SQLite format 3@ v#Windexgpl_acc_idxgplCREATE INDEX gpl_acc_idx on gpl (gpl)tablegplgplCREATE TABLE gpl ( ID REAL, title TEXT, gpl TEXT, status TEXT, submission_date TEXT, last_update_date TEXT, technology TEXT, distribution TEXT, organism TEXT, manufacturer TEXT, manufacture_protocol TEXT, coating TEXT, catalog_number TEXT, support TEXT, description TEXT, web_link TEXT, contact TEXT, data_row_count REAL, supplementary_file TEXT, bioc_package TEXT )?#Windexgse_acc_idxgseCREATE INDEX gse_acc_idx on gse (gse)mAtablegsegseCREATE TABLE gse ( ID REAL, title TEXT, gse TEXT, status TEXT, submission_date TEXT, last_update_date TEXT, pubmed_id INTEGER, summary TEXT, type TEXT, contributor TEXT, web_link TEXT, overall_design TEXT, repeats TEXT, repeats_sample_list TEXT, variable TEXT, variable_description TEXT, contact TEXT, supplementa }N M3#'-/357999IGKKMRUXVXXZggmrrrx{~~Um8|vpjd^XRLF@:4.(" ztnhb\VPJD>82,& RMHC>94/*%  ~xrlf`ZTNHB<60*$P2؁)ׁ(ց'Ձ&ԁ%Ӂ$ҁ#с"Ё!΁ ́́ˁʁɁȁǁƁŁāÁ k\jehMgekdO-ca``d/^y]!-[nZJ7YWgVD8TSYTQ1P~NUML1wJSIj%HFpE]KD&BwA"P?>)- {nw GSE418ZnM GSE934)nL GSE850nK GSE784nJ GSE719qnI GSE6566nH GSE594nv GSE527ny GSE490nu GSE411Sunt GSE4049 8nG GSE3993 ns GSE3921 nr GSE3849 nq GSE3791 Ynp GSE373-nn GSE3660 no GSE3588 nm GSE3524 unl GSE3463 >nF GSE3402 nk GSE3326 nj GSE3254 ni GSE3194 \nh GSE313ng GSE3065 ne GSE3004 nf GSE2934 ~nd GSE2852 Cnc GSE2792 nE GSE2710nb GSE2642na GSE256n` GSE25n_ GSE243nO GSE2365n^ GSE2280n] GSE2208In\ GSE2143n[ GSE208nP GSE2009nZ GSE1924anY GSE1840nX GSE1767nW GSE1693nV GSE1599lnU GSE1515n{ GSE175633n GSE4586o GSE6400 GSE1815o GSE8121\ GSE4586nz GSE13132&-g|vpjd^XRLF@:4.("  zupkfa\WRMHC>94/*%  ~xrlf`ZTNHB<60*$o܁oہoځoفo؁oׁoցoՁoԁoӁoҁoсoЁoρo΁óóoˁoʁ oɁ oȁ oǁ oƁ oŁoāoÁoooooooo~o}o|o{ozoyoxowovouotosoroqopooonomolokojoiohogofoeodocoboao`o_o^o]o\o[oZoYoXoWoUoToSoRoQoOoMoLoKoJoIoHoG=yrX/v˫" utgæ='vh=PwA3K@ɜ6?)$~(}na|O|0I{\=z)yy>xxw[ vv tumtdt([sakrWqׅ8qC"p1o4o߁{jYH7&}l[J:)sbQ@/ GPL513E GPL91Q GPL758,GPL7 GPL639 GPL605 GPL5054 { GPL4975 C GPL49( GPL4836  GPL4766 GPL4678 L GPL4603  GPL4528 GPL4454 GPL439. 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GDS1270a GDS30 GDS2070Xc GDS33 GDS932M GDS860 GDS773 GDS680 GDS594a GDS507& GDS41 GDS307 GDS1095 }wqke_YSMGA;5/)# {uoic]WQKE?93-'! ysmga[UOIC=71+% ng \t[hZeY_XRWBV6U%TSRQ{PpOaNNMCL4K)JI H|GkF_EQDJC;B+A@ ?~>t=k82,& ix.tzl]OA2$xiZL=/ teWH:,seWH:,ߊފ݉܉qۉcډUىF؉8׉*։Չ Ԉӈq҈cшUЈFψ7Έ)͈̈ ˇ|ʇmɇ_ȇQLJCƇ4Ň&ćÇ †{l]O@2$whYJ;,rcTF9,xk^QD7( }oaSE7) qcUG9?9h\ByYEL!`_9tN(^0!H*WGSE12351-GPL7142_series_matrix.txt.gz/"GGSE10560_series_matrix.txt.gz.!f!EGSE9630_series_matrix.txt.gz'!-!EGSE9196_series_matrix.txt.gz&N!)UGSE8782-GPL5577_series_matrix.txt.gz% )UGSE8457-GPL5518_series_matrix.txt.gz# !EGSE7994_series_matrix.txt.gz! )UGSE7576-GPL5276_series_matrix.txt.gz  !EGSE7095_series_matrix.txt.gz CGSE662_series_matrix.txt.gz &OGSE620-GPL97_series_matrix.txt.gz r!EGSE5713_series_matrix.txt.gzQ [!EGSE5220_series_matrix.txt.gz C)UGSE4741-GPL3637_series_matrix.txt.gz -!EGSE4316_series_matrix.txt.gz  CGSE393_series_matrix.txt.gz!EGSE3555_series_matrix.txt.gz !EGSE3164_series_matrix.txt.gz !EGSE2667_series_matrix.txt.gz!| CGSE214_series_matrix.txt.gzu!)UGSE1684-GPL1408_series_matrix.txt.gz"GGSE11680_series_matrix.t!)UGSE4741-GPL3637_series_matrix.txt.gz#2wfUD3"xgVE4#yhWF5$z@" GSE3526 " GSE3484 [" GSE3443 " GSE3394 " GSE3335 " GSE3284 f" GSE3237 *" GSE3193 " GSE3155 " GSE3100 r" GSE3044 4" GSE2991 " GSE2948 " GSE2879 |" GSE2821 ?" GSE2742 " GSE2701" GSE2649" GSE2585I" GSE2522 " GSE2472" GSE2422" GSE2361U" GSE2298" GSE2242" GSE2189" GSE2131a" GSE2084"" GSE2031" GSE1962" GSE1899m" GSE18300" GSE1772" GSE1709" GSE1635x" GSE1564;" GSE1481" GSE1429" GSE1365" GSE1309I" GSE1261 " GSE1209" GSE1155" GSE1100R" GSE1097" GSE1097" GSE15665:~# GSE4911" GSE2879 |#y GSE6346;#[ GSE7631 z GSE3890" GSE124245*$xgVE5$n]L<, paRC4%# GPL1216 # GPL1094*# GPL97 # GPL96 1# GPL96U# GPL96q# GPL96# GPL91# GPL91O# GPL90!# GPL870 # GPL85 ^# GPL83 # GPL81 # GPL81# GPL81<# GPL81w# GPL76# GPL715# GPL656# GPL6347G# GPL599# GPL570 G# GPL570# GPL513# GPL513# GPL4032# GPL341 C# GPL340i# GPL3394# GPL3236 # GPL3095 q# GPL3022 # GPL2927 # GPL284# GPL2780 +# GPL2720 J# GPL2671 I# GPL2641(# GPL260# GPL254O# GPL223\# GPL2046# GPL1998G# GPL198# GPL1951# GPL1901 # GPL1843# GPL1789 # GPL1722P# GPL1530$' GPL4559$~ GPL81 $` GPL5875.# GPL339F# GPL198"t&"t`L8$~jp\H4  lXD0$!2005-07-08$!2005-06-29*$!2008-02-28~$!2008-02-19P$!2008-02-12$!2008-01-30%!2008-01-22%!2008-01-08I$!2007-08-13>$!2007-04-03$!2006-12-15$!2006-12-07N$!2006-09-08$!2006-07-27K$!2006-07-27%!2006-07-27$!2006-07-27$!2006-05-22%!2006-03-30$!2006-02-28%!2006-01-043$!2005-12-20l$!2005-11-25$!2005-10-28$!2005-10-28!$!2005-10-28% !2005-10-28%!2005-10-21f%!2005-10-04%!2005-07-28% !2005-07-20$!2005-06-27$!2005-05-29$!2005-05-29$!2005-05-29M$!2005-05-29$!2005-05-29 $!2005-05-29{$!2005-05-29%!2009-05-126%!2008-11-212%!2008-03-18)%m!2007-10-241!%=!2007-05-01% !2006-07-28 % !2005-10-28! &P sgseweb_link[Values separated by ';tab', if more than one] Web link(s) to sudy and/or supplementary information about the study0 Qgsecontactcontact information for this studyc #-gsecontributor[Values separated by ';tab', if more than one] People contributed to this study hEgsetypekeyword(s)generally describing the type of study, e.g., time course, dose response, comparative genomic hybridization, ChIP-chip, cell type comparison, disease state analysis, stress response, genetic modification, etc.E{gsesummarya description of the goals and objectives of this study]%gsepubmed_id[Values separated by ';tab', if more than one] NCBI PubMed identifier (PMID)(-/gselast_update_datedate last updated$+)gsesubmission_datedate submitted$;gsestatusdate released to publicB}gsegseunique accession number approved and issued by GEO, NCBI4]gse&O_&NP&MC&L6&K/&J#&I&H&G &Tzc)QjH>Sc+wB({funding, or donated+gsmsource_name_ch10'gsmchannel_count/ gsmtype.-gsmlast_update_date-+gsmsubmission_date,gsmstatus+ gsmgpl* gsmgse) gsmgsm( gsmtitle' gsmID&%gplbioc_package%1gplsupplementary_file$)gpldata_row_count#gplcontact"gplweb_link!#gpldescription gplsupport)gplcatalog_numbergplcoating5gplmanufacture_protocol%gplmanufacturergplorganism%gpldistribution!gpltechnology-gpllast_update_date+gplsubmission_dategplstatus gplgpl gpltitle gplID1gsesupplementary_file5gsevariable_descriptiongsevariable3gserepeats_sample_listgserepeats )gseoverall_design gseweb_link gsecontact #gsecontributor gsetypegsesummarygsepubmed_id-gselast_update_date+gs&S5gsmextract_protocol_ch2>&R%gplmanufacturerxqjc\UNG@92+$|ung`YRKD=6/(! yrkd]VOHA:3,% ]WQKRJQ嗎JQPQwP^PSYOrO O&9NKN]M;McM0L˔bLgeL(KtK9|JՓ|JpyJ zI|IC"Hޒ Hz H<GQGLEF葩OFeF\E\EViDADRD(fCďzC_B!B5B2IA͎]Ai;AD@t@;?׍M?r~?U> >E[=7=|v=;@;H;!::X 9V9Y9+i8ƉG8b#7Q774u6Ј{6k6^55>4ه64u?4 33G}22~f2#1x1Qo0f00#q/x/Z}.#..---Ȅu-dv,q,),6m+҃}+m2+ 7*l*@m)ۂ)w) (|(ңPqCS?Sc  Nat Genet 2001 Nov;29(3):263-4 and it's web supplement.; Specimen procurement, labeling, hybridization and imaging protocols from Nat Genet 2001 Nov;29(3):263-4 web supplement:; Specimens. We obtained GM03563, GM00143, GM05296, GM07408, GM01750, GM03134, GM13330, GM03576, GM01535, GM07081, GM02948, GM04435, GM10315, GM13031 and GM01524 cell strains from the NIGMS Human Genetics Cell Repository (Coriell Institute for Medical Research), and cultured them under the recommended conditions. We cultured cell lines BT474, HCT116, T47D, MPE600, COLO320, SW837, MDA-MB-231, MDA-MB-453 and HT29 under the recommended conditions. To isolate DNA from confluent cell cultures, we collected cells from T75 flasks and then incubated them overnight at 55 C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 g/l proteinase K. We added 1 ml of saturated NaCl solution and 10 ml of ethanol to the cell lysate an(13creation timestamp2009-11-10 01:55:22)schema version1.0hen dissolved the DNA in 1 ml of H2O. We isolated DNA from breast tumor specimens as described previously.; DNA labeling. We labeled DNA by nick translation or random priming. For nick translation, we used a 400 l reaction containing 10 g DNA, 50 mM Tris, pH 7.6, 5 mM MgCl2, 0.02 mM each dATP, dTTP and dGTP, 0.2 mM Cy3- or Cy5-dCTP (Amersham), 0.2 U DNA Polymerase I (Gibco BRL), and 30 l DNAseI/PolI enzyme mix (Gibco BRL). We incubated the reaction at 15 C for 60 min after which we stopped the reaction by incubation at 70 C for 10 min. We removed unincorporated nucleotides using a Sephadex G-50 spin column. We labeled genomic DNA by random priming in a 100 l reaction containing 0.003 - 0.6 g DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1 mM Tris, pH 7.6, 0.1 mM EDTA, 0.2 mM each of dATP, dTTP and dGTP, 0.1 mM dCTP, 0.4 mM Cy3 or Cy5-dCTP (Amersham) and 160 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL). We incubated the DNA with the random primers solution at 100 C for 10 min in a total volume of 84 l, prior to adding the other reagents and then incubated the 100 l reaction overnight at 37 C. We removed unincorporated nucleotides using a Sephadex G-50 column.; Hybridization. We combined test and reference DNAs (~2 g of input genomic DNA for nick translation or ~0.6 g of input genomic DNA for random prime labeling) with Cot-1 DNA (80-100 g; Gibco BRL) and precipitated them with ethanol. We collected the precipitate by centrifugation and allowed the precipitate to dry in air for 10 min before re-dissolving it in a 50 l hybridization mixture containing 50% formamide, 2 x SSC, 10% dextran sulfate, 4% SDS and 500 g yeast tRNA, pH 7. We incubated the hybridization mixture at 70 C for 10-15 min to denature the DNA and subsequently continued incubation at 37 C for 60 min to allow blocking of repetitive sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 l of slide blocking solution containing 500 g salmon sperm DNA in 50% formamide, 2 x SSC, 10% dextran sulfate and 4% SDS, pH 7. We created an airtight hybridization chamber by placing a silicone gasket (PGC Scientific) around the array and rubber cement ring, placing a slide on top of it and clamping with binder clips. After a 30 min incubation at room temperature, we opened the chamber, removed approximately three-quarters of the blocking solution, added the denatured and re-annealed hybridization mixture and then re-sealed the chamber. We placed the arrays on a slowly rocking table (~1 rpm) at 37 C to allow hybridization to occur over 16-72 h. After hybridization, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed once in 50% formamide, 2 x SSC, pH 7 at 45 C for 15 min, and finally in PN buffer at room temperature for 15 min. After draining excess liquid from the arrays, we mounted them in a solution containing 90% glycerol, 10% PBS and 1 M DAPI, and then sea led them with a cover slip. We drained excess glycerol-DAPI solution onto a paper tissue.; Imaging and analysis. We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system, although we have also used commercial laser scanners for this purpose. We used ?UCSF SPOT? software (A.N.J. manuscript submitted) to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot. We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the September, 2000 freeze of the draft human genome sequence (http://genome.ucsc.edu). SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot. The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content (Tables A and B). We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.otherAntoine,M,Snijders; Norma Nowak; Richard Segraves; Stephanie Blackwood; Nils Brown; Jeffery Conroy; Greg Hamilton; Anna,K,Hindle; Bing Huey; Karen Kimura; Sindy Law; Ken Myambo; Joel Palmer; Bauke Ylstra; Jingzhu,P,Yue; Joe,W,Gray; Ajay,N,Jain; Daniel PinName: Donna,G,Albertson; Email: albertson@cc.ucsf.edu; Phone: 415 502-8463; Department: Comprehensive Cancer Center; Institute: University of California San Francisco; Address: ; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USA !K7!!CWqYoung and old muscle comparisonGSE17Public on Feb 01 20022002-02-012005-06-15bRNA was pooled from vastus lateralis biopsies obtained from 8 younger (21-24 yr) and 8 older (66-77 yr)men. Healthy subjects with no neuromuscular disease.otherS,,Welle; C,A,Thornton; Stephen Wellehttp://www.urmc.rochester.edu/smd/CRC/SWindex.htmlName: Stephen Welle; Email: stephen_welle@urmc.rochester.edu; Phone: 585-273-3117; Institute: University of Rochester; Address: ; City: Rochester; State: NY; Zip/postal_code: 14642; Country: USAmic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.; Study is described in more detail in Gasch AP et al.(2000) Mol Biol Cell 11:4241-57otherA,P,Gasch; P,T,Spellman; C,M,Kao; O Carmel-Harel; M,B,Eisen; G Storz; D Botstein; P,O,BrownName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ 77!!CYeast Stress ResponseGSE18Public on Feb 12 20022002-02-082005-05-29i9We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the geno" E7!!I SBF-MBF genomic distributionGSE19Public on Feb 12 20022002-02-082005-05-29The first 18 experiments are ordered according to the legend in Figure 3 of the published paper. Experiment 19 is the gene expression profile of the swi4 deletion strain compared to the wild-type strain.; This study is described in more detail in Iyer VR, et al.(2001) Nature 409:533-38otherV,R,Iyer; C,E,Horak; C,S,Scafe; D Botstein; M Snyder; P,O,BrownName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ PP-K7!!GGManipulation in phospate levelsGSE20Public on Feb 12 20022002-02-082005-05-29i=The arrays were used to study the effects of modifying phosphate levels in yeast, either through mutation, or chemical manipulation.; This study is described in more detail in Ogawa N et al.(2000) Mol Biol Cell 11:4309-21otherN,,Ogawa; J DeRisi; P,O,BrownName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ mRNA levels, that Snf/Swi controls some genes differently in rich and minimal media, and that Snf/Swi control is exerted at the level of individual genes rather than over larger chromosomal domains. In addition, this work shows that Snf/Swi controls mRNA levels of MATalpha-specific genes, likely via controlling transcription of the regulators MATalpha1 and MCM1. Finally, we provide evidence that Snf/Swi acts both as an activator and as a repressor of transcription, and that neither mode of control is an indirect effect of the other.; This study is described in more detail in Sudarsanam P et al.(2000) Proc Natl Acad Sci U S A 97:3364-9otherP,,Sudarsanam; V,R,Iyer; P,O,Brown; F WinstonName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ --HO7!!Ygsnf/swi mutants of S. cerevisiae.GSE21Public on Feb 12 20022002-02-082005-05-29The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrated to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome expression analysis, using DNA microarrays, to study mutants deleted for a gene encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi component. This analysis was performed on cells grown in both rich and minimal media. The microarray results, combined with Northern blot, computational, and genetic analyses, show that snf2Delta and swi1Delta mutations cause similar effects on& cA7!!!#UAlpha-factor block-releaseGSE22Public on Feb 12 20022002-02-082006-01-303qThese data are from a time series, where yeast were arrested in alpha-factor, then the alpha-factor was washed out, and the cells were release into fresh medium. Samples were taken every 7 minutes as the cells went through the cell cycle.; This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97time-courseP,T,Spellman; G Sherlock; M,Q,Zhang; V,R,Iyer; K Anders; M,B,Eisen; P,O,Brown; D Botstein; B FutcherName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ }37!!y#?cdc15 block-releaseGSE23Public on Feb 12 20022002-02-082006-01-303qYeast cells were blocked in telophase using a cdc15-2 temperature senstive mutant at restrictive temperature. The culture was then shifted to permissive temperature (25oC), and released into the cell cycle. Samples were then taken during the course of almost three full cell cycles.; This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97time-courseP,T,Spellman; G Sherlock; M,Q,Zhang; V,R,Iyer; K Anders; P,O,Brown; D Botstein; B FutcherName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ 3;7!!G#UElutriation time courseGSE24Public on Feb 12 20022002-02-082006-01-303qSmall G1 daughter yeast cells were isolated by centrifugal elutriation. They were then released into YEP ethanol, and followed through one cell cycle, with samples being taken every 30 minutes.; This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97time-courseP,T,Spellman; G Sherlock; M,Q,Zhang; V,R,Iyer; K Anders; M,B,Eisen; P,O,Brown; D Botstein; B FutcherName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ 77!!{UCyclin overexpressionGSE25Public on Feb 12 20022002-02-082005-05-293qYeast cells were arrested either in G1 (for CLN3 overexpression) or in G2/M (for CLB2 overexpression). The cyclin was then induced, and samples were taken.; This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97otherP,T,Spellman; G Sherlock; M,Q,Zhang; V,R,Iyer; K Anders; M,B,Eisen; P,O,Brown; D Botstein; B FutcherName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/logous to cystathionine gamma-lyase encoded by CYS3. Several genes that are differentially expressed in cells containing a constitutively active Mac1, designated Mac1up1, are not direct targets of Mac1. Induction or repression of these genes is likely a secondary effect of cells due to constitutive Mac1 activity. Elevated copper levels induced the expression of the metallothioneins CUP1 and CRS5, and two genes, FET3 and FTR1, in the iron uptake system. Cu-induced FET3 and FTR1 expression arises from an indirect Cu effect on cellular Fe pools.; This study is described in more detail in Gross C et al.(2000) J Biol Chem 275:32310-6otherC,,Gross; M Kelleher; V,R,Iyer; P,O,Brown; D,R,WingeName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ K7!!]uCopper regulon in S. cerevisiaeGSE26Public on Feb 12 20022002-02-082005-05-29In Saccharomyces cerevisiae, copper ions regulate gene expression through the two transcriptional activators, Ace1 and Mac1. Ace1 mediates Cu-induced gene expression in cells exposed to stressful levels of copper salts, whereas Mac1 activates a subset of genes under copper-deficient conditions. DNA microarray hybridization experiments revealed a limited set of yeast genes differentially expressed under growth conditions of excess copper or copper deficiency. Mac1 activates the expression of six S. cerevisiae genes, including CTR1, CTR3, FRE1, FRE7, YJL217w and YFR055w. Two of the last three newly identified Mac1 target genes have no known function, the third, YFR055w, is homo, of induction were observed. The transcription factor Ndt80 appeared to be important for induction of a large group of genes at the end of meiotic prophase. Consensus sequences known or proposed to be responsible for temporal regulation could be identified solely from analysis of sequences of coordinately expressed genes. The temporal expression pattern provided clues to potential functions of hundreds of previously uncharacterized genes, some of which have vertebrate homologs that may function during gametogenesis.; This study is described in more detail in Chu S, et al. 1998. Science 282:699-705time-courseS,,Chu; J DeRisi; M,B,Eisen; J Mulholland; D Botstein; P,O,Brown; I HerskowitzName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ dd57!!5#)Sporulation in yeastGSE27Public on Feb 12 20022002-02-082005-05-29K:Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct temporal patterns. u'7!!k#KDiauxic shiftGSE28Public on Feb 12 20022002-02-082005-05-29%9Exploring the metabolic and genetic control of gene expression on a genomic scale in yeast.; This study is described in more detail in DeRisi JL et al. 1997. Science 278:680-6time-courseJ,L,DeRisi; V,R,Iyer; P,O,BrownName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/ C7!!mAdaptive evolution in yeastGSE29Public on Feb 12 20022002-02-082005-05-29saA Saccharomyces cerevisiae population was cultured for many generations under conditions to which it is not optimally adapted. These experiments were designed to investigate adaptive evolution under natural selection.; This study is described in more detail in Ferea TL, et al. 1999. Proc Natl Acad Sci USA 96:9721-6otherT,L,Ferea; D Botstein; P,O,Brown; R,F,RosenzweigName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/expression patterns in the brain. In these experiments, mouse brains were dissected into 40 voxels, or cubes, by cutting 10 serial coronal sections and transecting each coronal section into fourths. Using microarrays, the gene expression pattern of 9000 genes was acquired for both a normal and a pharmacological model of Parkinson's disease (PD) mouse brain.; The mice used in these experiments were C57BL/6J males 10-24 weeks in age.; KeywordsotherVanessa,M,Brown; Alex Ossadtchi; Arshad,H,Khan; Simon Yee; William,P,Melega; Simon,R,Cherry; Richard,M,Leahy; Desmond,J,Smithhttp://www.pharmacology.ucla.edu/smithlab/genome_multiplexName: Vanessa,Marie,Brown; Email: dsmith@mednet.ucla.edu; Phone: 310-794-5711; Fax: 310-825-6267; Laboratory: Desmond Smith, M.D., Ph.D.; Department: Department of Molecular & Medical Pharmacology; Institute: UCLA; Address: 650 Charles E. Young Dr. South, CHS 23-151; City: Los Angeles; State: CA; Zip/postal_code: 90095; Country: USA; Web_link: http://www.pharmacology.ucla.edu/smithlab qqq37!!{1SAGE_HumanEpidermisGSE31Public on Feb 22 20022002-02-142005-06-15SAGE libraries from cultured, differentiated keratinocytes and human epidermis, both normal and affected by actinic keratosis; KeywordsotherFred,,Van Ruissen; Bastiaan,J,Jansen; Gys,J,De Jongh; Ivonne,M,Van Vlijmen-Willems; Joost Schalkwijk; Patrick,L,ZeeuwenName: Bastiaan Jansen; Email: bjhjansen@gmail.com; Department: Tumor Immunology; Institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen; Address: PO Box 9101; City: Nijmegen; Zip/postal_code: 6500 HB; Country: NetherlandsO7!!WMultiplex three dimensional brain gene expression mapping in a mouse model of Parkinson's diseaseGSE30Public on Mar 29 20022002-02-132005-05-29UVoxelation is a novel technology designed to produce high throughput, three-dimensional imaging of gene 2 at a genomic level.; In this study, transgenic fly strains carrying the otd coding sequence or the human Otx2 coding sequence under control of the heat inducible Hsp70 promoter were used [Leuzinger et al.: Equivalence of the fly orthodenticle gene and the human OTX genes in embryonic brain development of Drosophila. Development 1998; 125:1703-1710.]. Stage 10-17 embryos were given a 25-min heat pulse in order to overexpress the otd or Otx2 genes and allowed to recover for 25 min.; KeywordsorderedHaiqiong,,Montalta-He; Ronny Leemans; Thomas Loop; Martin Strahm; Ulrich Certa; Michael Primig; Dario Acampora; Antonio Simeone; Heinrich Reicherthttp://www.unibas.ch/dib/zoologie/research/neuro.htmlName: Thomas Loop; Email: thomas.loop@unibas.ch; Phone: +41612671616; Laboratory: Reichert Lab; Department: Institute of Zoology; Institute: University of Basel; Address: Klingelbergstrasse 50; City: Basel; Zip/postal_code: CH-4056; Country: Switzerland; Web_link: http://www.unibas.ch/dib/zoologie/research/neuro.html 99< 57!!31w Heatshock otd / OTX2GSE32Public on Feb 25 20022002-02-212005-06-15The homeobox genes of the orthodenticle (otd)/Otx family play conserved roles in embryogenesis of the head and brain. Gene replacement experiments show that the Drosophila otd gene and orthologous mammalian Otx genes are functionally equivalent, in that overexpression of either gene in null mutants of Drosophila or mouse can restore defects in cephalic and brain development. This suggests that otd and Otx genes can control a comparable subset of downstream target genes in either organism. Here we use quantitative transcript imaging to analyze this equivalence of Drosophila otd and human Otx gene action4damage. Among the damage-induced genes more than a hundred are novel. From those genes involved in DNA metabolism that have not been previously shown to be induced by DNA damage, for example, the mutS gene involved in mismatch repair is especially noteworthy. In addition to the SOS response, we observed the induction of other stress response pathways such as those of oxidative stress and osmotic protection. Among the genes that are down-regulated in response to DNA damage are numerous protein biosynthesis genes. Analysis of the gene expression data highlighted the essential involvement of sigmaS regulated genes and the general stress response network in the response to DNA damage.; KeywordsotherPavel,P,Khil; R. Daniel Camerini-OteroName: Natalya,A,Smirnova; Email: natalyas@intra.niddk.nih.gov; Phone: (301)-496-4053; Fax: (301)-496-9878; Laboratory: Genetics and Biochemistry Branch; Department: ; Institute: NIDDK; Address: 5 Memorial Dr.; City: Bethesda; State: MD; Zip/postal_code: 20892; Country: USA ]]!;7!!Y1!E. coli response to MMCGSE33Public on Feb 26 20022002-02-252005-05-29_Changes in gene expression after treatment of E. coli cultures with mitomycin C were assessed using gene array technology. Unexpectedly, a large number of genes (nearly 30% of all genes) displayed significant changes in their expression level. Analysis and classification of expression profiles of the corresponding genes allowed us to assign this large number of genes into a dozen to two dozen small clusters of genes with similar expression profiles. This assignment allowed us to describe systematically the changes in the level of gene expression in response to DNA 6 U"=7!!m#'g"Prp4-1 temperature shiftGSE34Public on Apr 16 20022002-03-192005-10-28^Prp4-1 and wt strains were grown at 26°C to A600 of 1.0, then an equal volume of 48°C media was added to bring the temperature to 37°C. Both strains were allowed to grow at 37°C and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.; Keywordstime-courseTyson,A,ClarkName: Manuel Ares; Email: ares@biology.ucsc.edu; Phone: 831 459-4628; Institute: UC Santa Cruz; Address: ; City: Santa Cruz; State: CA; Zip/postal_code: 95064; Country: USA ;_D&+7!!7'{=&BY_wild_parentsGSE38Public on May 01 20022002-04-262005-05-29&Expression analysis of BY4716(isogenic to S288c) and a wild isolate collected by R. Mortimer. Each strain was g?7!!e{>mRNAs translated at eIF4FGSE62Public on Jun 27 20022002-06-242005-05-29cIdentification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5' end-dependent scanning Z;=a7!!QA=Molecular portraits of human breast tumorsGSE61Public on Jun 27 20022002-06-242005-05-29JSet of 65 surgical specimens of human breast tumors from 42 different individuals, using complementary DNA microarrays representing 8,102 human genes. Gene expression variation patterns within this set prYa<G7!!3 G;
  • Brain:

    • ; GSM2558: Control
    ; GSM2559: Control
    ; GSM2560: Fungal oil (AA)
    ; GSM2561: Fungal oil (AA)
    ; GSM2562: Fish oil (DHA)
    ; GSM2563: Fish oil (DHA)
    ; GSM2564: Fish and Fungal oil (DHA + AA)
    ;
  • Liver:

    • ; GSM2565: Control
    ; GSM2566: Control
    ; GSM2567: Control
    ; GSM2568: Control
    ; GSM2569: Fungal oil (AA)
    ; GSM2570: Fungal oil (AA)
    ; GSM2571: Fish oil (DHA)
    ; GSM2572: Fish oil (DHA)
    ; GSM2573: Fish + Fungal oil (DHA +AA)
    ; GSM2574: Fish + Fungal oil (DHA +AA)
    ; orderedA,,Berger; D,M,Mutch; B German; D Vilanova; Matthew-Alan Robertshttp://www.Lipidworld.com/articles/browse.aspName: David Vilanova; Email: david.vilanova@rdls.nestle.com; Phone: +41217858723; Institute: Nestle Research Center; Address: ; City: Lausanne; Zip/postal_code: 1012; Country: Switzerlande life cycle (sporozoites, merozoites, trophozoites and gametocytes) by multidimensional protein identification technology. Functional profiling of over 2,400 proteins agreed with the physiology of each stage. Unexpectedly, the antigenically variant proteins of var and rif genes, defined as molecules on the surface of infected erythrocytes, were also largely expressed in sporozoites. The detection of chromosomal clusters encoding co-expressed proteins suggested a potential mechanism for controlling gene expression.orderedL,,Florens; M,P,Washburn; J,D,Raine; R,M,Anthony; M Grainger; J,D,Haynes; J,K,Moch; N Muster; J,B,Sacci; D,L,Tabb; A,A,Witney; D Wolters; Y Wu; M,J,Gardner; A,A,Holder; R,E,Sinden; J,R,Yates; D,J,Caruccihttp://www.plasmodb.org/Name: Laurence Florens; Email: florens@scripps.edu; Phone: 858-784-8876; Department: Department of Cell Biology; Institute: The Scripps Research Institute; Address: SR-11, 10550 North Torrey Pines Road; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA r\y7!! #=!\Proteomic view of the Plasmodium falciparum life cycleGSE92Public on Dec 23 20022002-11-082005-05-29The completion of the Plasmodium falciparum clone 3D7 genome provides a basis on which to conduct comparative proteomics studies of this human pathogen. Here, we applied a high-throughput proteomics approach to identify new potential drug and vaccine targets and to better understand the biology of this complex protozoan parasite. We characterized four stages of the parasitz h]W7!!W'=m]Wing imaginal disc spatial expressionGSE93Public on Jan 08 20032002-11-132005-05-29ӍWing imaginal discs were dissected to generate body wall and wing/hinge fragments. Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays. Comparisons between the sample groups allow the identification of genes with localized expression patterns.; Keywordsrepeat sampleMiranda,J,Butler; Thomas,L,Jacobsen; Donna,M,Cain; Michael,G,Jarman; Michael Hubank; Robert,S,Whittle; Roger Phillips; Amanda Simcox; J Robert,S,WhittleName: Amanda Simcox; Email: simcox.1@osu.edu; Phone: 614 292 8857; Fax: 614 292 4466; Department: Molecular Genetics; Institute: Ohio State University; Address: 484 W 12th Ave; City: Columbus; State: OH; Zip/postal_code: 43210; Country: USAort gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.otherM,N,Arbeitman; E,E,Furlong; F Imam; E Johnson; B,H,Null; B,S,Baker; M,A,Krasnow; M,P,Scott; R,W,Davis; K,P,Whitehttp://genome.med.yale.edu/Lifecycle/Name: Kevin,P,White; Email: kevin.white@yale.edu; Phone: 203-785-5572; Fax: 203-785-6333; Department: Department of Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar Street; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA 0_7!!MgA_Gene expression analysis reveals chemical-specific profilesGSE95Public on Nov 20x^W7!!]mW^Life cycle of Drosophila melanogasterGSE94Public on Jan 06 20032002-11-192005-05-29y/Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we rep} 20022002-11-192005-05-29GThe application of gene expression profiling technology to examine multiple genes and signaling pathways simultaneously promises a significant advance in understanding toxic mechanisms to ultimately aid in protection of public health. Public and private efforts in the new field of toxicogenomics are focused on populating databases with gene expression profiles of compounds where toxicological and pathological endpoints are well characterized. The validity and utility of a toxicogenomics is dependent on whether gene expression profiles that correspond to different chemicals can be distinguished. The principal hypothesis underlying a toxicogenomic or pharmacogenomic strategy is that chemical-specific patterns of altered gene expression will be revealed using high-density microarray analysis of tissues from exposed organisms. Analyses of these patterns should allow classification of toxicants and provide important mechanistic insights. This report provides a verification of this hypothesis. Patterns of gene expression corresponding to liver tissue derived from chemically exposed rats revealed similarity in gene expression profiles between animals treated with different agents from a common class of compounds, peroxisome proliferators [clofibrate (ethyl-p-chlorophenoxyisobutyrate), Wyeth 14,643 ([4-chloro-6(2,3-xylidino)-2-pyrimidinylthio]acetic acid), and gemfibrozil (5-2[2,5-dimethylphenoxy]2-2-dimethylpentanoic acid)], but a very distinct gene expression profile was produced using a compound from another class, enzyme inducers (phenobarbital).otherhttp://dir.niehs.nih.gov/microarray/datasets/Name: Hisham,K,Hamadeh; Email: hhamadeh@amgen.com; Phone: 805-447-4818; Fax: 805-499-4687; Laboratory: At time of data generation: National Institute of Environmental; Department: Toxicology; Institute: Currently at: Amgen Inc.; Address: One Amgen Center Drive, Mailstop 5-1-A; City: Thousand Oaks; State: CA; Zip/postal_code: 91320; Country: USAate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.otherA,I,Su; M,P,Cooke; K,A,Ching; Y Hakak; J,R,Walker; T Wiltshire; A,P,Orth; R,G,Vega; L,M,Sapinoso; A Moqrich; A Patapoutian; G,M,Hampton; P,G,Schultz; J,B,Hogeneschhttp://expression.gnf.orgName: John,R,Walker; Email: jwalker@gnf.org; Phone: 858-812-1636; Fax: 858-812-1746; Laboratory: RNA Profiling Group; Department: ; Institute: Genomics Institute of the Novartis Research Foundation; Address: 10675 John Jay Hopkins; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA; Web_link: http://expression.gnf.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE96/GSE96_RAW.tar q`k7!!?S?)-`Large-scale analysis of the human transcriptomeGSE96Public on Dec 06 20022002-11-222005-05-29fHigh-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.otherA,I,Su; M,P,Cooke; K,A,Ching; Y Hakak; J,R,Walker; T Wiltshire; A,P,Orth; R,G,Vega; L,M,Sapinoso; A Moqrich; A Patapoutian; G,M,Hampton; P,G,Schultz; J,B,Hogeneschhttp://expression.gnf.orgName: John,R,Walker; Email: jwalker@gnf.org; Phone: 858-812-1636; Fax: 858-812-1746; Laboratory: RNA Profiling Group; Department: ; Institute: Genomics Institute of the Novartis Research Foundation; Address: 10675 John Jay Hopkins; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA; Web_link: http://expression.gnf.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE97/GSE97_RAW.tar qak7!!?S?)-aLarge-scale analysis of the mouse transcriptomeGSE97Public on Dec 06 20022002-11-222005-05-29fHigh-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustr RR+b7!!W'QEbzzMex67 co-IPed RNA vs. zz co-IPed RNA (zzMex67IP_v_zzIP)GSE98Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA IPed with zzMex67 to that from RNA co-IPed with zz tag alone (control IP)repeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/; research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA rc}7!!U-Q EczzYra1 co-IPed RNA vs. zz co-IPed RNA (zzYra1IP_v_zzIP)GSE99Public on Nov 25 20022002-11-252005-06-15Comparison of cDNA from RNA IPed with zzYra1 to that from RNA co-IPed with zz tag alone (control IP)equivalent probeHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA TT)d7!!E'Q EdzzMex67 co-IPed RNA vs. Total RNA (zzMex67IP_v_TotalRNA)GSE100Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA IPed with zzMex67 to that from total RNA; resulting analysis gives Mex67 binding level relative to total abundance for each mRNArepeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA XX%e{7!!A'Q EezzYra1 co-IPed RNA vs. Total RNA (zzYra1IP_v_TotalRNA)GSE101Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA IPed with zzYra1 to that from total RNA; resulting analysis gives Yra1 binding level relative to total abundance for each mRNArepeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA mf7!!9'Q EfzzYra1 co-IPed RNA vs. zzMex67 co-IPed RNA (zzYra1IP_v_zzMex67IP)GSE102Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA co-IPed with zzYra1; to cDNA from RNA co-IPed with zzMex67repeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA NN/g7!!3'Q Egtotal RNA from mex67-6 at 37C vs. Mex67 WT at 37C (mex67-5TS_v_Mex67WT)GSE103Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA of mex67-5 temperature-sensitive mutant to RNA from Mex67 wildtype strain both at the non-permissive temperature of 37Crepeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USA TT)h7!!/'Q Ehtotal RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)GSE104Public on Nov 25 20022002-11-252005-05-29Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37Crepeat sampleHaley,,Hieronymus; Pamela,A,Silverhttp://research.dfci.harvard.edu/silverlab/research/hieronymus/Name: Haley Hieronymus; Email: hierony@fas.harvard.edu; Phone: 617-632-5105; Laboratory: Pamela A. Silver; Department: ; Institute: Harvard Medical School and Dana-Farber Cancer Institute; Address: 1 Jimmy Fund Way SM922; City: Boston; State: MA; Zip/postal_code: 02445; Country: USAed by 4 h of LPS treatment, and 13 genes were repressed. Genes other than cytokines and chemokines are regulated; interestingly, genes involved in cell growth regulation and survival, transcriptional regulation, and interferon response are among those induced, whereas genes involved in cytoskeletal regulation are predominantly repressed. In addition, we identified monocyte chemoattractant protein-1 as a novel LPS-regulated chemokine in neutrophils. Included in these lists are five clones with no defined function. These data suggest molecular mechanisms by which neutrophils respond to infection and indicate that the transcriptional potential of neutrophils is greater than previously thought.repeat sampleK,C,Malcolm; P,G,Arndt; E,J,Manos; D,A,Jones; G,S,WorthenName: K,C,Malcolm; Email: malcolmk@njc.org; Phone: 303-398-1640; Laboratory: Worthen; Department: Department of Medicine; Institute: National Jewish Medical and Research Center; Address: ; City: Denver; State: CO; Zip/postal_code: 80206; Country: USA tti_7!!)'iLipopolysaccharide-stimulated neutrophilsGSE105Public on Mar 10 20032002-12-092005-06-15DNeutrophil gene transcription following lipopolysaccharide exposure.; Microarray analysis of lipopolysaccharide-treated human neutrophils.; Neutrophils respond to infection by degranulation, release of reactive oxygen intermediates, and secretion of chemokines and cytokines; however, activation of neutrophil transcriptional machinery has been little appreciated. Recent findings suggest that gene expression may represent an additional neutrophil function after exposure to lipopolysaccharide (LPS). We performed microarray gene expression analysis of 4,608 mostly nonredundant genes on LPS-stimulated human neutrophils. Analysis of three donors indicated some variability but also a high degree of reproducibility in gene expression. Twenty-eight verifiable, distinct genes were inducle mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks; of age. 14 days after ovariectomy, mice were injected; subcutaneously with progesterone dissolved in sesame oil (Sigma;; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine; horns at various times after injection. 8 uterine horns from 4 mice were; pooled to form one sample. Total RNA preparation, cRNA labeling and; hybridization were performed according to recommendations by; Affymetrix.time-courseMylene,W,Yao; Hyunjung Lim; Daniel,J,Schust; Sung,E,Choe; Anna Farago; Yueyun Ding; Sebastien Michaud; George,M,Church; Richard,L,MaasName: Richard,L.,Maas; Email: maas@rascal.med.harvard.edu; Phone: 617-732-5856; Fax: 617-732-5123; Laboratory: Division of Genetics; Department: Medicine/Division of Genetics; Institute: Brigham and Women's Hospital/Harvard Medical School; Address: 20 Shattuck St, Room 1019A; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA T$FT|ni7!!KugnBovine Glomerular and Aortic Endothelial CellsGSE110Public on Dec 10 20022002-12-ymU7!!'[1mOVX/oil/6h/UTX 129 WT vs. Hoxa-10-/-GSE109Public on Dec 10 20022002-12-102005-05-29Female mice useSlS7!!1lOVX/P4/6h/UTX 129 WT vs. Hoxa-10-/-GSE108Public on Dec 10 20022002-12-102005-05-29Female mice used were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in para!k?7!!C#1kOVX/P4/UTX 129/SvImJ WT BGSE107Public on Dec 10 20022002-12-102005-05-29Fema!j?7!!C#1jOVX/P4/UTX 129/SvImJ WT AGSE106Public on Dec 10 20022002-12-102005-05-29Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks; of age. 14 days after ovariectomy, mice were injected; subcutaneously with progesterone dissolved in sesame oil (Sigma;; 0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine; horns at various times after injection. 8 uterine horns from 4 mice were; pooled to form one sample. Total RNA preparation, cRNA labeling and; hybridization were performed according to recommendations by; Affymetrix.time-courseMylene,W,Yao; Hyunjung Lim; Daniel,J,Schust; Sung,E,Choe; Anna Farago; Yueyun Ding; Sebastien Michaud; George,M,Church; Richard,L,MaasName: Richard,L.,Maas; Email: maas@rascal.med.harvard.edu; Phone: 617-732-5856; Fax: 617-732-5123; Laboratory: Division of Genetics; Department: Medicine/Division of Genetics; Institute: Brigham and Women's Hospital/Harvard Medical School; Address: 20 Shattuck St, Room 1019A; City: Boston; State: MA; Zip/postal_code: 02115; Country: USAllel experiments.; 14 days after ovariectomy, mice were injected subcutaneously with; progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse),; followed by sacrifice and removal of uterine horns at 6 hours after; injection. 8 uterine horns from 4 mice were pooled to form one; sample. Total RNA preparation, cRNA labeling and hybridization were; performed according to recommendations by Affymetrix.; The 6 samples were obtained and processed in two batches: (1: GSM3047 and GSM3041), and (2: GSM3048, GSM3049, GSM3042, and GSM3043).otherMylene,W,Yao; Hyunjung Lim; Daniel,J,Schust; Sung,E,Choe; Anna Farago; Yueyun Ding; Sebastien Michaud; George,M,Church; Richard,L,MaasName: Richard,L.,Maas; Email: maas@rascal.med.harvard.edu; Phone: 617-732-5856; Fax: 617-732-5123; Laboratory: Division of Genetics; Department: Medicine/Division of Genetics; Institute: Brigham and Women's Hospital/Harvard Medical School; Address: 20 Shattuck St, Room 1019A; City: Boston; State: MA; Zip/postal_code: 02115; Country: USAd were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in parallel experiments. 14 days after ovariectomy, mice were injected with sesame oil; (Sigma; 0.1mL/mouse), followed by sacrifice and removal of uterine; horns at 6 hours after injection. 8 uterine horns from 4 mice were; pooled to form one sample. Total RNA preparation, cRNA labeling and; hybridization were performed according to recommendations by; Affymetrix. All 6 samples were collected and processed in parallel.otherMylene,W,Yao; Hyunjung Lim; Daniel,J,Schust; Sung,E,Choe; Anna Farago; Yueyun Ding; Sebastien Michaud; George,M,Church; Richard,L,Maas; Hyunhung Lim; Sebastein MichaudName: Richard,L.,Maas; Email: maas@rascal.med.harvard.edu; Phone: 617-732-5856; Fax: 617-732-5123; Laboratory: Division of Genetics; Department: Medicine/Division of Genetics; Institute: Brigham and Women's Hospital/Harvard Medical School; Address: 20 Shattuck St, Room 1019A; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA102005-05-29VSAGE libraries were prepared from mRNA of cultured bovine glomerular and aortic endothelial cells. Cells both cell lines were positive for acetylated LDL uptake and vWF expression, and were proven to be free of non-endothelial cells. Cultures were studied at passage 9-10. The cells were confluent, cultured in parallel, under identical conditions. Cells were plated on gelatin coated cell culture plastic in RPMI 1640 medium containing 10% FBS and streptomycin/penicillin. The last medium change was 48 hours prior to mRNA harvest.; KeywordsotherBarbara,J,Ballermann; Guerkan Sengolge; Wencheng LuoName: Barbara,Jutta,Ballermann; Email: bjballer@aecom.yu.edu; Phone: 718-430-3252; Fax: 718-430-8369; Laboratory: Endothelial Cell Biology; Department: Medicine; Institute: Albert Einstein College of Medicine; Address: 1300 Morris Park Ave; City: Bronx; State: NY; Zip/postal_code: 10461; Country: USAnd clinical subgroups. As a result, we found 796 differentially expressed genes and ESTs between GIST and smooth muscle tissue, including promising new candidate genes for the pathogenesis of GIST. Furthermore, we identified differences in gene expression between GIST of different site, size, and immunohistochemical expression of CD34 and SMA. Our data show that alterations in gene expression are associated with morphologically and clinically detectable features of GIST and provide new aspects for the understanding of these tumors.; KeywordsotherF,,Bergmann; A von Heydebreck; W Huber; A Buness; J Höer; C Langer; B Gunawan; L Füzesi; A Poustka; H Sültmannwww.dkfz-heidelberg.de/abt0840/whuber/gistfilterName: Wolfgang Huber; Email: w.huber@dkfz.de; Phone: +49-6221-424709; Fax: +49-6221-423470; Department: Molecular Genome Analysis; Institute: German Cancer Research Center; Address: Im Neuenheimer Feld 280; City: Heidelberg; Zip/postal_code: 69120; Country: Germany; Web_link: www.dkfz-heidelberg.de/abt0840 3oS7!!momsoDistinctive gene expression patterns in gastrointestinal stromal tumors identified with cDNA arraysGSE112Public on Apr 10 20032002-12-112005-10-28Gastrointestinal stromal tumors (GIST) are phenotypically and clinically heterogeneous mesenchymal tumors. Using the cDNA array technique, we analyzed the gene expression profiles of 22 GIST and 7 non-neoplastic gastrointestinal smooth muscle specimens, in order to detect molecular differences between GIST and non-neoplastic tissue, and to detect differences between GIST of various phenotypic a yp'7!!'1 pCT18_LT2_STv2GSE113Public on Mar 07 20032002-12-132005-05-29comparative DNA hyb of CT18 and LT2 gDNA to the Salmonella chip STv2repeat sampleSteffen,,Porwollik; Jonathan Frye; L,D,Florea; Felisa Blackmer; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA q57!!;'1 qCT18_log_overnight_1GSE114Public on Mar 07 20032002-12-132005-05-29comparative hybridization of gDNA from logarithmic and stationary CT18 cultures on STv2repeat sampleSteffen,,Porwollik; Jonathan Frye; L,D,Florea; Felisa Blackmer; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA r37!!Q'1 rLT2_log_overnight_1GSE115Public on Mar 07 20032002-12-132005-05-29comparative hybridization of Typhimurium LT2 gDNA from logarithmic and stationary cultures on STv2repeat sampleSteffen,,Porwollik; Jonathan Frye; L,D,Florea; Felisa Blackmer; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA sG7!!C#3 sTY2_hydrogen_peroxide_2mM_RNAGSE116Public on Mar 08 20032002-12-142005-05-29Gene expression in Salmonella enterica sv Typhi TY2 after exposure to 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Steffen Porwollik; L,D,Florea; Felisa Blackmer; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA @t#7!!I'MUtP7 wildtypeGSE117Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P7. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian Zuo; Qiang HuangName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA 5u%7!!K'3UuP10 wildtypeGSE118Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P10. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA 5v%7!!K'3UvP14 wildtypeGSE119Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P14. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA 5w%7!!K'3UwP18 wildtypeGSE120Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P18. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA FxY7!!9}xType 2 diabetes and insulin resistanceGSE121Public on Dec 17 20022002-12-172005-05-29wGlobal transcript profiling to identify differentially expressed skeletal muscle genes in insulin resistance, a major risk factor for Type II (non-insulin-dependent) diabetes mellitus. Compared gene expression profiles of skeletal muscle tissues from 18 insulin-sensitive versus 17 insulin-resistant equally obese, non-diabetic Pima Indians.otherX,,Yang; R,E,Pratley; S Tokraks; C Bogardus; P,A,PermanaName: Paska Permana; Email: ppermana@phx.niddk.nih.gov; Phone: 602-200-5345; Fax: 602-200-5335; Laboratory: Clinical Diabetes and Nutrition Section; Department: Phoenix Epidemiology and Clinical Research Branch; Institute: NIDDK, NIH; Address: 4212 N. 16th St.; City: Phoenix; State: AZ; Zip/postal_code: 85016; Country: USA 5y%7!!K'3UyP21 wildtypeGSE122Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P21. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA  z#7!!}'3UzP7 knockoutGSE123Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P7. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA {%7!!'3U{P10 knockoutGSE124Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P10. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA |%7!!'3U|P14 knockoutGSE125Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P14. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA }%7!!'3U}P18 knockoutGSE126Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P18. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA ~%7!!'3U~P21 knockoutGSE127Public on Apr 15 20042002-12-172005-05-29Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P21. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.repeat sampleQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA W7!!c3URp1 knockout mice retinal developmentGSE128Public on Apr 15 20042002-12-172006-03-28Mice were a mixed background between 129/SvEv and C57BL/6.; Rp1 knockout mice (Rp1-/-) and wildtype littermates examined.; At P7, P10, P14, P18 and P21, mice were sacrificed and retinas removed.; Each RNA sample included a pool of neural retinas from 3-4 mice.; Retinas were all collected at 1-2 pm.otherQian,,Huang; Jiewu Liu; Wei Liu; Kyeogmi Cheon; Jason Higdon; Cheng Cheng; Jian ZuoName: Jiewu Liu; Email: jiewu.liu@gmail.com; Phone: 901-495-3893; Laboratory: Jian Zuo's Lab; Department: Department of Developmental Neurobiology; Institute: St. Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA &"&x7!!'coDrosophila melanogaster CantonS blue gut larvae vs. white prepupaeGSE130Public on Jan 27 20032002-12-242005-06-15xDrosophila melanogaster CantonS blue gut larvae vs. white prepupaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/Zu7!!u'coDrosophila yakuba white prepupae vs. blue gut larvaeGSE129Public on Jan 27 20032002-12-242005-06-15xDrosophila yakuba white prepupae vs. blue gut larvaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/ 7!!'coDrosophila melanogaster Netherlands2 blue gut larvae vs. white prepupaeGSE131Public on Jan 27 20032002-12-242005-06-15xDrosophila melanogaster Netherlands2 blue gut larvae vs. white prepupaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/ x7!!'coDrosophila melanogaster OregonR blue gut larvae vs. white prepupaeGSE132Public on Jan 27 20032002-12-242005-06-15xDrosophila melanogaster OregonR blue gut larvae vs. white prepupaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/ ^y7!!y'coDrosophila simulans blue gut larvae vs. white prepupaeGSE134Public on Jan 27 20032002-12-242005-06-15xDrosophila simulans blue gut larvae vs. white prepupaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/|7!!'coDrosophila melanogaster Samarkand blue gut larvae vs. white prepupaeGSE133Public on Jan 27 20032002-12-242005-06-15xDrosophila melanogaster Samarkand blue gut larvae vs. white prepupaerepeat sampleScott,A,Rifkin; Junhyong Kim; Kevin,P,WhiteName: Scott,A,Rifkin; Phone: 617-496-5540; Laboratory: Hartl Lab; Department: OEB; Institute: Harvard University; Address: 16 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: kim.bio.upenn.edu/~scott/to Kit(+)/EpoR-high/CD71(+)/Ter119(-) proerythroblasts [stage I]; Kit-low/EpoR(+)/CD71-high/Ter119(+) polychromatophilic erythroblasts [stage II]; and Kit(-)/EpoR-low/CD71-low/Ter119-high/lowFALS normoblasts [stage III]. Primary splenic (pro)erythroblasts were prepared at 80, 100 and 120 hours post thiamphenicol dosing, and were purified by MACS using a transgenic erythroid-restricted “EE” tag. For each stage, duplicate hybridizations were performed. GSM3371 and GSM3372 are results from stage I hybridizations; GSM3373 and GSM3374 are results for stage II; and GSM3375 and GSM3376 are results for stage III. The order of listed genes is organized based first on average p-value among all six hybridizations in ascending order, and second on fold-increases in expression levels from stage I to stage II (descending order).; ; B] METHOD DETAILS (as a supplement to Zhang et al., submitted) B1-B6 below:; ; B.1/ ERYTHROID PROGENITOR CELL PREPARATIONS: Thiamphenicol (TAP) (Sigma, St. Louis, MO) was administered on day 1 to 8-week old Gata1-“EE” mice [1] (15 mg per gram weight in 0.4 mL of water) as a subcutaneous implant in Spectra Por 2 tubing (Spectrum, Houston, TX) [2]. On days 2 through 4, mice were phlebotomized (80mL blood per day), and TAP implants were removed on day 6. Splenocytes were prepared at 80, 100, or 120 hours post TAP withdrawal by disruption of spleens in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 2% fetal bovine serum (FBS) and 0.1 U/mL Epo. Cells were passed through a 70 um strainer (Falcon, Franklin Lakes, NJ), collected at 300 x g for 10 minutes, resuspended in 1 mL of phosphate-buffered saline (PBS, 140 mM NaCl, 2.7 mM KCl, 8.1 mM Na2HPO4, 1.2 mM KH2PO4, pH 7.4), exposed for 2 minutes to 9 mL of 0.8% NH4Cl, 0.01 mM Na2EDTA buffered at pH 7.5 with KHCO3. Cells then were collected through 50% FBS in PBS, and washed in DMEM.; B.2/ MACS: Splenocytes (3x10^8 cells per 3 spleens per preparation) in 3 mL of 5mM Na2EDTA, 0.5 % BSA in PBS, pH 7.2 (PBE) were incubated for 5 minutes at 15°C with murine IgG Fc fragment (5 μg per mL) (Pierce, Rockford, IL), and pre-absorbed for 20 minutes at 15°C with anti-mouse IgG2a+2b magnetic microbeads (100 μL per mL) (Miltenyi, Bergisch Gladbach, Germany). Samples were passed through a magnetized MACS-LS column (non-specific adsorption) and unbound cells were collected, washed and resuspended (at 1 x 10^8 cells per mL) in 3 mL of PBE buffer. Cells then were incubated at 15°C for 15 minutes with monoclonal antibody EGFR.1 (5 μg per mL) (PharMingen, San Diego, CA), washed in 20 mL of 2°C PBE buffer, resuspended in PBE at 1 x 10^8 cells per mL, and incubated for 20 minutes at 15°C with anti-mouse IgG2a+2b magnetic microbeads (200 μL per mL). Bead-tagged (pro)erythroblasts were washed in 2°C PBE buffer, resuspended in 3 mL PBE, and applied to a MACS-LS column. Columns were washed six times with 3 mL of PBE, and EE-positive cells were recovered in 5 mL of PBE buffer. Overall, 6 x 10^6 stage I, II and III (pro)erythroblasts were purified from 12, 4, and 3 mice, respectively.; B.3/ RNA ISOLATION AND ANALYSIS: Purified (pro)erythroblasts (6 x 10^6 cells) were lysed in 1 mL Trizol reagent (Life Technologies, Gaithersburg, MD). Chloroform (0.2 mL) was added and samples were vortexed and microcentrifuged at 7,500 rpm for 15 minutes at 4°C. The aqueous phase (approximately 0.5 mL) was recovered, and extracted using 0.5 mL of Trizol LS reagent plus 0.1 mL of chloroform. From the recovered epi-phase (750 μL), RNA was precipitated using isopropanol (750 μL), collected (10 minutes at 4°C, 12,000 rpm), washed with 80% ethanol, air-dried, and dissolved in 35 μl of 70°C DEPC-treated water. In Northern blotting, RNA samples were electrophoresed in 6% formaldehyde 1.2% agarose gels, blotted to Nytran membranes (Schleicher and Schuell, Keene, NH), and fixed (312 nm radiation for 3 minutes; 2 hours at 80°C under vacuum). In hybridizations, Redivue deoxyadenosine 5'-(α-32P)-triphosphate labeled probes were prepared by random priming (Prime-a-Gene System, Promega, Madison, WI) using 25 ng of the following cDNA fragments: murine Epo receptor, 880 bp Bgl II to Xba I fragment of pUC19ER-DpI3K [3]; murine beta-major globin, 1,100 bp Bgl II to Xba I fragment of pGEM7-betamaj-globin [4]; murine Kit, 1,500 bp BamH I to Nhe I fragment of pRep4DEB-cKit [5]; murine Gata-1, Xho I fragment of pBluescript-GATA-1 [6]; 32P-labeled probes were isolated using Sephadex G-50 microcolumns (Pharmacia Biotech, Piscataway, NJ). Hybridizations were for 4 hours at 68°C using 2 × 10^6 cpm of probe per mL in QuickHyb solution (Stratagene, La Jolla, CA). Membranes were exposed to X-OMAT AR film (Kodak, Rochester, NY) and were assayed quantitatively by phosphor imaging (Storm 860 system, Molecular Dynamics, Sunnyvale, CA).; B.4/ BIOTIN-cRNA PREPARATION, AND ARRAY HYBRIDIZATIONS: First-strand cDNA was synthesized with a T7-oligo (dT) 24 primer (5'-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT) 24-3') (Geneset, La Jolla CA) and Superscript II reverse transcriptase (Invitrogen, Carsbad, CA) (1 hour, 42°C). DNA polymerase I (cat# 18010-017, Invitrogen) and RNase H (cat# 18021-041, Invitrogen) were used in second strand syntheses (2 hours, 16°C). Products were extracted in Tris-phenol: chloroform: isoamyl (25:24:1) using a phase-lock gel (cat# 175850, Eppendorf 5-prime, Boulder, CO). Precipitation was with 0.5 volumes of 7.5M NH4Ac, 5 μg of glycogen and 2.5 volumes of -20°C absolute ethanol. Double stranded -cDNA (1 μg in 10 µl DEPC-treated water) was used per T7 RNA pol transcription (Enzo BioArray High Yield biotin-UTP and -CTP RNA Labeling Kit) (cat# 42655, Farmingdale, NY). Products were purified using QIAGEN RNeasy columns (cat# 72104) (Valencia, CA). For each sample (16 μg total RNA) approximately 60 μg of purified biotin-labeled cRNA was recovered. Labeled cRNA was fragmented for 35 min at 94°C in 500 mM potassium acetate (C2H3KO2), 150 mM magnesium acetate (C4H6MgO4), 200 mM Tris-acetate (C4H11NO3 • CH3COOH), pH 8.1. Each sample (diluted 1:10 in hybridization buffer) was first hybridized to a Test2 Genechip to confirm full-length transcript representation. Replicate hybridizations were to Affymetrix murine U74Av2 arrays, and data were analyzed using Affymetrix Genechip 5.1 software.; B.5/ ANALYSES OF PROFILING OUTCOMES: Transcripts expressed (detected) at each stage were identified based on a detection p-value of <0.05 in one replicate, and <0.1 in the other. 3'/5' ratios of housekeeping genes confirmed uniform biotin cRNA syntheses. Pair-wise comparisons among stages included 4659 transcripts detected in at least one stage, and employed averages of log expression values from duplicate hybridizations for each gene. In these comparisons, modulation is defined by vertical distances from a regression (no-modulation) trendline. For the above 4659 detected transcripts, mean expression values were normalized to account for chip/sample variability by subtracting the stage mean, and dividing by the stage standard deviation. The three normalized values of each gene (one for each stage) then were standardized by subtracting the gene mean and dividing by the gene standard deviation. Non-modulated genes (less than two-fold change) then were removed from further consideration. Clustering of the resulting data was performed by K-means (S+ package), a partitioning algorithm that pursues a minimum of the within-clusters sums of squares (WSS, which measures square Euclidean distances between cluster points and the cluster average within each cluster) [7]. Principal component analysis (PCA) was used to visualize K-means clustering results. PCA is a common method for reduction of dimensionality. WhorderedDiya,,Zhang; Don,M,WojchowskiName: Diya Zhang; Email: WOJCHD@mmc.org , diya@northwestern.edu; Phone: (207) 885-8258; Fax: (207) 885-8179; Laboratory: Dr. Don M. Wojchowski; Department: Molecular Medicine; Institute: Maine Medical Center Research Institute; Address: 81 Research Drive; City: Scarborough; State: ME; Zip/postal_code: 04074; Country: USA; Web_link: www.mmcri.org }77!!!Somatic embryogenesisGSE136Public on Apr 14 20032002-12-302005-06-15Examination of cotyledons after 7, 14, 21 and 28 days on 40mg/L 2,4-D.otherFrancoise,,Thibaud-Nissen; Robin,T,Shealy; Anupama Khanna; Lila,O,VodkinName: Lila,O.,Vodkin; Email: l-vodkin@uiuc.edu; Phone: 217-244-6147; Fax: 217-333-4582; Laboratory: Lila Vodkin; Department: Crop Sciences; Institute: University of Illinois; Address: 1201 W. Gregory Dr.; City: Urbana; State: IL; Zip/postal_code: 61801; Country: USA q7!!9GCErythroid Progenitor Cell Gene Expression ProfilesGSE135Public on May 02 20042002-12-262006-09-08A] DESCRIPTION - GENE EXPRESSION PROFILES were analyzed (via Affymetrix MG-U74Av2 arrays) at three distinct stages of late erythroid progenitor cell development. Stages correspond kk#7!!%mNatural variation in human gene expression assessed in lymphoblastoid cellsGSE137Public on Apr 22 20032002-12-312005-05-29•Lymphoblastoid cells from 35 unrelated individuals used to examined variation in gene expression. Identified genes whose transcript levels differed greatly among unrelated individuals.otherV,G,Cheung; L,K,Conlin; T,M,Weber; M Arcaro; K,Y,Jen; M Morley; R,S,SpielmanName: Michael Morley; Email: mmorley@mail.med.upenn.edu; Phone: 215-590-7673; Laboratory: Dr. Vivian Cheung Lab; Institute: Children's Hospital of Philadelphia; Address: ; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USA particular, the 5-HT2A receptor has been implicated in the modulation of the mechanisms related to psychosis. We compared gene response patterns in the somatosensory cortical brain area, which has a high density of 5-HT2A receptors and has been implicated in the action of hallucinogenic drugs. Mice (strain 129Sv) were injected with DOI (2 mg/kg or 10 mg/kg) or vehicle, animals were sacrificed after 1 h, and somatosensory cortex samples dissected on ice for RNA extraction. Seven independent microarray hybridizations from seven different DOI- or vehicle-treated mouse pairs were performed.otherJavier,,González-Maeso; Tony Yuen; Barbara,J,Ebersole; Elisa Wurmbach; Alena Lira; Jay,A,Gingrich; Stuart,C,Sealfonhttp://www.mssm.edu/labs/sealfon/Name: Elisa Wurmbach; Email: Elisa.Wurmbach@mssm.edu; Phone: 212-241-9779; Laboratory: Sam Waxman; Department: Hematology/Oncology; Institute: Mount Sinai School of Medicine; Address: 1 Gustave L. Levy Place; City: New York; State: NY; Zip/postal_code: 10029; Country: USA ))K 7!!5uO-Effect of serotonergic hallucinogen in mouse somatosensory cortexGSE138Public on Apr 29 20032002-12-312005-10-28ݚTo investigate the gene program activated by serotonergic hallucinogens in mouse somatosensory cortex, the effects of the 5-HT2A agonist (±)2,5-dimethoxy 4-iodoamphetamine (DOI) on gene expression was studied. The 5-HT2A serotonin receptor is a member of the 5-HT2 receptor subfamily of G protein–coupled receptors. The 5-HT2A receptor is thought to modulate processes related to cognition, appetite, mood, anxiety, sleep, and sexual behavior. Abnormal function of this receptor has been implicated in neuropsychiatric disorders such as major depression and schizophrenia. In  y7!!)qi1Rat muscle tissue group comparisons (skeletal-extraocular, skeletal-hindlimb, o 7!!7YKGene-expression profile comparisons distinguish seven organs of maizeGSE141Public on Jan 08 200{ I7!!a3+Effect of varying illuminationGSE139Public on Apr 21 20032002-12-312005-06-15Rhodobacter sphaeroides 2.4.1 illuminated with either lumiline bulbs at 10W/m2 or tungsten bulbs at 100W/m2.; Sparged with 95%N/5%CO2.otherJung,H,Roh; William,E,Smith; Samuel Kaplanwww.rhodobacter.orgName: Samuel Kaplan; Email: Samuel.Kaplan@uth.tmc.edu; Phone: 713-500-5505; Fax: 713-500-5499; Department: Microbiology and Molecular Genetics; Institute: University of Texas Health Science Center at Houston; Address: 6431 Fannin, JFB 1.765; City: Houston; State: TX; Zip/postal_code: 77030; Country: USA; Web_link: www.rhodobacter.org32003-01-072005-06-150A maize array was fabricated with 5,376 unique expressed sequence tag (EST) clones sequenced from 4-day-old roots, immature ears and adult organ cDNA libraries. To elucidate organ relationships, relative mRNA levels were quantified by hybridization with embryos, three maize vegetative organs (leaf blades, leaf sheaths and roots) from multiple developmental stages, husk leaves and two types of floral organs (immature ears and silks).; Clustering analyses of the hybridization data suggest that maize utilizes both the PEPCK and NADP-ME C(4) photosynthetic routes as genes in these pathways are co-regulated. Husk RNA has a gene-expression profile more similar to floral organs than to vegetative leaves. Only 7% of the genes were highly organ specific, showing over a fourfold difference in at least one of 12 comparisons and 37% showed a two- to fourfold difference. The majority of genes were expressed in diverse organs with little difference in transcript levels. Cross-hybridization among closely related genes within multigene families could obscure tissue specificity. As a first step in elucidating individual gene-expression patterns, we show that 45-nucleotide oligo probes produce signal intensities and signal ratios comparable to PCR probes on the same matrix.; Gene-expression profile studies with cDNA microarrays provide a new molecular tool for defining plant organs and their relationships and for discovering new biological processes in silico. cDNA microarrays are insufficient for differentiating recently duplicated genes. Gene-specific oligo probes printed along with cDNA probes can query individual gene-expression profiles and gene families simultaneously.otherY,,Cho; J Fernandes; S,H,Kim; V WalbotName: Yangrae Cho; Email: yacho@sequence.stanford.edu; Phone: 650-812-1976; Fax: 650-812-1975; Laboratory: V. Walbot; Department: Biological Sciences; Institute: Stanford University; Address: 385 Serra Mall; City: Stanford University; State: CA; Zip/postal_code: 94305-8221; Country: USAsmooth-stomach, and cardiac; Porter lab)GSE142Public on Apr 02 20032003-01-082005-06-15&Comparison of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall). Affymetrix microarray chip RG-U34A was used. MAS version 5 was used to analyze the muscle group differences. Data form part of publication: FASEB Journal 17: 1370-1372, 2003 (full length article available at http://www.fasebj.org/cgi/doi/10.1096/fj.02-1108fje).otherJ,D,Porter; A,P,Merriam; P Leahy; B Gong; S KhannaName: Sangeeta Khanna; Email: sxk128@po.cwru.edu; Phone: 216-844-1429; Fax: 216-844-4792; Laboratory: John D. Porter (john.porter@case.edu); Department: Neurology; Institute: Case Western Reserve University; Address: 11100 Euclid Avenue; City: Cleveland; State: OH; Zip/postal_code: 44106; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE142/GSE142_RAW.tars. An initial screen of the cDNA clone arrays lead to the identification of 753 unique ESTs. Many showed sequence similarity to known metabolic and regulatory genes; however, no function could be ascribed to over 50% of the ESTs. Gene expression analysis of Aspergillus parasiticus grown under conditions conducive and non-conductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs. Twenty-four genes were more highly expressed during aflatoxin biosynthesis and 18 genes were more highly expressed prior to aflatoxin biosynthesis. No predicted function could be ascribed to 18 of the 24 genes whose elevated expression was associated with aflatoxin biosynthesis.; Keywords; Keywordstime-courseGregory,R,OBrian; Ahmad,M,Fakhoury; Gary,A,PayneName: Ahmad Fakhoury; Email: amfakhou@siu.edu; Phone: 919-515-6995; Laboratory: Payne; Department: Plant Pathology; Institute: North Carolina State University; Address: ; City: Raleigh; State: NC; Zip/postal_code: 27695; Country: USA QQ# C7!!=#maDifferential expression of Aspergillus genes during the induction of aflatoxin biosynthesisGSE204Public on Jan 15 20032003-01-152005-05-29fGene expression analysis of A. parasiticus grown under conditions conducive and nonconductive for aflatoxin production was evaluated using glass slide microarrays containing the 753 ESTs.; ; ; A complex regulatory network governs the biosynthesis of aflatoxin. While several genes involved in aflatoxin production are known, their action alone cannot account for its regulation. Arrays of clones from an Aspergillus flavus cDNA library and glass slide microarrays of ESTs were screened to identify additional gene HA7!!'wEMouse T helper cell clonesGSE205Public on Jun 12 20032003-01-152005-07-21(Regulatory T cells overexpress a subset of Th2 gene transcripts. A comparison of murine CD4+ Th1, Th2 and Tr1/Treg clones with identical TCR specificity for the male transplantation antigen H-Y.; KeywordsotherDiana,,Zelenika; Elizabeth Adams; Susan Humm; Luis Graca; Sara Thompson; Steve Cobbold; Herman Waldmann; Chun-Yen LinName: Steve Cobbold; Email: stephen.cobbold@path.ox.ac.uk; Phone: +44-(0)1865-275504; Fax: +44-(0)1865-275501; Laboratory: Therapeutic Immunology Group; Department: Sir William Dunn School of Pathology; Institute: University of Oxford; Address: South Parks Road; City: Oxford; State: Oxfordshire; Zip/postal_code: OX1 3RE; Country: United Kingdom; Web_link: http://www.molbiol.ox.ac.uk/pathology/tig/welcome.html TT(M7!!?ECD4/CD25 subsets of mouse spleenGSE206Public on Jun 12 20032003-01-152005-05-29v7A comparison of CD4+CD25+ and CD4+CD25- splenic T cells. Although both subsets have regulatory T cell activity in an induced transplantation tolerance model, the CD4+CD25+ subsets are apparently 10 fold enriched in regulatory T cells. SAGE analysis is performed and compared both on resting and CD3 activated populations.otherLuis,,Graca; Sara Thompson; Chun-Yen Lin; Elizabeth Adams; Steve Cobbold; Herman WaldmannName: Steve Cobbold; Email: stephen.cobbold@path.ox.ac.uk; Phone: +44-(0)1865-275504; Fax: +44-(0)1865-275501; Laboratory: Therapeutic Immunology Group; Department: Sir William Dunn School of Pathology; Institute: University of Oxford; Address: South Parks Road; City: Oxford; State: Oxfordshire; Zip/postal_code: OX1 3RE; Country: United Kingdom; Web_link: http://www.molbiol.ox.ac.uk/pathology/tig/welcome.html `+7!!S#3[KHDMTX_MP-1 pairGSE207Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a-7!!S#3[KHDMTX_MP-10 pairGSE208Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-2 pairGSE209Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-3 pairGSE210Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-4 pairGSE211Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-5 pairGSE212Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-6 pairGSE213Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-7 pairGSE214Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-8 pairGSE215Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `+7!!S#3[KHDMTX_MP-9 pairGSE216Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]%7!!S#3[KHDMTX-1 pairGSE217Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^'7!!S#3[KHDMTX-10 pairGSE218Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^'7!!S#3[KHDMTX-11 pairGSE219Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^'7!!S#3[KHDMTX-12 pairGSE220Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^'7!!S#3[KHDMTX-13 pairGSE221Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^'7!!S#3[KHDMTX-14 pairGSE222Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^ '7!!S#3[KHDMTX-15 pairGSE223Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm,,111117B?@FKIMQRzzzzzzz`z`azzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz ^!'7!!S#3[KHDMTX-16 pairGSE224Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^"'7!!S#3[KHDMTX-17 pairGSE225Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^#'7!!S#3[KHDMTX-18 pairGSE226Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^$'7!!S#3[KHDMTX-19 pairGSE227Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]%%7!!S#3[KHDMTX-2 pairGSE228Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^&'7!!S#3[KHDMTX-20 pairGSE229Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^''7!!S#3[KHDMTX-21 pairGSE230Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ^('7!!S#3[KHDMTX-22 pairGSE231Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ])%7!!S#3[KHDMTX-3 pairGSE232Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]*%7!!S#3[KHDMTX-4 pairGSE233Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]+%7!!S#3[KHDMTX-5 pairGSE234Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm|~~ #(-27<AFKPUZ_dinsx} "',16;@EJOTY^chmrw|      !#$%'()L  |W  # $ &F&U!#$%'()*+-/0135 7!8"9&='>(?)@*A+B,C-D.E/F0I1J2K5O6P7Q8R:U;X>\?]@^A_B`CaDbEcFdGeHfIgLjMkNmPnQoRpSrVuWvXwYx[{\|]~_`abcdefghinopqrstuvwxyz{|}~ ÁāŁƁǁȁofWflrx~ &,28>DJPV\bhntz "(.4:@FLRX^djpv|"ʁˁ́́΁ Ё!с"ҁ#Ӂ$ԁ%Ձ&ց'ׁ(؁)ف*ʁˁ́́΁ Ё!с"ҁ#Ӂ$ԁ%Ձ&ց'ׁ(؁)ف*ځ+݁,ށ-߁./0123456789:;<=>?@ABCDEFGHIJKLMNOQRSTUV W X Y Z [\]^_befgjm n!o"p#q$r%s&t'u(v)w*x,z.{/|1789:;<=> B C D E FHKMNOPQTUV ],%7!!S#3[KHDMTX-6 pairGSE235Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]-%7!!S#3[KHDMTX-7 pairGSE236Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ].%7!!S#3[KHDMTX-8 pairGSE237Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ]/%7!!S#3[KHDMTX-9 pairGSE238Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `0+7!!S#3[KLDMTX_MP-1 pairGSE239Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a1-7!!S#3[KLDMTX_MP-10 pairGSE240Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a2-7!!S#3[KLDMTX_MP-11 pairGSE241Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a3-7!!S#3[KLDMTX_MP-12 pairGSE242Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a4-7!!S#3[KLDMTX_MP-13 pairGSE243Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm b5/7!!S#3[KLDMTX_MP-14 pairGSE244Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a6-7!!S#3[KLDMTX_MP-15 pairGSE245Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm a7-7!!S#3[KLDMTX_MP-16 pairGSE246Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `8+7!!S#3[KLDMTX_MP-2 pairGSE247Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `9+7!!S#3[KLDMTX_MP-3 pairGSE248Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `:+7!!S#3[KLDMTX_MP-4 pairGSE249Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `;+7!!S#3[KLDMTX_MP-5 pairGSE250Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `<+7!!S#3[KLDMTX_MP-6 pairGSE251Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `=+7!!S#3[KLDMTX_MP-7 pairGSE252Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `>+7!!S#3[KLDMTX_MP-8 pairGSE253Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm `?+7!!S#3[KLDMTX_MP-9 pairGSE254Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm Z@7!!S#3[KMP-1 pairGSE255Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm [A!7!!S#3[KMP-10 pairGSE256Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm [B!7!!S#3[KMP-11 pairGSE257Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm [C!7!!S#3[KMP-12 pairGSE258Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZD7!!S#3[KMP-2 pairGSE259Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZE7!!S#3[KMP-3 pairGSE260Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZF7!!S#3[KMP-4 pairGSE261Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZG7!!S#3[KMP-5 pairGSE262Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZH7!!S#3[KMP-6 pairGSE263Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZI7!!S#3[KMP-7 pairGSE264Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZJ7!!S#3[KMP-8 pairGSE265Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm ZK7!!S#3[KMP-9 pairGSE266Public on Apr 21 20032003-01-152005-05-29څpre- and post-treatment sample pairtime-courseM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm JJ2L7!!3[KLDMTX_MPGSE267Public on Apr 21 20032003-01-162005-05-29څprimary ALL cells from bone marrow aspirates taken two days after in vivo treatment with low-dose methotrexate and mercaptopurineotherM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm __M7!!k3[KHDMTXGSE268Public on Apr 21 20032003-01-162005-05-29څprimary ALL cells from bone marrow aspirates taken two days after in vivo treatment with high-dose methotrexateotherM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm II3N7!!3[KHDMTX_MPGSE269Public on Apr 21 20032003-01-162005-05-29څprimary ALL cells from bone marrow aspirates taken two days after in vivo treatment with high-dose methotrexate and mercaptopurineotherM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm jjO7!![3[KMPGSE270Public on Apr 21 20032003-01-162005-05-29څprimary ALL cells from bone marrow aspirates taken two days after in vivo treatment with mercaptopurineotherM,H,Cheok; W Yang; C,H,Pui; J,R,Downing; C Cheng; C,W,Naeve; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm aQ[7!!ea5T and B lymphocyte development profilesGSE272Public on Jan 29 20032003-01-282005-07-21SFExpression profiles of seven consecutive stages of mouse thymocyte development were generated. Previously known expression patterns of several genes were confirmed. Ten percent (1,304 of more than 13,000) of the monitored genes were found witwP_7!!CYDrosophila Eye Development - Larval StageGSE271Public on Jan 21 20032003-01-212005-09-28Analysis of gene expression during Drosophila eye formation.otherLydia,,Michaut; Susanne Flister; Martin Neeb; Kevin,P,White; Ulrich Certa; Walter,J,GehringName: Lydia Michaut; Email: Lydia.Michaut@unibas.ch; Phone: +41612672054; Fax: +41612672078; Department: Cell Biology; Institute: Biozentrum; Address: Klingelbergstrasse 70; City: Basel; Zip/postal_code: 4056; Country: Switzerlandh 99% confidence to be differentially expressed across all T cell developmental stages. When compared with 1,204 genes differentially expressed in five consecutive B lineage developmental stages of bone marrow, >40% (546 genes) appeared to be shared by both lineages. However, when four pools of functionally distinct cell stages were compared between B and T cell development, DJ-rearranged precursor cells and resting immature precursor cells before and after surface Ag receptor expression shared less than 10%, mature resting lymphocytes between 15 and 20%, and only cycling precursors responding to precursor lymphocyte receptor deposition shared >50% of these differentially expressed genes.otherReinhard,,Hoffmann; Ludovica Bruno; Thomas Seidl; Antonius Rolink; Fritz Melchers; Ton Rolink; Martin NeebName: Reinhard Hoffmann; Email: reinhard.hoffmann@lrz.tum.de; Phone: +49-89-4140-4155; Institute: Institute for medical microbiology; Address: Trogerstr. 30; City: Munich; Zip/postal_code: 81675; Country: Germany R;7!!/yQAging primary myoblastsGSE273Public on Jan 10 20052003-01-302005-05-29Comparison of primary myoblasts isolated from 8- and 23-month-old DBA/2JNIA mice.otherM,L,Beggs; R Nagarajan; J,M,Taylor-Jones; C,A,PetersonName: Marjorie,L,Beggs; Email: BeggsMarjorieL@uams.edu; Phone: 501-526-5809; Laboratory: Charlotte Peterson, Ph.D.; Department: Geriatrics; Institute: University of Arkansas for Medical Sciences; Address: 629 S. Elm Street; City: Little Rock; State: AR; Zip/postal_code: 72205; Country: USA TT(Si7!!- 9Overexpression of the plant LAMMER kinase PK12GSE274Public on Feb 05 20032003-02-032005-06-15XpComparison of plants that overexpress PK12 and non-transformed plants. Plants were grown for 10 days under long day conditions (GSM3816-GSM3819) or plants were grown for 21 days under long day conditions (GSM3820-GSM3823) . Hybridization was performed on arrays from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K (GSM3816-GSM3819) or 9K (GSM3820-GSM3823)Arabidopsis ESTs. The 4 samples corresponding to each array represent 2 repetitions of 2 independent biological experiments.; Keywords; Keywordsequivalent probeSigal,,Savaldi-Goldstein; Olga Davydov; Dvora Aviv; Robert FluhrName: Robert Fluhr; Email: robert.fluhr@weizmann.ac.il; Phone: 972-8-9342175; Department: Plant Sciences; Institute: Weizmann Institute of Science; Address: ; City: Rehovot; Zip/postal_code: 76100; Country: Israelehensive manner, genome-wide oligonucleotide arrays were used to analyze differential gene expression in wild-type embryos versus embryos in which gcm is misexpressed throughout the neuroectoderm. Transcripts were analyzed at two defined temporal windows during embryogenesis. This first genome-wide analysis of gene expression events downstream of a key developmental transcription factor presents a novel level of insight into the repertoire of genes that initiate and maintain cell fate choices in CNS development.otherB,,Egger; R Leemans; T Loop; L Kammermeier; Y Fan; T Radimerski; M,C,Strahm; U Certa; H Reicherthttp://www.zoo.unibas.ch/resreich1.htmlName: Boris Egger; Email: Boris.Egger@stud.unibas.ch; Phone: ++41-(0)61-267 16 16; Fax: ++41-(0)61-267 16 13; Laboratory: Dr. Heinrich Reichert; Department: University of Basel; Institute: Institute of Zoology; Address: Klingelbergstrasse 50; City: Basel; State: BS; Zip/postal_code: 4056; Country: Switzerland; Web_link: http://www.zoo.unibas.ch/resreich1.html ww}T?7!!UM[_Gliogenesis in DrosophilaGSE276Public on Feb 04 20032003-02-042005-07-21In Drosophila, the glial cells missing (gcm) gene encodes a transcription factor that controls the determination of glial versus neuronal fate. In gcm mutants, presumptive glial cells are transformed into neurons and, conversely, when gcm is ectopically misexpressed, presumptive neurons become glia. Although gcm is thought to initiate glial cell development through its action on downstream genes that execute the glial differentiation program, little is known about the identity of these genes. To identify gcm downstream genes in a compr   rU 7!! 5-Effect of uniconazole-P on wt and pkl mutant germinating seedsGSE277Public on Jul 07 20032003-02-052005-06-15`Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl). Each experimental condition (wt, pkl, Uwt and Upkl) has four true replicates for a total of 16 chips.; Keywords; Keywords; Keywords; Keywords; KeywordsotherS Jr,,Dean Rider; J,T,Henderson; R,E,Jerome; H,J,Edenberg; J Romero-Severson; J OgasName: Jeanne Romero-Severson; Email: romeros@fnr.purdue.edu; Phone: 765-496-6801; Department: ; Institute: Purdue University; Address: ; City: West Lafayette; State: IN; Zip/postal_code: 47907; Country: USA iVQ7!!g1Pancreas and islet gene expressionGSE278Public on Feb 05 20032003-02-052005-10-28Gene expression of pancreatic exocrine cells, pancreatic islets and hand-selected pancreatic islets examined.otherH,,Inoue; C Cras-Méneur; Y Zhou; M Ohsugi; E Bernal-Mizrachi; D Pape; S,W,CliftonName: Corentin Cras-Méneur; Email: ccrasmen@im.wustl.edu; Phone: 314-747-0414; Laboratory: M. A. Permutt; Department: Metabolism Division; Institute: Washington University School of Medicine; Address: 660 S. Euclid; City: Saint Louis; State: MO; Zip/postal_code: 63110; Country: USA; Web_link: http://www.wustl.edu/ tWY7!!{'Mammary tissue gene expression studiesGSE279Public on Feb 07 20032003-02-072005-06-15*A series of experiments to establish a bovine developing mammary gland gene expression signature, identify genes differentially expressed in bovine lactating mammary gland, and to establish the false positive rate of the BMAM microarray; Keywordsrepeat sampleSteven,P,Suchyta; Sue Sipkovsky; Robert,G,Halgren; Paul,M,CoussensName: Steven,Paul,Suchyta; Email: suchytas@msu.edu; Phone: 517-355-8443; Laboratory: Center for Animal Functional Genomics; Department: Animal Science; Institute: Michigan State University; Address: B215 Anthony Hall; City: East Lansing; State: MI; Zip/postal_code: 48824; Country: USA; Web_link: http://nbfgc.msu.edu ffXE7!!-#sQMouse EE uterine time courseGSE280Public on Apr 09 20032003-02-112005-06-15Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1 mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose. Two replicates of each sample are provided. In addition, one time=0 sample is included.; Keywordstime-courseK,C,Fertuck; J,E,Eckel; C Gennings; T,R,ZacharewskiName: Tim Zacharewski; Email: tzachare@msu.edu; Phone: 517-355-1607; Fax: 517-353-9334; Department: Biochemistry & Molecular Biology, National Food Safety & Toxicol; Institute: Michigan State University; Address: 223 Biochemistry Bldg.; City: East Lansing; State: MI; Zip/postal_code: 48824-1319; Country: USA; Web_link: http://www.bch.msu.edu/~zacharet/ 3Y77!!%5iInflammatory myopathyGSE281Public on Feb 12 20032003-02-112005-06-15Molecular profiles of muscle tissue in patients with inflammatory myopathiesotherS,A,Greenberg; D Sanoudou; J,N,Haslett; I,S,Kohane; L,M,Kunkel; A,H,Beggs; A,A,AmatoName: Steven,Alan,Greenberg; Email: sagreenberg@partners.org; Phone: 617 732-8641; Fax: 617 730-2885; Laboratory: Division of Neuromuscular Disease; Department: Neurology; Institute: Brigham and Women's Hospital; Address: 75 Francis Street; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA 44HZG7!!'};Interferon induction by shRNAGSE282Public on Feb 21 20032003-02-122005-06-15CmEmbryonic lung fibroblasts (HLF) infected with either control lentivirus (GSM3892), or lentivirus expressing MRG15 and MRGX small hairpin RNAs from the H1 polIII promoter (GSM3891). The MRG15 shRNA induces an interferon response that is unrelated to silencing of MRG15.otherA,J,Bridge; S Pebernard; A Ducraux; A,L,Nicoulaz; R IggoName: Richard Iggo; Email: Richard.Iggo@st-andrews.ac.uk; Phone: +44 1334 463558; Fax: +44 1334 463482; Department: Bute Medical School; Institute: University of St Andrews; Address: Westburn Lane; City: St Andrews; State: Fife; Zip/postal_code: KY16 9TS; Country: United Kingdom I[?7!!GE17sage gene RNAi experimentGSE283Public on Jul 23 20032003-02-182005-05-29tComparisons between the salivary glands upon the RNAi of sage gene vs. the control.; KeywordsotherTong-Ruei,,Li; Kevin,P,Whitehttp://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703001928Name: Tong-Ruei Li; Email: tong-ruei.li@yale.edu; Phone: 203-785-4474; Laboratory: Kevin White; Department: Department of Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St. Rm#NSB386; City: New Haven; State: CT; Zip/postal_code: 06511; Country: USA \a7!!yCSkin irradiation and vitamin A supplementsGSE284Public on Mar 20 20032003-02-202005-05-297Analysis of gene expression in skin of rats subjected to electron irradiation and the effect of vitamin A supplements.otherF,J,BurnsName: Fredric,J.,Burns; Email: burns@env.med.nyu.edu; Phone: 845-731-3551; Fax: 845-351-2118; Laboratory: Radiation Cancer; Department: Environmental Medicine; Institute: NYU School of Medicine; Address: 550 First Ave.; City: New York; State: NY; Zip/postal_code: 10016; Country: USA n]7!!%'s11hr C-CA1GSE285Public on Feb 26 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA n^7!!%'s12hr C-CA1GSE286Public on Feb 26 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA n_7!!%'s14hr C-CA1GSE287Public on Feb 26 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA 00ob#7!!#'s12hr C+S-CA1GSE290Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shocoa#7!!#'s11hr C+S-CA1GSE289Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shocn`7!!%'s16hr C-CA1GSE288Public on Feb 27 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USAk. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USAk. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USAk. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA 1"1me7!!%'s11hr C-DGGSE293Public on Feb 27 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USAod#7!!#'s16hr C+S-CA1GSE292Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shococ#7!!#'s14hr C+S-CA1GSE291Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA mf7!!%'s12hr C-DGGSE294Public on Feb 27 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA mg7!!%'s14hr C-DGGSE295Public on Feb 27 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA 11nj!7!!#'s12hr C+S-DGGSE298Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shockni!7!!#'s11hr C+S-DGGSE297Public on Feb 27 20032003-02-262005-05-29C + S: Context + Shockmh7!!%'s16hr C-DGGSE296Public on Feb 27 20032003-02-262005-05-29C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. All three sample treatments are identical but prepared separately.repeat sampleJonathan,M,Levenson; Sangdun Choi; Sun-Young Lee; Yun Anna Cao; Kim Worley; Hui Zheng; Melvin,I,Simon; David SweattName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA b"bi7!!}1C>Spleen vs Leukotriene B4 (LTB4) Treated B cellGSE390Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Leukotriene B4 (LTB4) labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org  ?S7!!g1C?Spleen vs MIP3-alpha Treated B cellGSE391Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with MIP3-alpha labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.orgof3flrx~ &,28>DJPV\bhntz "(.4:@FLRX^djpv|XY Z![#\$]%^&`(c)d*e+f,g-h.i/XY Z![#\$]%^&`(c)d*e+f,g-h.i/j0k1l2m3n4o5p6q7r8s9t:u;v<w=x>y?{@|A}B~CDEFGHIJLPQSTUVWXYZ[]abcdehjklmno‚rłsƂtǂvȂwɂxʂz˂|͂}΂~ςփ׃؃݃߃    ! "%&'()+,-./!0#1&3*4-728 )@q7!!1C@Spleen vs NGF (Nerve Growth Factor) Treated B cellGSE392Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with NGF (Nerve Growth Factor) labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org A[7!!o1CASpleen vs Neuropeptide Y Treated B cellGSE393Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Neuropeptide Y labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org +Bs7!!1CBSpleen vs Platelet activating factor Treated B cellGSE394Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Platelet activating factor labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org C_7!!s1CCSpleen vs Prostaglandin E2 Treated B cellGSE395Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Prostaglandin E2 labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org %Dm7!!1CDSpleen vs Sphingosine-1-phosphate Treated B cellGSE396Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Sphingosine-1-phosphate labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org LE7!!'1CESpleen vs SDF1 alpha (Stromal cell derived factor-1) Treated B cellGSE397Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with SDF1 alpha (Stromal cell derived factor-1) labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org HF7!!#1CFSpleen vs SLC (Secondary lymphoid-organ chemokine) Treated B cellGSE398Public on Apr 14 20032003-04-112005-06-15total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with SLC (Secondary lymphoid-organ chemokine) labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org  GU7!!i1CGSpleen vs Terbutaline Treated B cellGSE399Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Terbutaline labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org LH7!!'1CHSpleen vs TGF-beta (transforming growth factor-beta) Treated B cellGSE400Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with TGF-beta (transforming growth factor-beta) labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org -Iu7!! 1CISpleen vs Tumor necrosis factor-alpha Treated B cellGSE401Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells treated with Tumor necrosis factor-alpha labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org  JU7!!g1CJSpleen vs Untreated, cultured B cellGSE402Public on Apr 14 20032003-04-112005-05-29total RNA from mouse (male c57BL/6) spleen labeled with Cy3 vs total RNA from mouse (male c57BL/6) B cells untreated and cultured, labeled with Cy5- time course with repeatsorderedRebecca,,Hart; Mi Sook Chang; Jong-Woo Kim; Yun Anna Cao; Sun Young Lee; Angela Alexander; Joella Grossoehme; Zhen Yan; Robert Hsueh; Sangdun ChoiName: Sangdun Choi; Email: schoi@its.caltech.edu; Phone: 626-395-8732; Laboratory: Alliance for Cellular Signaling Molecular Biology Laboratory; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA; Web_link: www.signaling-gateway.org L{7!!%#gk%LEffect of glutamine concentration on hepatoma cell lineGSE404Public on Apr 16 20fK7!!#]]KcAMP-induced differentiation of endometrial stromal cellsGSE403Public on Apr 14 20032003-04-142005-06-15ݾTimecourse of cAMP-induced decidualization of endometrial stromal cells.time-courseE,P,Tierney; S Tulac; J Huang; L GiudiceName: Said Talbi; Email: talbi@stanford.edu; Phone: 650-701-0451; Department: Reproductive Endocrinology; Institute: Stanford University School of Medicine; Address: ; City: Stanford; State: CA; Zip/postal_code: 94025; Country: USA032003-04-142005-10-28oA mouse hepatoma cell line (Hepa1-6 cells, ATCC) was grown in T-25 tissue culture flasks (Corning) at 37ºC in 5% CO2 under two conditions. The first condition was the control, which contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine, 1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second condition was identical to the first, however the glutamine concentration was altered periodically.; ; Once the cells had grown to confluency, the experiment began at 9:30 PM by exchanging the medium in all flasks. The control flasks received the same medium, containing 4 mM glutamine, while the experimental flasks received identical medium with no glutamine. Twenty-four hours later, the medium was exchanged again, however this time all flasks received medium containing 4 mM glutamine. The first medium exchange was repeated at 48 hours into the experiment, while the second was repeated at 72 hours into the experiment. Hence the glutamine concentration of the experimental flasks oscillated between 0 mM and 4 mM glutamine over 96 hours, while the glutamine concentration of the control flasks remained constant at 4 mM glutamine. At regular intervals, the flasks were sampled. Total RNA was isolated, medium samples were retained, and isotopic measurements were performed from flasks fed different labelled compounds. All samples taken during the experiment were analyzed.; ; The total RNA harvested was labeled and hybridized to DNA microarrays to measure the abundance of transcripts present. Total RNA control samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was aliquoted into a 6 uL volume. If concentration of the RNA was necessary, this was conducted using a speed vacufuge (Eppendorf) at 60ºC for 10 minutes. The RNA sample was then mixed with 2 uL of 10X Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP, dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20 (Invitrogen), and 2 uL of Superscript II reverse transcriptase (Invitrogen). This reaction mixture was incubated at 42ºC for approximately two hours. Following the reverse transcription reaction, the RNA template was degraded by addition of 2 uL of 1 N NaOH and incubation at 65 ºC for 10 minutes. The alkaline conditions were then neutralized by addition of 2 uL of 1 N HCl. Samples from identical time points that were to be compared on DNA microarrays were then mixed. The combined sample was cleaned to remove extra primers and nucleotides using a QIAquick Nucleotide Removal kit as described by the manufacturer's instructions. Once cleaned, the sample was concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65ºC. Following concentration, the sample was resuspended in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), 1 uL was; removed for quantitation, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 ºC using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), and then in 1X SSC, and finally 0.1X SSC. Each wash step was conducted for 20 minutes under high agitation. The arrays were dried by centrifugation and scanned using GenePix 4000B scanner (Axon Instruments). The resulting data was downloaded and formatted in Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.).; ; The arrays used for hybridization were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). These arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). Briefly, the library was resuspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed using 32 pins (Telechem), at approximately 50% humidity. Once printed, the probes were crosslinked to the glass slides using a UV Stratalinker (Stratagene). The slides were then blocked for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric acid, pH 8.0. They were cleaned by rinsing in 250 mL of milli-Q water (X2), followed by 250 mL of 95% ethanol. They were finally dried using filtered air and stored in the dark at room temperature.; Keywordstime-courseM,,Wong; R Raab; J Kelleher; G Stephanopouloshttp://web.mit.edu/cheme/gnswebpage/index.shtmlName: R.,Michael,Raab; Email: rmraab@mit.edu; Phone: 617-258-0349; Fax: 617-253-3122; Laboratory: Laboratory for Bioinformatics and Metabolic Engineering; Department: Chemical Engineering; Institute: Massachusetts Institute of Technology; Address: 77 Massachusetts Avenue; City: Cambridge; State: MA; Zip/postal_code: 02139; Country: USA; Web_link: http://web.mit.edu/cheme/gnswebpage/index.shtmloscopic analysis were immediately snap-frozen in liquid nitrogen and at no time prior to or during subsequent sample manipulation were the samples allowed to thaw. Standard laboratory procedures to eliminate the presence of RNases, including the use of RNase free plastic-ware, heat baked glassware, molecular biology grade chemicals and DEPC-treated solutions, were adopted. Frozen biopsies were crushed to a fine powder under liquid nitrogen using a manual crusher with a teflon head (Omnilab) and total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol, with minor modifications that improved RNA yields and purity in our hands. In brief, crushed biopsy samples were lysed in an appropriate volume of Buffer RLT (typically 600 µL/20 mg tissue). To facilitate complete lysis, samples were allowed to stand at room temperature for 5-10 min before vortexing. The lysate was homogenized by addition to a QIA shredder column (Qiagen) and centrifuged at 14,000 rpm for 2 min. The resulting supernatant was centrifuged at 14,000 rpm for 3 min to pellet any cell debris. One volume of 70% ethanol was added to the cleared lysate, added to the RNeasy column and centrifuged at 10,000 rpm for 15 sec. Bound RNA was washed with the addition of RW1 buffer to the column and allowed to stand at room temperature for 10 min followed by centrifugation at 10,000 rpm for 15 sec. DNase 1 incubation mix (Stock: 273 kunits; RNase-free DNase Set, Qiagen) was added directly to the spin column membrane and digestion of any contaminating genomic DNA was carried out at room temperature for 30 min. The column was washed with RWI buffer and the DNase treatment step was repeated. The bound RNA was washed with RW1 buffer and centrifuged at 10,000 rpm for 15 sec three times, followed by two additional wash and centrifugation steps with RPE buffer. Finally, purified RNA was eluted off the column with RNase-free water. RNA concentration and purity was determined spectrophotometrically at A260/A280 and was determined to be intact as assessed by formaldehyde gel electrophoresis. The presence of genomic DNA contamination was assessed by PCR amplification of GAPDH using standard PCR conditions and the following primers: GAPDH_F2-5’- ACCCACTCCTCCACCTTTGAC-3’, GAPDH_R2- 5’-CTGTTGCTGTAGCCAAATTCGT-3’. RNA was re-treated with DNase if necessary. Upon confirming the quality of the RNA (intact and free of genomic DNA), 15 µg of total RNA from each of the five biological replicates was used for expression screening on either the Affymetrix or the clone-based filter platform.parallel sampleNancy,,Mah; Anders Thelin; Tim Lu; Susanna Nikolaus; Tanja Kühbacher; Yesim Gurbuz; Holger Eickhoff; Günther Klöppel; Hans Lehrach; Björn Mellgård; Christine,M,Costello; Stefan Schreiber; Nicola Dierkeshttp://www.mucosa.de/comparison/Name: Nancy Mah; Email: n.mah@mucosa.de; Phone: +0049-431-597-3725; Institute: Christian-Albrechts-University Kiel; Address: ; City: Kiel; Zip/postal_code: D-24105; Country: Germany Z?Pi7!!U#OPStationary phase - ypl230w mutant and wildtypeGSE408Public on Apr 15 20032003-04-152005-05-29gWild type and ypl230w mutOY7!!G#OOHypo-osmotic shock - ppt1 and wildtypeGSE407Public on Apr 15 20032003-04-152005-05-29gWild type and ppt1NY7!!Q#ONHeat shock - kin82 mutant and wildtypeGSE406Public on Apr 15 20032003-04-152005-10-28gWild type and kin82 mutM{7!!E++MyMMicroarray Comparison Using Normal Human Colonic MucosaGSE405Public on Dec 14 20032003-04-152005-10-28yThis series represents a group of five samples (from sigmoid colon biopsies of clinically normal Patients A-E) profiled by a publicly available cDNA-based platform (GPL284) and a commercial oligonucleotide-based platform (GPL91).; ; Sample RNA extraction:; ; Biopsies taken during endant under heat shock.; ; Cells grown at 25°C were collected by centrifugation, resuspended in an equal volume of 37°C medium, and returned to 37°C for growth. Samples were collected at 0, 5, 15, 30 and 60 minutes after transfer to 37°C.; ; Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.time-courseEran,,Segal; Michael Shapira; Aviv Regev; Dana Pe'er; David Botstein; Daphne Koller; Nir FriedmanName: Eran Segal; Email: eran@cs.stanford.edu; Phone: 650-725-8784; Department: Computer Science; Institute: Stanford University; Address: Gates Building 1A; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://cs.stanford.edu/~eran mutant under hypo-osmotic shock.; ; Cultures were grown with 1M sorbitol for ~20 hours, cells were collected by centrifugation and resuspended in YPD at time zero. Samples were collected at 0, 7, 15, 30 and 60 minutes after transfer to YPD.; ; Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.time-courseEran,,Segal; Michael Shapira; Aviv Regev; Dana Pe'er; David Botstein; Daphne Koller; Nir FriedmanName: Eran Segal; Email: eran@cs.stanford.edu; Phone: 650-725-8784; Department: Computer Science; Institute: Stanford University; Address: Gates Building 1A; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://cs.stanford.edu/~eranant under stationary phase.; ; Cultures were grown to OD600 of 0.27 (Ypl230w mutants) and 0.4 (congenic wild-type; DBY8778), at which point time zero samples were collected. Samples were further collected at 2 (or 3), 5, 7, 9, and 24 hours.; ; Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs.time-courseEran,,Segal; Michael Shapira; Aviv Regev; Dana Pe'er; David Botstein; Daphne Koller; Nir FriedmanName: Eran Segal; Email: eran@cs.stanford.edu; Phone: 650-725-8784; Department: Computer Science; Institute: Stanford University; Address: Gates Building 1A; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://cs.stanford.edu/~eran Q[7!!S#aQIMR-90 cells: Collagen Mesh Time CourseGSE409Public on Sep 10 20032003-04-172007-03-05O'A series of chips with some repeated measurments. Each chip represents a pool of 4 collagen/chondroitin sulfate tissue engineering scaffold meshes seeded with 1 x 10^6 IMR-90 Human Fibroblasts.; ; mRNA was isolated at 30 minutes, 1, 2, 4, 8, 12, 24, 48, and 72 hours after seeding.; Keywordstime-courseCatherine,M,Klapperich; Carolyn,R,BertozziName: Catherine Klapperich; Email: catherin@bu.edu; Phone: 617-358-0253; Laboratory: Laboratory for Biomedical Materials Research; Department: Biomedical and Manufacturing Engineering; Institute: Boston University; Address: 44 Cummington St. 7th Floor; City: Boston; State: MA; Zip/postal_code: 02215; Country: USA lSA7!!u'3K1SEffect of SOCS3 on the transcriptional response of bone marrow-derived macrop Ru7!!I#aRIMR-90 cells: Tissue Culture Polystyrene Time CourseGSE410Public on Sep 10 20032003-04-172007-03-05O'IMR-90 Human Fibroblasts were seeded onto TCPS dishes. mRNA was isolated at 1, 2, 4, 8, 12, 24, 48 and 96 hours. This time course was used as a control for gene expression studies on collagen/chondroitin sulfate tissue engineering scaffold materials using the same cell line.; Keywordstime-courseCatherine,M,Klapperich; Carolyn,R,BertozziName: Catherine Klapperich; Email: catherin@bu.edu; Phone: 617-358-0253; Laboratory: Laboratory for Biomedical Materials Research; Department: Biomedical and Manufacturing Engineering; Institute: Boston University; Address: 44 Cummington St. 7th Floor; City: Boston; State: MA; Zip/postal_code: 02215; Country: USAhages to IL-6GSE411Public on Apr 17 20032003-04-172005-06-15žJEffects of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6.; ; Fetal liver cells from SOCS3+/+ or SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages. Macrophages were either unstimulated, or stimulated for 100 or 400 minutes with 10 ng/ml IL-6.; Keywordsrepeat sampleR,,Lang; A Pauleau; E Parganas; Y Takahashi; J Mages; J Ihle; R Rutschman; P MurrayName: Roland Lang; Email: Roland.Lang@lrz.tum.de; Phone: ++49-89-41406248; Fax: ++49-89-41407461; Department: Institute of Medical Microbiology, Immunology and Hygiene; Institute: Technical University Munich; Address: Trogerstr. 4A; City: Munich; Zip/postal_code: 81675; Country: Germanyftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE411/GSE411_RAW.taring genes included those involved in apoptosis, mismatch repair, cell cycle control and stress response. Only 14% of genes that changed when these medications were given as single agents also changed when they were given together. These data indicate that lymphoid leukemia cells of different molecular subtypes share common pathways of genomic response to the same treatment, that changes in gene expression are treatment-specific and that gene expression can illuminate differences in cellular response to drug combinations versus single agents.otherM,H,Cheok; W Yang; Ching-Hon Pui; J,R,Downing; C Cheng; M,V,Relling; W,E,Evanshttp://www.stjuderesearch.org/data/ALL2Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htm 8T]7!!c)[KTTreatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cellsGSE412Public on Apr 21 20032003-04-212005-05-29څTo elucidate the genomics of cellular responses to cancer treatment, we analyzed the expression of over 9,600 human genes in acute lymphoblastic leukemia cells before and after in vivo treatment with methotrexate and mercaptopurine given alone or in combination. Based on changes in gene expression, we identified 124 genes that accurately discriminated among the four treatments. Discriminat dUS7!!##MUKidneys of Dahl salt sensitive ratsGSE413Public on Aug 20 20032003-04-232005-05-29Gene expression profiling of kidney tissue from 5 week old Dahl salt sensitive rats and congenic strain of Chr.10 Dahl salt sensitive rats.otherAlan,Y,DengName: Alan,Y,Deng; Email: alan.deng@umontreal.ca; Phone: 514-890-8000 ext.15522; Laboratory: Chief of Molecular Genetics; Institute: Research Centre-CHUM; Address: ; City: Montreal; Zip/postal_code: H2W 1T8; Country: Canada LVW7!! #5VTime course of aortic gene expressionGSE414Public on Sep 19 20032003-04-232005-06-15After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint).time-courseRadu,D,Rudic; Peter McNamara; Satchidananda Panda; John Hogenesch; Garret FitzGeraldName: Radu,Daniel,Rudic; Email: rudicrd@spirit.gcrc.upenn.edu; Phone: 215 898-0255; Fax: 215 573-9004; Laboratory: Garret FitzGerald Lab; Department: Center of Experimental Therapeutics; Institute: University of Pennsylvania; Address: 421 Curie Boulevard; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USA ^WQ7!!1CWMouse models of cardiac remodelingGSE415Public on Aug 22 20032003-04-252005-05-29We employed the Affymetrix GeneChip technology to evaluate the patterns of expression in two different in vivo models of cardiac remodeling and in two different regions (left ventricle free wall and septum) of the heart. Mice underwent transverse aortic constriction (TAC); myocardial infarction (MI) or Sham operation and RNA from the left ventricle free wall and the septum was isolated 1 week later.otherName: Maria Mirotsou; Email: mmirotsou@rics.bwh.harvard.edu; Phone: 617-7328155; Institute: Brigham and Women's Hospital, Harvard Medical School; Address: ; City: Boston; State: MA; Zip/postal_code: 02115; Country: USAen. RNA extracted from BM samples was used for microarray analysis. The blast cell infiltration both at diagnosis and relapse was 75% and mononuclear cell were isolated using a Lymphoprep™ density gradient (1.077 g/ml, Nycomed Pharma, Oslo, Norway).; RNA was extracted from blast cells at diagnosis and relapse and both samples were hybridized on an MWG 30K Human Array A (MWG, München) after direct labeling using two different fluorochromes (Cy3 and Cy5) for the respective samples.; KeywordsotherAndrea,,Rinaldi; Geertruy te Kronnie; Liza Franceschini; Silvio Bicciato; Carlo Di Bello; Giuseppe Bassohttp://www.dpci.unipd.it/PersPages/SBicciato/SBicc_Home.htmName: Silvio Bicciato; Email: silvio.bicciato@unipd.it; Phone: +39-049-827-5544; Fax: +39-049-827-5555; Laboratory: Laboratory of Bioengineering; Department: Chemical Engineering Processes; Institute: University of Padova; Address: via Marzolo, 9; City: Padova; Zip/postal_code: 35131; Country: Italy; Web_link: http://www.dpci.unipd.it/Bioengineering.htmzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz zzzzzzzzzz!z#z&$z&'*z-+z-.-0zzuuuuuuuu><uuuuuuuFuuuuuJuuOuQuSuuTWuW[Yuu\]`uucueuuuu ]X97!!u]SXB-ALL relapse analysisGSE416Public on Jun 13 20032003-04-292005-10-28A comparison of RNA expression profiles from leukemic cells of 8 single B-ALL patients at diagnosis and relapse. For all patients, clonality of the blast cells at diagnosis and relapse was demonstrated to be the same (Germano, G., del Giudice, L., Palatron, S., Giarin, E., Cazzaniga, G., Biondi, A., Basso, G., Clonality profile in relapsed precursor-B-ALL children by GeneScan and sequencing analyses. Consequences on minimal residual disease monitoring. Leukemia, 2003, in press).; The study protocol was approved by the Research committee of the AIEOP and written informed consent was obtained from all participants before samples were tak iiY57!!/1YKc167_RNA_Quant_EvalGSE417Public on May 27 20032003-04-292005-05-29Three different amounts, 20 ug (GSM6155), 40 ug (GSM6157) and 80ug (GSM6158), of total Kc167 RNA were used in homotypic labelings to determine the optimal amount of RNA necesary to produce the most useable data using the CDMC_Drosophila_7k2 array. See Neal et al. 2003 for results and discussion.; Keywords; Keywords; KeywordsotherScott,J,Neal; Meredith,L,Gibson; Anthony,K,So; Jon,T,Westwoodwww.flyarrays.comName: Scott,J,Neal; Email: sneal@utm.utoronto.ca; Phone: 905-569-4664; Laboratory: Canadian Drosophila Microarray Centre; Department: Zoology Department; Institute: University of Toronto; Address: 3359 Mississauga Road; City: Mississauga; State: ON; Zip/postal_code: L5L 1C6; Country: Canada; Web_link: http://www.flyarrays.comftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE417/GSE417_RAW.tar gZQ7!!'/1ZKc167_Inter-slide_Variability_TestGSE418Public on May 27 20032003-04-292005-05-29A large batch of Drosophila Kc167 total RNA was prepared and was used for 3 homotypic hybridizations in order to evaluate the inter-slide variability using the CDMC_Drosophila_7k2 platform. See Neal et al. 2003 for results and discussion.; Keywords; Keywords; KeywordsotherScott,J,Neal; Meredith,L,Gibson; Anthony,K,So; Jon,T,Westwoodwww.flyarrays.comName: Scott,J,Neal; Email: sneal@utm.utoronto.ca; Phone: 905-569-4664; Laboratory: Canadian Drosophila Microarray Centre; Department: Zoology Department; Institute: University of Toronto; Address: 3359 Mississauga Road; City: Mississauga; State: ON; Zip/postal_code: L5L 1C6; Country: Canada; Web_link: http://www.flyarrays.comftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE418/GSE418_RAW.tar ]][77!!1/1[SL2_vs_Kc167_Dif_ExprGSE419Public on May 27 20032003-04-292005-05-29The expression profiles of Drosophila Kc167 and SL2 cells were compared on the CDMC_Drosophila_7k2 array platform. Three independent RNA samples from each cell line were isolated and compared in a pairwise fashion. Dye-flip experiments were also performed. See Neal et al. 2003 for results and discussion.; Keywords; Keywords; KeywordsotherScott,J,Neal; Meredith,L,Gibson; Anthony,K,So; Jon,T,Westwoodwww.flyarrays.comName: Scott,J,Neal; Email: sneal@utm.utoronto.ca; Phone: 905-569-4664; Laboratory: Canadian Drosophila Microarray Centre; Department: Zoology Department; Institute: University of Toronto; Address: 3359 Mississauga Road; City: Mississauga; State: ON; Zip/postal_code: L5L 1C6; Country: Canada; Web_link: http://www.flyarrays.comftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE419/GSE419_RAW.targ and those associated with the mechanical regulation of vascular structure (cytoskeletal-cell membrane-extracellular matrix). Although previous studies have concentrated on the contribution of the latter group toward arterial stiffness, our data suggest that changes in expression of signaling molecules play an equally important role. Alterations in the profiles of signaling molecules could be involved in the regulation of cell cytoskeletal organization, cell-matrix interactions, or the contractile state of the cell. CONCLUSIONS: Although the influence of smooth muscle contraction/relaxation on arterial stiffness could be controversial, our provocative data would suggest that further studies on this subject are indicated.otherStephane,,Laurent; Richard PrattName: Richard,E.,Pratt; Email: rpratt@rics.bwh.harvard.edu; Phone: 617-732-8799; Fax: 617-975-0995; Department: Medicine; Institute: Brigham and Women's Hospital; Address: 75 Francis Street; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA V1]17!!Kw]Aging in rat heartGSE421Public on Aug 28 20032003-04-302005-06-15Myocardial aging leads to a reduction of beta-adrenergic receptor-induced metabolic and contr\-7!!SM\Aortic stiffnessGSE420Public on Aug 28 20032003-04-302005-05-29ݶBACKGROUND: Previous genomic studies with human tissues have compared differential gene expression between 2 conditions (ie, normal versus diseased) to identify altered gene expression in a binary manner; however, a potentially more informative approach is to correlate the levels of gene expression with quantitative physiological parameters. METHODS AND RESULTS: In this study, we have used this approach to examine genes whose expression correlates with arterial stiffness in human aortic specimens. Our data identify 2 distinct groups of genes, those associated with cell signalinactile responsiveness. We hypothesize that a change in the patterns of gene expression is important in these age-related events. To test this, hearts were harvested from young and aged male rats (3-4 and 20-22 mo, respectively). Total mRNA was extracted and prepared for hybridization to Affymetrix U34A GeneChips. Filtering criteria, involving fold change and a statistical significance cutoff were employed, yielding 263 probe pairs exhibiting differential signals. Of the 163 annotated genes, at least 56 (34%) were classified as signaling/cell communication. Of these 56, approximately half were directly involved in G protein-coupled receptor signaling pathways. We next determined which of these changes might be involved in anti-adrenergic activity and identified 19 potentially important gene products. Importantly, we observed a decrease in beta1-adrenergic receptor and adenylyl cyclase mRNAs, whereas the mRNA encoding beta-arrestin increased. Furthermore, the results demonstrate an increase in mRNAs encoding the adenosine A1 receptor and phospholipase D, which could increase anti-adrenergic effects. Moreover, the mRNAs encoding the muscarinic M3 receptor, nicotinic acetylcholine receptor beta3, and nicotinic acetylcholine receptor-related protein were increased as was the mRNA encoding guanylate kinase-associated protein. Interestingly, we also observed eight mRNAs whose abundance changed three- to sixfold with aging that could be considered as being compensatory. Although these results do not prove causality, they demonstrate that cardiac aging is associated with changes in the profiles of gene expression and that many of these changes may contribute to reduced adrenergic signaling.; Keywords; KeywordsotherJames,,Dobson; John Fray; Jack Leonard; Richard PrattName: Richard,E.,Pratt; Email: rpratt@rics.bwh.harvard.edu; Phone: 617-732-8799; Fax: 617-975-0995; Department: Medicine; Institute: Brigham and Women's Hospital; Address: 75 Francis Street; City: Boston; State: MA; Zip/postal_code: 02115; Country: USAo Adenomas and Carcinomas in the APC(Min/+) Mouse.; ; Samples used in analysis:; * GSM6191-GSM6196 (WT): Ilea epithelial cells from C57/BL6 wild-type samples; * GSM6197-GSM6201 (Adenoma): Epithelial cells from crypts of adenomas of APC(Min/+) mice; * GSM6202-GSM6206 (Carcinoma): Epithelial cells from crypts of carcinomas of APC(Min/+) mice; ; Using a PixCell IIe instrument (Arcturus), ~30,000 laser firings per sample were used to collect cells of interest. RNA was extracted from captured cells by PicoPure (Arcturus) technique, followed by 2 rounds of RiboAmp amplification (Arcturus), with incorporation of biotinylated nucleotides (Enzo) in the IVT of round 2. All protocols were as per manufacturers instructions. 15ug of labeled cRNA from individual samples were hybridized to respective MG_U74Av2 chips (Affymetrix) and washed/stained using the standard EukGEWS2v4 protocol (Affymetrix). Chips were scanned and analyzed using MAS 5 (Affymetrix) and data scaled to TI=500.; ; Pairwise comparisons using the Mann-Whitney test were performed in DMT 3 (Affymetrix), comparing:; * WT vs Adenoma (n=6 x n=5; 83.3% concordance); * WT vs Carcinoma (n=5 x n=5; 84% concordance); * Adenoma vs Carcinoma (n=5 x n=5; 84% concordance); ; This resulted in the identification of differentially expressed transcripts. Fold changes were calculated from signal-log-ratios. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx web portal (Affymetrix).; Keywords; Keywords; Keywords; Keywords; KeywordsorderedNicholas,F,Paoni; Matthew,W,Feldman; Linda,S,Gutierrez; Victoria,A,Ploplis; Francis,J,Castellinohttp://www.nd.edu/~transgen/APCmin/Name: Matthew Feldman; Email: mfeldman@nd.edu; Phone: 574-631-3539; Fax: 574-631-4048; Laboratory: Keck Center for Transgene Research; Department: Chemistry and Biochemistry; Institute: University of Notre Dame; Address: 251 Nieuwland Science Hall; City: Notre Dame; State: IN; Zip/postal_code: 46556; Country: USA BdCaE7!!SE=aAcute myeloid leukemia studyGSE425Public on Apr 15 20042003-05-072006-11-02,Acute myeloid leukemia study.; ; Supplementary Table 1: Clinical, morphological, cytogenetic andJ` 7!!E7`Colon carcinoma cell line CC531 response to butyrate and aspirinGSE424Public o;_/7!![C?_Yeast aging studyGSE423Public on Jun 03 20032003-05-062005-05-29wWild type an.^G7!!MS^Epithelium transition profileGSE422Public on Sep 12 20032003-04-302005-08-29Y_Transcriptional Profiling of the Transition from Normal Intestinal Epithelia td sgs1 null yeast were grown under DNA damaging (with MMS) conditions or without treatment to log phase and their transcriptional profiles compared .; ; The human aging diseases Werner and Bloom syndromes are a result of mutation of the WRN and BLM genes, respectively. The SGS1 gene of Saccharomyces cerevisiae is homologous to the human WRN and BLM genes of the RecQ DNA helicase family. Deletion of SGS1 results in accelerated yeast aging and a reduction in life span as well as cell cycle arrest. We demonstrate that SGS1 deletion, DNA damage, and stress show similar transcriptional responses in yeast. Our comparative analysis of the genome-wide expression response of SGS1 deletion, stress and DNA damage indicates parallel transcriptional responses to cellular insult and aging in yeast.otherR,C,Fry; T Sambandan; C RhaName: Rebecca Fry; Email: rfry@mit.edu; Phone: 617-452-2015; Institute: MIT; Address: ; City: Cambridge; State: MA; Zip/postal_code: 02139; Country: USAn May 19 20032003-05-062005-06-15PTemporal analysis of colon carcinoma cell line CC531 response to 4.5 mM butyrate or 3 mM aspirin. Samples taken at 2, 6, 12, 16 and 24 hours.; ; The CC531 cell line has been widely used to study different aspects of tumor growth and metastasis and provides an excellent experimental platform to develop novel antitumor strategies. To characterize the CC531 model at the molecular level, we screened for mutations in genes covering important signal-transduction pathways that are known to play major roles during colon carcinogenesis, the wnt and the ki-ras signaling pathways. We found both a prototypic beta-catenin (Ctnnb1) mutation (Thr(41)Ile) and a ki-ras (G12D) mutation, providing unambiguous evidence for the constitutive activation of these pathways in CC531 cells. We further established comprehensive gene expression profiles of CC531 cells and investigated the molecular response to 2 antitumor drugs, butyrate and aspirin. Using oligonucleotide microarrays, we screened the expression levels of 7,700 genes and identified a total of 398 genes whose expression was significantly changed upon treatment with butyrate. When using aspirin, 121 genes were significantly altered. Interestingly, 36 genes were regulated by both butyrate and aspirin and 35 of them were regulated in the same direction. We found 7 differentially expressed genes, cyclin D1, cyclin E, c-myc, Fosl1, c-fos, Cd44 and follistatin, which are known targets of the beta-catenin and/or the ras pathway. In all cases, butyrate and aspirin reversed the changes in expression normally found in response to active signaling of these oncogenic pathways.otherA,,Germann; S Dihlmann; M Hergenhahn; M von Knebel Doeberitz; R KoestersName: Anja Germann; Email: a.germann@dkfz-heidelberg.de; Phone: +49-6221-422467; Laboratory: Division of Molecular Pathology; Department: Department of Pathology; Institute: University Heidelberg; Address: INF 220-221; City: Heidelberg; Zip/postal_code: 69120; Country: Germany molecular; genetic information on 116 AML patient samples.; ; Supplementary Table 2: Summary of the distribution of clinical and molecular; genetic characteristics within the AML sample set.; ; Supplementary Table 3: Fluorescence ratios of the 6,283 well-measured and; variably-expressed genes.; ; Supplementary Table 4: Clinical and laboratory characteristics of normal; karyotype predominant subtypes I and II.; ; Supplementary Table 5: Supervised analysis of group-specific gene expression; signatures.; ; Supplementary Table 6: Gene-expression outcome class predictor.; ; Supplementary Table 7: Multivariate proportional hazards analysis.otherL,,Bullinger; K Dohner; E Bair; S Frohling; R,F,Schlenk; R Tibshirani; H Dohner; J,R,PollackName: Jonathan Pollack; Email: pollack1@stanford.edu; Phone: 650-736-1987; Fax: 650-736-0073; Laboratory: Pollack Lab; Department: Pathology; Institute: Stanford University; Address: 269 Campus Drive, CCSR3245A; City: Stanford; State: CA; Zip/postal_code: 94305-5176; Country: USA ccbg7!!9UObFibroblast Gene Expression: Hacia LaboratoryGSE426Public on May 08 20032003-05-082005-05-29hData files from Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"; KeywordsotherMazen,W,Karaman; Maryls,L,Houck; Leona,G,Chemnick; Shailender Nagpal; Daniel Chawannakul; Dominck Sudano; Brian,L,Pike; Vincent,V,Ho; Oliver,A,Ryder; Joseph,G,Haciahttp://lichad.usc.edu/supplement/Name: Shailender Nagpal; Email: nagpal@usc.edu; Phone: 323-630-8690; Institute: University of Southern California; Address: ; City: Los Angeles; State: CA; Zip/postal_code: 90033; Country: USA CC9c[7!!WOcHuman Fibroblast Set: Hacia LaboratoryGSE427Public on May 08 20032003-05-082005-05-29hData from human fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"; KeywordsorderedMazen,W,Karaman; Maryls,L,Houck; Leona,G,Chemnick; Shailender Nagpal; Daniel Chawannakul; Dominick Sudano; Brian,L,Pike; Vincent,V,Ho; Oliver,A,Ryder; Joseph,G,Haciahttp://lichad.usc.edu/supplement/Name: Shailender Nagpal; Email: nagpal@usc.edu; Phone: 323-630-8690; Institute: University of Southern California; Address: ; City: Los Angeles; State: CA; Zip/postal_code: 90033; Country: USA @@rI7!![arLeprosy lesion gene expressionGSE443Public on Jun 08 20032003-06-032005-05-29Ĉ7qA7!!5{qSex-biased gene expressionGSE442Public on Jun 02 20032003-06-022005-06-15InÍ^pC7!!e+[)pYeast glucosamine treatmentGSE441Public on May 30 20032003-05-302005-06-15OWe did transcription profiling on the effect of glucosamine in Saccharomyces cerevisiae using Research Genetics strains BY4741 (wild type) and 5251 (fks1). Yeast cells exposed to glucosamine in YPD growth medium show a significant increase in chitin content in the lateral cell wall. Likewise, cell wall stress caused by a gene deletion e.g., fks1 also results in elevated chitin. By comparing our data for fks1 with those from the literature we confirmed a strong induction of genes responsive to cell wall integrity, environmental stress as well as genes involved in cell signaling. Wild type cells treated with 15 mM glucosamine forvestigatation into how genes with sex-differential expression profiles are distributed among the chromosomes in Drosophila. Assayed the expression of 14,142 predicted transcripts in competitive hybridizations and found a dramatic underrepresentation of X-chromosome genes showing high relative expression in male. This is the first report of sex-biased expression of the full (predicted) genome. Findings indicate that there is significant sex-biased expression, especially in gonads. Genes showing sex-biased gene expression profiles are likely to have sex-biased functions.otherM,,Parisi; R Nuttall; D Naiman; G Bouffard; J Malley; J Andrews; S Eastman; B OliverName: Brian Oliver; Email: Brian_Oliver@nih.gov; Phone: 301-496-5495; Fax: 301-496-5239; Department: LCDB; Institute: National Institutes of Health, NIDDK; Address: 50 South Drive; City: Bethesda; State: MD; Zip/postal_code: 20892-8028; Country: USA; Web_link: http://www.niddk.nih.gov/intram/people/boliver.htmDLeprosy presents as a clinical and immunological spectrum of disease. With the use of gene expression profiling, we observed that a distinction in gene expression correlates with and accurately classifies the clinical form of the disease. Genes belonging to the leukocyte immunoglobulin-like receptor (LIR) family were significantly up-regulated in lesions of lepromatous patients suffering from the disseminated form of the infection. In functional studies, LIR-7 suppressed innate host defense mechanisms by shifting monocyte production from interleukin-12 toward interleukin-10 and by blocking antimicrobial activity triggered by Toll-like receptors. Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens.otherName: Joshua Bleharski; Email: jrbleharski@yahoo.com; Phone: 310-231-3530; Institute: UCLA; Address: ; City: Los Angeles; State: CA; Zip/postal_code: 90095; Country: USA csw7!!Q+C=sEffect of Vitamin D on gene expression by CaCO2 cellsGSE444Public on Oct 26 20042003-06-042006-03-28The raw data are presented. The computations in the manuscript were based on the fold-changes reported by the MAS 4.0 software, not on ratios taken from raw dataparallel sampleLarry,A,Sonna; Richard WoodName: Larry,Allen,Sonna; Email: larry.sonna@na.amedd.army.mil; Phone: 508-233-4194; Laboratory: Environmental Genomics; Department: Thermal and Mountain Medicine Division; Institute: USARIEM; Address: 42 Kansas Street; City: Natick; State: MA; Zip/postal_code: 01760; Country: USA yytq7!!'G?tAlpha Thalassaemia Myelodysplasia Syndrome (ATMDS)GSE445Public on Jun 06 20032003-06-062005-05-293?A 10K cDNA microarray was used to compare granulocyte RNA from one ATMDS patient to pooled granulocyte RNA from 7 healthy controls.repeat sampleAndrea,,Pellagatti; Richard Gibbons; Jacqueline Boultwood; James,S,Wainscoat; Douglas,R,HiggsName: Andrea Pellagatti; Email: andreapellagatti@yahoo.co.uk; Phone: 00441865220485; Laboratory: LRF Molecular Haematology Unit; Department: NDCLS; Institute: University of Oxford, John Radcliffe Hospital; Address: ; City: Oxford; Zip/postal_code: OX3 9DU; Country: United Kingdom D0v{7!!9+)vLungs from ovalbumen sensitized and challenged C57 miceGSE447Public on Jun 10 20032003-06-092005-05-29Profile of gene expression of lungs from ovalbumen sensitized and challenged C57 mice.parallel sampleName: Dean Sheppard; Email: deans@itsa.ucsf.edu; Phone: 415-206-5901; Department: Medicine; Institute: UCSF; Address: UCSF Box 0854; City: San Francisco; State: CA; Zip/postal_code: 94143-0854; Country: USA8u{7!!I+)uLungs from ovalbumen sensitized and challenged C3H miceGSE446Public on Jun 10 20032003-06-092005-05-29Profile of gene expression in lungs of ovalbumen sensitized and challenged C3H mice.; Keywordsparallel sampleName: Dean Sheppard; Email: deans@itsa.ucsf.edu; Phone: 415-206-5901; Department: Medicine; Institute: UCSF; Address: UCSF Box 0854; City: San Francisco; State: CA; Zip/postal_code: 94143-0854; Country: USA   rwO7!!+#swWS1 response to high dose of UV-CGSE448Public on Aug 09 20032003-06-102005-05-29The transcriptional response to 50 J/m2 of UV-light (254 nm) was assessed with HGU95AV2 Affymetrix probe arrays at 6, 12, 18 and 24 hours after exposure. Mock-treated samples were assessed at 6 and 24 hours.time-courseMassimiliano,,Gentile; Leena Latonen; Marikki LaihoName: Massimiliano Gentile; Email: massimiliano.gentile@helsinki.fi; Phone: +358-9-47448726; Fax: +358-9-1912 5554; Laboratory: Biomedicum Bioinformatics Unit; Department: Biomedicum Bioinformatics Unit; Institute: Biomedicum Helsinki; Address: Haartmaninkatu 8; City: Helsinki; State: Finland; Zip/postal_code: 000 14; Country: Finland; Web_link: http://www.bioinfo.helsinki.fi   qxM7!!+#sxWS1 response to low dose of UV-CGSE449Public on Aug 09 20032003-06-102005-05-29The transcriptional response to 10 J/m2 of UV-light (254 nm) was assessed with HGU95AV2 Affymetrix probe arrays at 6, 12, 18 and 24 hours after exposure. Mock-treated samples were assessed at 6 and 24 hours.time-courseMassimiliano,,Gentile; Leena Latonen; Marikki LaihoName: Massimiliano Gentile; Email: massimiliano.gentile@helsinki.fi; Phone: +358-9-47448726; Fax: +358-9-1912 5554; Laboratory: Biomedicum Bioinformatics Unit; Department: Biomedicum Bioinformatics Unit; Institute: Biomedicum Helsinki; Address: Haartmaninkatu 8; City: Helsinki; State: Finland; Zip/postal_code: 000 14; Country: Finland; Web_link: http://www.bioinfo.helsinki.fi N zW7!!+)zLungs from bleomycin-treated A/J miceGSE451Public on Jun 11 20032003-06-102005-05-29Profile of gene expression of lungs from bleomycin-treated A/J mice.parallel sampleName: Dean Sheppard; Email: deans@itsa.ucsf.edu; Phone: 415-206-5901; Department: Medicine; Institute: UCSF; Address: UCSF Box 0854; City: San Francisco; State: CA; Zip/postal_code: 94143-0854; Country: USA.y{7!!5+)yLungs from ovalbumen sensitized and challenged A/J miceGSE450Public on Jun 11 20032003-06-102005-05-29Profile of gene expression in lungs of ovalbumen sensitized and challenged A/J mice.parallel sampleName: Dean Sheppard; Email: deans@itsa.ucsf.edu; Phone: 415-206-5901; Department: Medicine; Institute: UCSF; Address: UCSF Box 0854; City: San Francisco; State: CA; Zip/postal_code: 94143-0854; Country: USA iO|17!!u'}|fhCMV-H vs fhCMV-TGSE453Public on Sep 09 20032003-06-102005-05-29Cytomegalovirus (CMV) strains with different in vivo and in vitro characteristics may induce different patterns of cellular gene expression. CMV strain fhCMV-H, which spreads rapidly through cell culture, was isolated from a hematopoetic stem cell̃{]7!!+){Lungs from bleomycin-treated 129svJ miceGSE452Public on Jun 11 20032003-06-102005-05-29Profile of gene expression of lungs from bleomycin-treated C129svJ mice.parallel sampleName: Dean Sheppard; Email: deans@itsa.ucsf.edu; Phone: 415-206-5901; Department: Medicine; Institute: UCSF; Address: UCSF Box 0854; City: San Francisco; State: CA; Zip/postal_code: 94143-0854; Country: USA transplant patient who died of CMV-mediated marrow failure. In contrast fhCMV-T was isolated from a patient who survived CMV complications and does not spread rapidly in vitro. Fibroblasts were infected with both strains, which had been engineered to express GFP upon cellular infection, and the cellular gene expression profile was compared to that of noninfected controls at 24h. The gene expression profile of HFF exposed to UV-inactivated virus from the 2 strains was also tested, to differentiate the effects of the initial engagement with virus coat proteins such as glycoprotein B and gene modulation by active virus.; Keywordsrepeat sampleLynn,,Graf; Julie Randolph-Habecker; Beverly Torok-StorbName: Lynn Graf; Email: lgraf@fhcrc.org; Phone: 206-667-4545; Fax: 206-667-5978; Laboratory: Torok-Storb; Department: Clinical Research Division; Institute: Fred Hutchinson Cancer Research Center; Address: 1100 Fairview Ave. N. D1-100; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USA; Web_link: none }{7!!O ?}Circadian rhythm in Clock mutant and Cry deficient miceGSE454Public on Nov 08 20032003-06-112005-05-29OMolecular analysis of circadian rhythm in mice. Liver tissue of wildtype, Clock mutant and Cry deficient C57BL/6 8- to 10-week-old male mice examined.; KeywordsotherK,,Ooishi; K Miyazaki; K Kadota; R Kikuno; T Nagase; G Atsumi; N Ohkura; T Azama; M Mesaki; S Yukimasa; H Kobayashi; C Iitaka; T Umehara; M Horikoshi; T Kudo; Y Shimizu; M Yano; M Monden; K Machida; J Matsuda; S Horie; T Todo; N Ishida; Katsutaka Ooishi; Name: Norio Ishida; Email: n.ishida@aist.go.jp; Phone: +81-29-861-6053; Institute: National Institute of Advanced Industrial Science and Technology; Address: ; City: Tsukuba; Zip/postal_code: 135-0064; Country: Japan xx~m7!!e'3~Porcine brain library whole brain vs whole brainGSE456Public on Jun 13 20032003-06-122005-05-29*series of experiments assesing false positive and background of pig brain library (PBL) microarray; Keywordsrepeat sampleWilliam,,Nobis; Xiaoning Ren; Steven,P,Suchyta; Adroaldo,J,Zanella; Paul,M,CoussensName: Steven,Paul,Suchyta; Email: suchytas@msu.edu; Phone: 517-355-8443; Laboratory: Center for Animal Functional Genomics; Department: Animal Science; Institute: Michigan State University; Address: B215 Anthony Hall; City: East Lansing; State: MI; Zip/postal_code: 48824; Country: USA; Web_link: http://nbfgc.msu.edu y17!!%%Deletions_TETs_WTsGSE457Public on Jun 12 20032003-06-122005-05-29Analysis of noncoding RNA processing phenotypes in mutant yeast strains, with isogenic wildtype strains as controls two-color microarrays, total RNA labeled directly with Alexa Ulysis 546 and 648 dyes, dye-swap, eight replicates of each oligo per slide, Lowess smoother, Hedge et al. 2002 protocols, see Peng, Robinson et al., 2003.otherName: Timothy,Richard,Hughes; Email: t.hughes@utoronto.ca; Phone: 416-946-8260; Fax: 416-978-8528; Department: Banting and Best Department of Medical Research; Institute: University of Toronto; Address: 112 College St.; City: Toronto; State: ON; Zip/postal_code: M5G 1L6; Country: Canada; Web_link: http://hugheslab.med.utoronto.ca/ reverse transcriptase to yield Cy5 fluorescence-labeled test cDNA probe. After a 2-h reverse transcription reaction at 42oC, RNA was degraded by addition of 1.5 µl of an alkaline solution (1N NaOH / 20 mM EDTA), and neutralized by addition of 1.5 µl 1N HCl. The labeled control cDNA probe and test cDNA probe were then mixed and washed by centrifugation with TE (Tris-EDTA, pH 7.0) first and then with TE, 20 µg Salmon sperm DNA, 20 µg polyA and 20 µg yeast RNA in a Microcon YM-30 column (Millipore, Bedford, MA). The concentrated probe mix was adjusted with TE to a volume of 24.8 µl, denatured at 100oC for 2 min, spun for a few min and made to a final hybridization volume of 31 µl with 5.27 µl 20XSSC and 0.93 µl 10% SDS and kept at room temperature until used. Before hybridization, microarray glass slides were immersed in 0.2% SDS for 2 min followed by two washes each 2 min in autoclaved Milli Q water, and subjected to blocking in 180 ml of Methyl Pyrrolidinone (Aldrich) containing 2.7 g Succinic Anhydride (WAKO, Japan) and 15.3 ml 1M Boric acid (pH 8.0) solution for 20 min. Slides were then washed with autoclaved Milli Q water, and the spotted cDNA targets (microarray) were denatured in boiling water for 2 min. The slides were dehydrated in 100% ethanol for 2 min and air dried by spinning at a low speed. The mixture of labeled probes, for example, the control (Cy3) and test (Cy5), were then applied to the microarray, placed a cover slip carefully and incubated at 65oC for 14 – 16 h in a custom slide chamber with humidity maintained by a small reservoir of 3 x SSC. In addition, 3 - 6 µl of 3 x SSC was spotted at each corner of the slide, as far away from the array as possible. After incubation for 14 – 16 h at 65oC, the slides were washed in 2 x SSC / 0.03% SDS for 2 min, followed by washing in 2 x SSC, 1 x SSC and 0.2 x SSC, each for 2 min with gentle agitation, and air dried by spinning at a low speed. All hybridizations were performed in duplicate except those of days 19 and 27, where no reverse labeling was done. In addition, day 245 of pregnancy had three samples hybridized with two of them being labeled using the same dye combination and the other is reverse labeled. In the reverse labeling procedure, for example, the control liver cDNA and test liver cDNA, which had been first labeled with fluorescent dyes Cy3 and Cy5, respectively, were then labeled with Cy5 and Cy3, respectively. The microarray hybridization images were immediately scanned by GenePix 4000B (Axon Instrument, Union City, CA). The images acquired by scan were analyzed by GenePix Pro 4.0 software. The absolute feature (microarray spot) and background intensity of Cy3 and Cy5 for each feature on the array was obtained for the hybridized images. The local background intensity of each spot was smoothed by the local weight regression smoother (lowess smoother) and subtracted from feature intensity data. The subtracted intensity data were subjected to non-parametric regression and local variance normalization. The non-parametric regression can reduce intensity-depended biases. Compared with the linear regression, the accuracy is improved, if the points in scatter plot of Cy3 vs. Cy5 were not distributed around the straight line. The local variance normalization controls the noise (background) in the raw data to a greater extent where the normalized data, in many cases, did not show significant fold-differences in comparison with background-subtracted raw intensity ratios, which frequently displayed higher fold-differences. Thus, the variance method that we employed to bovine liver array data has produced much reliable normalized ratios. To group liver genes with similar expression patterns throughout bovine pregnancy, two clustering algorithm were employed. The hierarchical clustering algorithm was performed using the software, Cluster 3.0, created and made freely available by Dr. Michiel de Hoon (http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) based on the original version written by Dr. Michael Eisen (http://rana.lbl.gov/), and the software TreeView (http://rana.lbl.gov/). For hierarchical clustering, genes with either 2 or more than 2-fold induction or 2 or more than 2-fold repression at least at one point of the sampling period were selected. All ratio values were log transformed (base 2) to treat inductions or repressions of identical magnitude as numerically equal but with opposite sign, and subjected to centroid linkage clustering. Self-Organizing Maps (SOMs) algorithm was performed using the software GeneCluster 2 made freely available by Whitehead Institute Center for Genome Research (http://www-genome.wi.mit.edu/cancer/software/genecluster2/gc2.html). The SOMs were performed on the present data to better visualization of clusters of genes with their expression patterns plotted on an x-y axis. For SOMs, genes with either 1.5-fold (and above) induction or 1.5-fold (and above) repression at least at one point of the sampling period were selected. The minimum fold difference i.e., 1.5-fold, chosen for the analyses in the present study was based on the calculation that the technical variation contributing to the expression level of each individual gene due either to different labeling efficiencies of cyanine dyes or labeling procedure or both, was found to be within the range of 1.41-fold induction or repression. Therefore, either the induction or the repression of a particular gene by 1.5-fold or above was considered significant.; Keywords; Keywords; Keywords; Keywordstime-courseChandana,B,Herath; Satoshi Shiojima; Hiroko Ishiwata; Susumu Katsuma; Tadashi Kadowaki; Koichi Ushizawa; Kei Imai; Toru Takahashi; Akira Hirasawa; Gozoh Tsujimoto; Kazuyoshi Hashizume; Satoshi SatoshiName: Chandana Herath; Email: herath@affrc.go.jp; Phone: 0081-29-838-8633; Fax: 0081-29-838-8606; Laboratory: Reproductive Biology and Technology; Department: Development Biology; Institute: National Institute of Agrobiological Sciences; Address: Ikenodai 2; City: Tsukuba City, Ibaraki; Zip/postal_code: 305-8602; Country: Japan %7!!9#BLI_maternalGSE458Public on Nov 14 20032003-06-172005-10-28The objective of the present study was to use our own fabricated bovine liver cDNA microarray to profile genome-wide expression patterns of genes in the liver of cow throughout pregnancy. Ten-microgram of pooled liver total RNA obtained from nonpregnant cycling cows was reverse transcribed in the presence of cyanine-3-fluorescent dye (Cy3)-conjugated dUTP (Amersham Pharmacia Biotech) by using Superscript II reverse transcriptase (Life Technologies, Rockville, MD) to yield Cy3 fluorescence-labeled control cDNA probe. Similarly, liver total RNA obtained from cows on days 19, 27, 49, 58, 150 and 245 of pregnancy was separately reverse transcribed in the presence of Cy5-conjugated dUTP by using Superscript II HG7!!EaACalorie restriction and agingGSE459Public on Jun 23 20032003-06-172005-05-29Gene expression profiles of kidney tissue from control-fed 5-month-old, control-fed 30-month-old and calorie restricted 30 month-old C57BL/6 mice.; KeywordsotherT,,Kayo; Y Higami; R Weindruch; T,A,ProllaName: Tsuyoshi Kayo; Email: tkayo@facstaff.wisc.edu; Phone: 608-265-5205; Fax: 608-262-2976; Laboratory: Genetics/Biotechnology Center; Department: ; Institute: University of Wisconsin-Madison; Address: 445 Henry Mall; City: Madison; State: WI; Zip/postal_code: 53706; Country: USA qOq 7!!)C=Analysis of transcription in the Drosophila melanogaster testisGSE462Public onڇ|_7!!U#_G3Response to LiCl of galactose grown cellsGSE461Public on Jun 23 20032003-06-192م-=7!!/wMurine dermal burn woundGSE460Public on Jun 23 20032003-06-182005-06-15Investigation into murine dermal burn wound.; Mouse thermal injury induced, and skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury.otherRobert,J,Feezor; Heather,N,Paddock; Henry,V,Baker; Juan,C,Varela; Lyle,L,Moldawer; Gregory,S,Schultz; David,W,MozingoName: Robert,Joseph,Feezor; Email: feezor@surgery.ufl.edu; Phone: 352 265 0494; Fax: 352 265 0676; Laboratory: Moldawer; Department: Surgery; Institute: University of Florida; Address: 1600 SW Archer Road, Room 6116; City: Gainesville; State: FL; Zip/postal_code: 32610; Country: USA; Web_link: www.surgery.ufl.edu/research005-10-28/Wild type strain CEN.PK113-7D was grown in an aerobic batch cultivation with a start concentration of 20 g/L galactose. During exponential growth at a biomass concentration of 3 g dry weight/L LiCl was added to a concentration of 10 mM. Just before addition of LiCl (time 0) and 20, 40, 60 and 140 minutes after addition of LiCl samples were taken for transcription analysis. Lithium inhibits phosphoglucomutase whereby both galactose uptake and growth is strongly affected.; Keywordstime-courseChristoffer,,Bro; Birgitte Regenberg; Gilles Lagniel; Jean Labarre; Mónica Montero-Lomelí; Jens Nielsenwww.cpb.dtu.dk/data/licl.htmlName: Christoffer Bro; Email: cb@biocentrum.dtu.dk; Phone: +45 45252696; Laboratory: Center for Process Biotechnology; Department: BioCentrum-DTU; Institute: Technical University of Denmark; Address: Building 223; City: Kgs. Lyngby; Zip/postal_code: DK-2800; Country: Denmark Jul 16 20032003-06-252005-10-28AIdentification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.otherJusten,,Andrews; Gerard,G,Bouffard; Chris Cheadle; Jining Lü; Kevin,G,Becker; Brian OliverName: Brian Oliver; Email: oliver@helix.nih.gov; Phone: 301-496-5495; Fax: 301-496-5239; Department: LCDB; Institute: NIDDK, NIH; Address: 6 Center Drive; City: Bethesda; State: MD; Zip/postal_code: 20892; Country: USA; Web_link: http://www.niddk.nih.gov/intram/people/boliver.htmled separately with Cy5 and Cy3 monoreactive fluors, respectively. The Universal RNA consists of a mixture of RNA from 10 different human cell lines with a broad expression coverage of over 80% of the sequences on the array, allowing comparison of expression patterns of multiple different samples of different origin. The Cy5- and Cy3-labeled cDNAs were combined for hybridization to the microarray. Fluorescent array images were collected for both Cy3 and Cy5, and image-intensity data were extracted and analyzed to obtain expression ratios to Universal RNA for each stromal cell line. From these the expression in the 2 lines could be compared.otherL,,Graf; M Iwata; B Torok-StorbName: Mineo Iwata; Email: miwata@fhcrc.org; Phone: 206-667-4545; Fax: 206-667-5978; Laboratory: Torok-Storb; Department: Clinical Research; Institute: Fred Hutchinson Cancer Research Institute; Address: 1100 Fairview Ave. N. D1-100; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USA; Web_link: http://parma.fhcrc.org/MIwata ==77!!{K-Profiling of human bone marrow stromal cell lines HS-5 and HS-27aGSE463Public on Jul 16 20032003-06-252005-06-15The microarrays were constructed using a set of more than 17,000 sequence-verified clones from Research Genetics (Huntsville, AL). Of the 17,761 features (spots) on the microarray, 186 are control nonexpressed or nonhuman sequences or housekeeping genes. UniGene cluster IDs could be assigned by GenBank to 16,592 of the features as of June 1, 2001 (UniGene Build 133), indicating that they are representatives of nonredundant unique genes. Many have been functionally characterized, and chromosomal location and tissue expression patterns are known for others. Total RNA was isolated from semiconfluent cultures and reverse-transcribed into cDNA in a nucleotide mix containing amino-allyl deoxyuracil triphosphate (dUTP). The cDNA from stromal cells and Universal RNA (Stratagene, La Jolla, CA) was covalently couping SCI are well known.; ; Specific Aim: The goal of this project is to analyze the molecular events following spinal cord injury 1 cm above, below, and at the site of injury (T9), aiming at finding potential new targets to improve recovery and therapy.otherS,,Di Giovanni; S,M,Knoblach; C Brandoli; S,A,Aden; E,P,Hoffman; A,I,Fadenhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=211; http://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=212; http://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=213Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE464/GSE464_RAW.tar Jm7!!3Y%q1Expression profiling in the muscular dystrophiesGSE465Public on Jul 16 2003200r-7!!;!cq1CNS RegenerationGSE464Public on Jul 16 20032003-06-252006-07-27ESummary: Spinal cord injury (SCI) is a damage to the spinal cord induced by trauma or desease resulting in a loss of mobility or feeling. SCI is characterized by a primary mechanical injury followed by a secondary injury in which several molecular events are altered in the spinal cord often resulting in loss of neuronal function.; ; Hypothesis: Spinal cord injury (SCI) induces a cascade of molecular events including the activation of genes associated with transcription factors, inflammation, oxidative stress, ionic imbalance, apoptosis and neuroregeneration which suggests the existance of endogenous reparative attempts. However, not all mechanisms follow3-06-252005-08-23%This is a large series human Duchenne muscular dystrophy patient muscle biopsies, in specific age groups, using all available Affymetrix arrays (including a custom MuscleChip produced by the Hoffman lab). Both mixed groups of patients (5 patient biopsies per group) and individual biopsies were done.; ; Hypothesis: That the progression of DMD can be understood in terms of muscle molecular remodeling. otherY,W,Chen; P Zhao; R Borup; E,P,Hoffmanhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=29Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE465/GSE465_RAW.tar, calponin, mast cell chymase, and guanidinoacetate methyltransferase mRNA in the more benign mdx was also observed. Transcripts for oxidative and glycolytic enzymes in mdx muscle were not downregulated. These discrepancies could provide candidates for salvage pathways that maintain skeletal muscle integrity in the absence of a functional dystrophin protein in mdx skeletal muscle.otherB,S,Tseng; P Zhao; J,S,Pattison; S,E,Gordon; J,A,Granchelli; R,W,Madsen; L,C,Folk; E,P,Hoffman; F,W,Boothhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=1Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE466/GSE466_RAW.tar P}7!!)_#q1mRNA expression in regenerated mdx mouse skeletal muscleGSE466Public on Jul 16 20032003-06-262005-06-15%Despite over 3,000 articles published on dystrophin in the last 15 years, the reasons underlying the progression of the human disease, differential muscle involvement, and disparate phenotypes in different species are not understood. The present experiment employed a screen of 12,488 mRNAs in 16-wk-old mouse mdx muscle at a time when the skeletal muscle is avoiding severe dystrophic pathophysiology, despite the absence of a functional dystrophin protein. A number of transcripts whose levels differed between the mdx and human Duchenne muscular dystrophy were noted. A fourfold decrease in myostatin mRNA in the mdx muscle was noted. Differential upregulation of actin-related protein 2/3 (subunit 4), beta-thymosinession changes following high resistance contractions with two candidate mRNAs, basic fibroblast growth factor (bFGF) and elongation factor-1 alpha (EF1alpha), targeted to the heavier polysomal fractions after a bout of contractions. Gene profiling was performed using Affymetrix Rat U34A GeneChips with either total RNA or polysomal RNA at one and six hours following contractions. There were 18 genes that changed expression at one hour and 70 genes that were different (60 genes increased:10 genes decreased)at six hours after contractions. The model from this profiling suggests that following high resistance contractions skeletal muscle shares a common growth profile with proliferating cells exposed to serum. This cluster of genes can be classified as "growth" genes and is commonly associated with progression of the cell cycle. However, a unique aspect was that there was induction of a cluster of tumour suppressor or antigrowth genes. We propose that this cluster of "antigrowth" genes is induced by the stress of contractile activity and may act to maintain skeletal muscle in the differentiated state. From the profiling results, further experiments determined that p53 levels increased in skeletal muscle at 6 h following contractions. This novel finding of p53 induction following exercise also demonstrates the power of expression profiling for identification of novel pathways involved in the response to muscle contraction.otherY,W,Chen; G,A,Nader; K,R,Baar; M,J,Fedele; E,P,Hoffman; K,A,Esserhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=44Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE467/GSE467_RAW.tar **F s7!!m%q1Response of rat muscle to acute resistance exerciseGSE467Public on Jul 16 20032003-06-262005-06-15To further understand molecular mechanisms underlying skeletal muscle hypertrophy, expression profiles of translationally and transcriptionally regulated genes were characterized following an acute bout of maximally activated eccentric contractions. Experiments demonstrated that translational mechanisms contribute to acute gene exprwe assigned sample class to these tumors (M+ or M0) with 72% accuracy and to four additional independent tumors with 100% accuracy. We also assigned the metastatic medulloblastoma cell line Daoy to the metastatic class. Notably, platelet-derived growth factor receptor alpha (PDGFRA) and members of the downstream RAS/mitogen-activated protein kinase (MAPK) signal transduction pathway are upregulated in M+ tumors. Immunohistochemical validation on an independent set of tumors shows significant overexpression of PDGFRA in M+ tumors compared to M0 tumors. Using in vitro assays, we show that platelet-derived growth factor alpha (PDGFA) enhances medulloblastoma migration and increases downstream MAP2K1 (MEK1), MAP2K2 (MEK2), MAPK1 (p42 MAPK) and MAPK3 (p44 MAPK) phosphorylation in a dose-dependent manner. Neutralizing antibodies to PDGFRA blocks MAP2K1, MAP2K2 and MAPK1/3 phosphorylation, whereas U0126, a highly specific inhibitor of MAP2K1 and MAP2K2, also blocks MAPK1/3. Both inhibit migration and prevent PDGFA-stimulated migration. These results provide the first insight into the genetic regulation of medulloblastoma metastasis and are the first to suggest a role for PDGFRA and the RAS/MAPK signaling pathway in medulloblastoma metastasis. Inhibitors of PDGFRA and RAS proteins should therefore be considered for investigation as possible novel therapeutic strategies against medulloblastoma.otherT,J,MacDonald; K,M,Brown; B LaFleur; K Peterson; C Lawlor; Y Chen; R,J,Packer; P Cogen; D,A,Stephanhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=63Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE468/GSE468_RAW.tar d C7!!W%q1Asthma exacerbatory factorsGSE470Public on Jul 16 20032003-06-262005-08-24The e' a7!!5%q1Temporal profiling in muscle regeneration.GSE469Public on Jul 16 20032003-06-262005-06-15uTemporal expression profiling was utilized to define transcriptional regulatory pathways in vivo in a mouse muscle regeneration model. Potential downstream targets of MyoD were ide/ [7!!S%q1Expression profiling of medulloblastomaGSE468Public on Jul 16 20032003-06-262006-07-27'Little is known about the genetic regulation of medulloblastoma dissemination, but metastatic medulloblastoma is highly associated with poor outcome. We obtained expression profiles of 23 primary medulloblastomas clinically designated as either metastatic (M+) or non-metastatic (M0) and identified 85 genes whose expression differed significantly between classes. Using a class prediction algorithm based on these genes and a leave-one-out approach, ntified by temporal expression, promoter data base mining, and gel shift assays; Slug and calpain 6 were identified as novel MyoD targets. Slug, a member of the snail/slug family of zinc finger transcriptional repressors critical for mesoderm/ectoderm development, was further shown to be a downstream target by using promoter/reporter constructs and demonstration of defective muscle regeneration in Slug null mice.otherP,,Zhao; S Iezzi; E Carver; D Dressman; T Gridley; V Sartorelli; E,P,Hoffmanhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=80Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE469/GSE469_RAW.tarxacerbation of disease in asthmatics has been linked to both exposure to environmental agents as well as to the presence of virus in airways, particularly rhinovirus. The hypothesis tested in these experiments is that differences in gene expression profiles in epithelial cells derived from asthmatic and normal airways can be linked to enhanced responsiveness of the epithelium in its pro-inflammatory, immulogic or other activities that may lead to the exacerbation of disease.otherW,,Spannhakehttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=96Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE470/GSE470_RAW.tar-262006-07-275The extraocular muscles (EOM) are anatomically and physiologically distinct from other skeletal muscles. EOM are preferentially affected in mitochondrial myopathies, but spared in Duchenne's muscular dystrophy. The anatomical and pathophysiological properties of EOM have been attributed to their unique molecular makeup: an allotype. We used expression profiling to define molecular features of the EOM allotype. We found 346 differentially expressed genes in rat EOM compared with tibialis anterior, based on a twofold difference cutoff. Genes required for efficient, fatigue-resistant, oxidative metabolism were increased in EOM, whereas genes for glycogen metabolism were decreased. EOM also showed increased expression of genes related to structural components of EOM such as vessels, nerves, mitochondria, and neuromuscular junctions. Additionally, genes related to specialized functional roles of EOM such as the embryonic and EOM-specific myosin heavy chains and genes for muscle growth, development, and/or regeneration were increased. The EOM expression profile was validated using biochemical, structural, and molecular methods. Characterization of the EOM expression profile begins to define gene transcription patterns associated with the unique anatomical, metabolic, and pathophysiological properties of EOM.otherM,D,Fischer; J,R,Gorospe; E Felder; S Bogdanovich; F Pedrosa-Domellof; R,S,Ahima; N,A,Rubinstein; E,P,Hoffman; T,S,Khuranahttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=91Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE471/GSE471_RAW.tar aacM7!!C#q1Obesity and fatty acid oxidationGSE474Public on Jul 16 20032003-06-272006-07-2=A7!!a%qWPGA Human CD4+ LymphocytesGSE473Public on Jul 16 20032003-06-262005-06-15This project is based on the hygiene hypothesis that exposure to TB provides a protective mechanism against asthma through specific cytokines and the balance of Th1, Th2 cells. Additionally, expression changes are examined in patients with and without atopy in combination with asthma and PPD status. Expression levels were evaluated in CD4+ cells isolated from peripheral blood of 30 patients. Each patient was evaluated on the entire U133 Affymetrix GeneChip set.; HypothesilK7!!M7q1Congestive heart failure in dogGSE472Public on Jul 16 20032003-06-262005-08-23Canine ta- c7!!cq1Expression profiling of extraocular musclesGSE471Public on Jul 16 20032003-06chycardia-induced cardiomyopathy caused by several weeks of rapid ventricular pacing is a well-established animal model of congestive heart failure. However, little is known about the underlying changes in gene expression that occur in the canine myocardium after the induction of heart failure. This project aims to compare expression profiles in left ventricular free wall samples from control dogs and dogs with pacing-induced heart failure on the custom MuscleChip.otherT,P,Cappola; J,M,Harehttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=94Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE472/GSE472_RAW.tars: That CD4+ cells have specific diagnostic profiles based upon atopy and asthma state. Further information at http://www.hopkins-genomics.org/asthma/asthma001/index.html; Specific Aim: To define diagnostic genes from purified CD4+ blood cells have specific diagnostic profiles based upon atopy and asthma state. Further information at http://www.hopkins-genomics.org/asthma/asthma001/index.htmlotherG,,Diettehttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=98Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE473/CD4_Notes.pdf; ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE473/GSE473_RAW.tar8It has been found that fat oxidation is reduced in the skeletal muscle of obese humans. This study aims to identify the mRNA of proteins involved in fat oxidation that may be reduced in obese and morbidly obese individuals. Information gathered will help in understanding how obesity contributes to cardiovascular disease via insulin resistance.otherJ,A,Houmardhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=101Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE474/GSE474_RAW.tar zzW7!!o)'q1Chronic obstructive pulmonary diseaseGSE475Public on Jul 16 20032003-06-272005-08-23Diaphragm muscles in Chronic Obstructive Pulmonary Disease (COPD) patients undergo an adaptive fast to slow transformation that includes cellular adaptations. This project studies the signaling mechanisms responsible for this transformation.otherN,A,Rubinsteinhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=103Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE475/GSE475_RAW.tar005-06-15Ozone is a very common environmental pollutant and has been associated with the exacerbation of cardiopulmonary diseases like asthma. In this study the molecular mechanisms underlying the effect of ozone on airways hyperpermability were investigated. Two strains of mice, HeJ (Tlr4 mutant) and OuJ (wildtype) were exposed continuously to air or 0.3ppm of ozone. Lungs were removed and RNA was collected to generate expression profiles.otherStephan,,Kleebergerhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=109Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE476/GSE476_RAW.tar =h=VU7!!q71'q1Allergic response to ragweed in lungGSE483Public on Jul 16 20032003-06-272005-u7!!}!q1Vascular remodeling following pulmonary hypertensionGSE482Public on Jul 16 200G7!!!q1Allergen-induced goblet cellsGSE481Public on Jul 16 20032003-06-272005-08-24HiMQ7!!{9'q1Sleep apnea and glucose metabolismGSE480Public on Jul 16 20032003-06-272005-08x17!!)'q1Alveolar septationGSE479Public on Jul 16 20032003-06-272006-07-27The Mg-delta ls7!!wQ'q1Alveoli loss during caloric restriction time courseGSE478Public on Jul 16 2003.S7!![#q1Alternatively activated macrophagesGSE477Public on Jul 16 20032003-06-272005-08-24Similar to asthma, nematode infections are commonly associated with proL]7!!s3'q1Ozone effect on airways hyperpermabilityGSE476Public on Jul 16 20032003-06-272duction of Th2 cytokines and hyporesponsive T cells. This T cell phenotype has been reported to be induced by IL-4 dependent macrophages termed alternatively activated macrophages (AAM). Additionally, AAM have been implicated in several pulmonary diseases, including allergic asthma. This study examines the potential importance of AAM as immune regulatory cells in both infectious and noninfectious disease contexts. http://www.hopkins-genomics.org/asthma/asthma006/index.htmlotherAlan,,Scotthttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=107Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE477/GSE477_RAW.tar2003-06-272006-07-14޲Pulmonary alveoli are complex architectural units thought to undergo endogenous or pharmacologically induced programs of regeneration and degeneration. To study the molecular mechanism of alveoli loss mice were calorie restricted at different timepoints. Lungs were harvested and processed for RNA extraction.otherGloria,D,Massaro; Donald, ,Massarohttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=111Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE478/GSE478_RAW.tarstrain of fibrillin-1 deficient mice display an early defect in alveolar septation. This study attempts to identify expression patterns in the mutant mouse lung compared to their wild-type littermates that suggest pathways that are critical for normal septation. This experiment focuses on postnatal days 1 and 5. Other time points will be added at a later date.otherEnid,R,Neptunehttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=112Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE479/GSE479_RAW.tar-23This study examines the relationship between sleep apnea and glucose metabolism. Physiological studies have demonstrated that 5 days of exposure to intermittent hypoxia (similar to what occurs with sleep apnea) leads to significant improvements in glucose tolerance. Therefore, this study investigates the hypothesis that intermittent hypoxia may lead to upregulation of some novel peptide(s) that have a powerful glucose lowering action.otherChristopher,,O'Donnellhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=114Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE480/GSE480_RAW.targh numbers of goblet cells in airways contribute to the mucus obstruction characteristic of asthmatic airways. Allergen challenged mice exhibit robust expression of goblet cells within airway surface epithelium. This study looks at the temporal analysis of IL-13 exposed murine airways to elucidate pathways that result in differentiation of airway epithelial cells to goblet cells.otherMary,,Rosehttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=113Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE481/GSE481_RAW.tar32003-06-272005-08-23Hypoxia can induce vasoconstriction followed by vascular remodeling including hypertrophy and hyperplasia of pulmonary vascular smooth muscle and proliferation of endothelial cells. The goal of this project is to elucidate the genes involved in vascular remodeling following pulmonary hypertension. Total RNA was isolated from lungs of normoxic and hypoxic treated animals.otherDechun,,Lihttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=124Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE482/GSE482_RAW.tar08-23An important feature of human asthma and animal models of asthma is airway hyperresponsiveness. The symptoms of asthma are a narrowing of the airways caused by edema and the influx of inflammatory cells. The aim of this project is to determine the temporal relationship between gene expression and airway allergen challenge. 4 weeks old BALB/CJ mice were challenged on days 0,3,10 and 17 with PBS and ragweed pollen protein plus Alum.time series, allergenMarsha,,Wills-Karphttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=125Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE483/GSE483_RAW.tar272005-08-24It has been shown that dexamethasone (Dex) impairs the normal lung septation that occurs in the early postnatal period. Treatment with retinoic acid (ATRA) abrogates the effects of Dex. To understand the molecular basis for the Dex indiced inhibition of the formation of the alveoli and the ability of ATRA to prevent the inhibition of septation, gene expression was analyzed in 4-day old mice treated with diluent (control), Dex-treated and ATRA+Dex-treated.otherLinda,,Clerchhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=119Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE484/GSE484_RAW.tar "7!!_g?Replication and Protein binding profile of chromosome VI of S.cerevisiaeGSE486Public on Aug 27 20032003-06-272005-10-28ņLType of experiment: ChIP-chip (Chromatin immunoprecipitation on DNA chip) analyses of replication related, checkpoint related proteins and BrdU incorporated regions at 300bp resolution. Newly developed S.cerevisiae chromosome VI tiling array produced by affymetrix was used.; ; Experimental factors:Distribution of various replication and checkpoint related proteins on chromosome VI during S-phase (with or  q7!!O='q1Genetic basis of sensitivity to pulmonary fibrosisGSE485Public on Jul 16 20032`c7!!#'q1Alveoli septation inhibition and protectionGSE484Public on Jul 16 20032003-06-003-06-272006-07-27The murine pulmonary response is strain specific. Susceptible strains such as C57BL6/J experience an inflammatory response followed by progressive lung disease. Resistant strains such as Balb/c do not experience significant degrees of inflammation or fibrosis. This study aims to determine the genetic basis of sensitivity differences between strainsotherY,W,Chen; David, ,Mollerhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=121Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE485/GSE485_RAW.tarw/o hydroxy urea). Distribution of BrdU incorporated regions on chromosome VI during S-phase with hydroxy urea. Wild type, tof1 deletion mutant, mrc1 deletion mutant, rad9 deletion mutant, sml1 deletion mutant, and sml1 mec1 tel1 triple deletion mutant were also investigated. The results of 74 hybridization files presented in the paper are shown.; ; The type of reference used for the hybridizations, if any: For the analysis of FLAG tagged protein, we usually used Cdc45-3XHA as an internal reference. For the analysis of HA tagged protein, POL1-3XFLAG was usually analyzed simultaneously as a reference.; ; Hybridization design: Comparison of ChIP fraction with SUP fraction for protein binding profile. For the analyses of BrdU incorporated regions, anti BrdU antibody bound fraction was compared with SUP (Sup of purified DNA from cells at G1 phase) fraction. During a course of these experiments, we found that S-phase Sup fractions were essentially the same among different genetic backgrounds and did not affect the binding profiles. Based on this observation we use standardized Sups for all experiments. No locus was scored as significantly enriched in the control ChIP experiment using HU treated untagged cells.; ; Quality control steps taken: Confirmation of ChIP fraction by Western blotting. Confirmation by conventional ChIP PCR methods for selected locus. Or Duplication.; ; The origin of the biological sample:; Budding Yeast (Saccharomyces cerevisiae); ; Manipulation of biological samples and protocols used:For the preparation of HU-arrested cells, we synchronized yeast cells with alpha-factor (2mM) and then released cells into 200mM HU for 60 min. at 23°C. For the preparation of S-phase cells, cells were released into S-phase without HU and at 16°C collected at the time indicated. These cells were fixed by 1% Formaldehyde and then used for ChIP of protein of interest. For the analyses of BrdU incorporation, the same fraction of cells used for ChIP were fixed by ice cold buffer containing 0.1% Azide, and then used for detection of BrdU incorporated regions.; ; Protocol for preparing the hybridization extract:We disrupted 1.5X10^8 cells by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (http://inside.wi.mit.edu/young/pub/locationanalysis.html). Purified DNA was random primed and amplified by the protocol of Brown’s lab (http://www.microarrays.org). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).; For the analysis of BrdU incorporated regions, total DNA from 3X10^8 cells was purified by Qiagen Genomic-tip system (P/N10223, QIAGEN, Germany). DNA was sheared to 300bp by sonication, denatured, and mixed with 2ug of anti-mouse IgG1 dynabeads (P/N110.12, Dynal AS, Norway) bound anti-BrdU monoclonal antibody (2B1D5F5H4E2, MBL, Japan). Immunoprecipitation and purification of antibody bound DNA fraction was carried out following the protocol of Cimbora et al. (Mol. Cel. Biol. 20, 5581-5591, 2000). Purified DNA was random primed and amplified by the Brown’s lab protocol. 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling.; ; Labeling protocol:DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998); ; The protocol and conditions used during hybridization, blocking and washing: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).; ; Measurement data and specifications:Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus. For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array. In the case of BrdU experiment, loci c6-462 to c6-479 (Ty element) and c6-591 to c6-601 (YFR016c) were excluded from calculation, because those loci gave high background in IP fraction even without BrdU treatment. The software to present the result of discriminant analyses (makeps) is available at our web site.; ; KeywordsotherYuki,,Katou; Yutaka Kanoh; Masashige Bando; Hideki Noguchi; Hirokazu Tanaka; Toshihiko Ashikari; Katsunori Sugimoto; Katsuhiko Shirahigehttp://everythingchromosomevi.gsc.riken.go.jpName: Katsuhiko Shirahige; Email: kshirahi@bio.titech.ac.jp; Phone: +81-45-924-5812; Fax: +81-45-924-5814; Laboratory: Laboratory of Chromosome Structure and Inheritance; Department: Graduate School of Bioscience and Biotechnology; Institute: Tokyo Institute of Technology, Department of Biological Sciences; Address: 4259 Nagatsuta, Midori-ku; City: Yokohama City; State: Kanagawa; Zip/postal_code: 226-8501; Country: Japan; Web_link: http://shirahigelab.bio.titech.ac.jp/ovled in both the immuosuppressive and the energetic actions of corticosteroids.; ; Hypothesis: That pharmacodynamics can be derived from expression profiling data.; ; Specific Aim: The aim of this project is to identify distinct temporal patters of RNA expression in the liver of rats following a bolus dose of the corticosteroid methylprednisolone. 47 RG_U34A chips were used for 17 time points.otherRichard, ,Almonhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=127; http://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=127Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE487/GSE487_RAW.tar cc]Q7!!;#q1Sex differences in immune responseGSE488Public on Jul 16 20032003-07-012005-08"M7!!+;q1PGA Rat Liver MethylprednisoloneGSE487Public on Jul 16 20032003-07-012005-06-15oBSummary: The liver is the major site of gluconeogenesis, fat processing and distribution, as well as drug and xenobiotic metabolism. Altered gene expression in the liver is centrally inv-24In the field, adult male rodents are more frequently infected with hantaviruses than females. Early data suggests that sex steroid hormones modulate sex differences in host immune response. This project focuses on elucidating sex differences in gene expression in the lungs of infected males 15 and 40 days post infection with Seoul virus (naturally occurring hantavirus in Norway rats) relative to infected females 15 and 40 days post infection on 12 RG_U34 GeneChips.otherGreg,,Glasshttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=131Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE488/GSE488_RAW.tar MM/-7!!w%'q1Lung ventilationGSE489Public on Jul 16 20032003-07-012005-08-23This project focuses both on the separate and combined effects of large tidal volume ventilation and hyperoxia on gene expression in the lungs of anesthetized rats. Rats were either mechanically or spontaneously ventilated at either 21 or 100% oxygen and expression levels were evaluated on RG_U34 GeneChips.otherSkip,,Pearsehttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=130Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE489/GSE489_RAW.tar pp 7!!U+q1Pharmacogenomic effect of corticosteroid in skeletal muscleGSE490Public on Jul 16 20032003-07-012006-07-27The aim of this project is to identify distinct temporal patterns of RNA expression in the skeletal muscle of rats following a bolus dose of the corticosteroid methylprednisolone. 51 RG_U34A chips were used over 17 time points.otherRichard, ,Almonhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=128Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE490/GSE490_RAW.tar %%W!57!! A/'q1Effect of formula feeding and hypoxia on Necrotizing Enterocolitis (NEC) developmentGSE491Public on Jul 16 20032003-07-012005-08-23Necrotizing Enterocolitis (NEC) is an inflammation causing injury to the bowel in newborns. This project uses a rodent model that mimics the intestinal pathological changes seen in NEC to study the effect of formula feeding and hypoxia on NEC developmenttime series, diet, hypoxiaJeffrey,,Uppermanhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=129Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE491/GSE491_RAW.tar >>>"}7!!K)q1Effect of prostaglandin analogs on aqueous humor outflowGSE492Public on Jul 16 20032003-07-012006-07-27The purpose of this study is to discover genes that might increase aqueous humor outflow when human ciliary muscle or human trabecular meshwork cells are treated with the prostaglandin analogues latanoprost free acid or prostaglandin F2alpha. Five tissue donors were pooled on each chip.otherPaul, ,Russellhttp://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=132Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE492/GSE492_RAW.tar 20032003-07-012006-07-27'(Juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, is a systemic vasculopathy affecting young children. Epidemiology studies documenting an antecedent illness in the 3 mo before the first definite symptom (rash and/or weakness) of JDM are supported by immunologic data that suggest that the disease pathophysiology is Ag driven. The purpose of this study was to compare the gene expression profiles in muscle biopsies of four untreated DQA1*0501(+) JDM children with profiles from children with a known necrotizing myopathy (Duchenne muscular dystrophy), as well as an in vitro antiviral model (NF90), and healthy pediatric controls. Nearly half (47%) of the dysregulated genes in JDM were associated with the immune response. In particular, increased expression of IFN-alphabeta-inducible genes 6-16, myxovirus resistance protein p78, latent cytosolic transcription factor, LMP2, and TAP1 was observed. This profile is consistent with an IFN-alphabeta transcription cascade seen in the in vitro viral resistance model. The IFN-alphabeta-inducible profile was superimposed on transcription profiles reflective of myofiber necrosis and regeneration shared with Duchenne muscular dystrophy. Expressed genes were confirmed by quantitative real-time PCR (6-16), immunofluorescence (thrombospondin 4), and immunolocalization (IFN-gamma, p21).otherZ,,Tezak; E,P,Hoffman; J,L,Lutz; T,O,Fedczyna; D Stephan; E,G,Bremer; I Krasnoselska-Riz; A Kumar; L,M,Pachmanhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=171Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE493/GSE493_RAW.tar x  %77!!3'q1Hyperoxic lung injuryGSE495Public on Jul 16 20032003-07-012006-07-27Nrf2 is a  $E7!!/'q1Non-union skeletal fracturesGSE494Public on Jul 16 20032003-07-012006-07-27Nonx#+7!!;i'q1Gene expression profiling in DQA1*0501+ children with untreated dermatomyositisGSE493Public on Jul 16 -union skeletal fractures are characterized by their inability to heal six months after injury. Left untreated, the non-union fracture may cause advanced arthritis or loss of function in the affected limb. Arrays were used to identify the mechanisms that lead to lack of skeletal repair in non-unions. These profiles are the non-union callous samples pooled from five individualsotherDietrich,,Stephanhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=139Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE494/GSE494_RAW.tartranscription factor that binds to antioxidant response elements of the regulatory region of a number of antioxidant genes. A mutation in the Nrf2 gene increases susceptibility to hyperoxic lung injury. This project examines expression differences between wild type and Nrf2 knock out mice with the hope of providing insight to the downstream effector genes regulated by Nrf2.otherStephan,,Kleebergerhttp://pepr.cnmcresearch.org/PEPR/browse.do?action=list_prj_exp&projectId=118Name: Eric Hoffman; Email: ehoffman@cnmcresearch.org; Phone: 202-884-6011; Fax: 202-884-6014; Laboratory: Research Center for Genetic Medicine; Department: Children's Research Institute; Institute: Children's National Medical Center; Address: 111 Michigan Ave. 5th Floor; City: Washington; State: DC; Zip/postal_code: 20010; Country: USA; Web_link: pepr.cnmcresearch.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE495/GSE495_RAW.tar `&7!! Extraocular muscle, expression changes in critical period (Porter lab)GSE497Public on Jul 16 20032003-07-012005-07-21.Evaluation of extraocular muscle (EOM) critical period by expression profiling in dark reared rat. Data form part of publication: Investigative Ophthalmology and Visual Sciences 44: 3842-3855, 2003.otherGeorgiana,,Cheng; Michael,J,Mustari; Sangeeta Khanna; John,D,PorterName: Henry,J.,Kaminski; Email: henry.kaminski@case.edu; Phone: 216-368-0250; Fax: 216-368-1710; Laboratory: Henry J. Kaminski(henry.kaminski@case.edu); Department: Neurology; Institute: Case Western Reserve University; Address: 11100 Euclid Avenue; City: Cleveland; State: OH; Zip/postal_code: 44106-5068; Country: USA ii'57!!+KE2F1-regulated genesGSE498Public on Jul 16 20032003-07-012005-05-29fPIdentification of E2F1-regulated genes that modulate the transition from quiescence into DNA synthesis, or have roles in apoptosis, signal transduction, membrane biology, and transcription repression.otherWilliam,D,Cresshttp://www.med.usf.edu/~dcress/Name: William,Douglas,Cress; Email: cressd@moffitt.usf.edu; Phone: 813-979-6703; Fax: 813-632-1436; Laboratory: Cress; Department: Oncology; Institute: Moffitt Cancer Center; Address: 12902 Magnolia Drive; City: Tampa; State: FL; Zip/postal_code: 33612-9497; Country: USA; Web_link: http://www.med.usf.edu/~dcress/ vv(E7!!Y]'Granulosa cell tumorigenesisGSE499Public on Jul 16 20032003-07-012005-05-29KComparison of global changes in ovarian transcriptomes uniquely associated with either granulosa cell tumors or luteomas, and identification of new markers for this tumor phenotype. Luteinizing hormone hypersecreting mice studied.otherGabe,E,Owens; Ruth,A,Keri; John,H,NilsonName: John,H,Nilson; Email: jhn@po.cwru.edu; Phone: 216-368-4497; Laboratory: Nilson; Department: Pharmacology; Institute: Case Western Reserve University, School of Medicine; Address: 2109 Adelbert Road; City: Cleveland; State: OH; Zip/postal_code: 44106; Country: USA )37!!qE1CD34+ cell analysisGSE500Public on Jul 16 20032003-07-012005-05-29Comparison of gene expression in CD34+ cells from bone marrow and G-CSF-mobilized peripheral blood to investigate why the latter are optimal for allogeneic transplant recipients.otherLynn,,Graf; Beverly Torok-Storb; Heimfeld Shelly; Shelly Heimfeldhttp://parma.fhcrc.org/lgrafName: Lynn Graf; Email: lgraf@fhcrc.org; Phone: 206-667-4545; Fax: 206-667-5978; Laboratory: Torok-Storb; Department: Clinical Research Division; Institute: Fred Hutchinson Cancer Research Center; Address: 1100 Fairview Ave. N. D1-100; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USA; Web_link: noneftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE500/GSE500_RAW.tar r[+G7!!#CEucalyptus grandis BC progenyGSE502Public on Jul 16 20032003-07-012005-07-20rE *?7!!u}Cytomegalovirus infectionGSE501Public on Jul 16 20032003-07-012005-05-29Comparison of gene expression profiles of human foreskin fibroblasts (HFF) infected with 3 clinical isolates of cytomegalovirus strains representing three glycoprotein B genotypes.otherJulie,,Randolph-Habecker; Lynn Graf; Beverly Torok-StorbName: Lynn Graf; Email: lgraf@fhcrc.org; Phone: 206-667-4545; Fax: 206-667-5978; Laboratory: Torok-Storb; Department: Clinical Research Division; Institute: Fred Hutchinson Cancer Research Center; Address: 1100 Fairview Ave. N. D1-100; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USA; Web_link: noneThe gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5.; KeywordsorderedMatias,,Kirst; Ron SederoffName: Matias Kirst; Email: mkirst@unity.ncsu.edu; Phone: 919-513-0015; Department: ; Institute: Forest Biotechnology Group; Address: ; City: Raleigh; State: NC; Zip/postal_code: 27606; Country: USA ,U7!!IMacrophages infected with SalmonellaGSE503Public on Jul 16 20032003-07-022005-05-29Identification of host pathways affected by the Salmonella virulence transcription factor phoPotherName: Stanford Microarray Database; Email: array@genome.stanford.edu; Phone: 650-498-6012; Department: Stanford University, School of Medicine; Institute: Stanford Microarray Database (SMD); Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA; Web_link: http://genome-www5.stanford.edu/that additional genes are involved in the Pitx1-Tbx hierarchy. To examine the molecular distinctions coded for by these factors, and to identify novel genes involved in the determination of limb identity, we have used Serial Analysis of Gene Expression (SAGE) to generate comprehensive gene expression profiles from intact, developing mouse forelimbs and hindlimbs. To minimize the extraction of erroneous SAGE tags from low-quality sequence data, we used a new algorithm to extract tags from -analyzed sequence data and obtained 68,406 and 68,450 SAGE tags from forelimb and hindlimb SAGE libraries, respectively. We also developed an improved method for determining the identity of SAGE tags that increases the specificity of and provides additional information about the confidence of the tag-UniGene cluster match. The most differentially expressed gene between our SAGE libraries was Pitx1. The differential expression of Tbx4, Tbx5, and several limb-specific Hox genes was also detected; however, their abundances in the SAGE libraries were low. Because numerous other tags were differentially expressed at this low level, we performed a 'virtual' subtraction with 362,344 tags from six additional nonlimb SAGE libraries to further refine this set of candidate genes. This subtraction reduced the number of candidate genes by 74%, yet preserved the previously identified regulators of limb identity. This study presents the gene expression complexity of the developing limb and identifies candidate genes involved in the regulation of limb identity. We propose that our computational tools and the overall strategy used here are broadly applicable to other SAGE-based studies in a variety of organisms.otherElliott,H,Margulies; Sharon L,R,Kardia; Jeffrey,W,InnisName: Elliott,H,Margulies; Email: elliott@nhgri.nih.gov; Phone: 301-594-9210; Laboratory: Dr. Eric Green; Department: Genome Technology Branch; Institute: National Human Genome Research Institute; Address: ; City: Bethesda; State: MD; Zip/postal_code: 20892; Country: USA BB.-!7!!'{-Comparative molecular analysis of developing mouse forelimbs and hindlimbsGSE504Public on Jul 16 20032003-07-022005-06-15The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures, both within the same organism (e.g., hand vs. foot) and between different species (e.g., hand vs. wing). In the developing embryo, limb-specific expression of Pitx1, Tbx4, and Tbx5 regulates the determination of limb identity. However, numerous lines of evidence, including the fact that these three genes encode transcription factors, indicate ' corneal buttons were processed at the time of corneal transplantation. The endothelia of normal and Fuchs'-affected corneas were stripped, and total RNA was isolated. Serial analysis of gene expression (SAGE) was performed to identify and quantify gene transcripts. Genes over- and underexpressed by Fuchs' endothelium were limited to P < 0.01 by the method of Audic and Claverie. RESULTS: A total of 19,136 tags were identified with 9,530 from normal and 9,606 from Fuchs' endothelium. The expression of 18 transcripts was upregulated, and 36 transcripts were downregulated in Fuchs' endothelium compared with normal tissue. Upregulated transcripts included serum amyloid A1 and A2, metallothionein, and apolipoprotein D. Of the downregulated transcripts, 26 matched known genes, 3 matched expressed sequence tags (ESTs), and 7 were unknown to current databases. One downregulated transcript involved a newly reported bicarbonate transporter. Decreased transcripts related to antioxidants and proteins conferring protection against toxic stress were noted in Fuchs' versus normal endothelium including nuclear ferritin, glutathione S-transferase-pi, and heat shock 70-kDa protein. Nine different SAGE tags matching mitochondrial sequences accounted for 25% of the ESTs that were decreased in Fuchs' endothelium. CONCLUSIONS: SAGE analysis comparing normal to Fuchs' endothelium demonstrates diminished expression of mitochondrial, pump function, and antiapoptotic cell defense genes. A complete report of gene expression profiles of normal human corneal endothelium can be found in PMID 12583793.otherJohn,D,Gottsch; Gerami,D,Seitzman; Elliott,H,Margulies; Amanda,L,Bowers; Sean,W,Kim; Saurabh Saha; Albert,S,Jun; Walter,J,Stark; Sammy,H,Liucorneanet.wilmer.jhu.eduName: Elliott,H,Margulies; Email: elliott@nhgri.nih.gov; Phone: 301-594-9210; Laboratory: Dr. Eric Green; Department: Genome Technology Branch; Institute: National Human Genome Research Institute; Address: ; City: Bethesda; State: MD; Zip/postal_code: 20892; Country: USA OO!./7!!#%=-Serial analysis of gene expression in the corneal endothelium of Fuchs' dystrophyGSE505Public on Jul 16 20032003-07-022005-07-21dPURPOSE: To compare the gene expression profiles of normal human corneal endothelium with Fuchs' corneal endothelium, by using serial analysis of gene expression (SAGE). METHODS: Three pairs of normal human corneas were obtained from eye banks. Thirteen bisected Fuchsesent transcriptional alterations in response to HCMV infection. Expression kinetics by 5' nuclease fluorigenic real-time PCR of selected genes revealed partial protection of infected cells against initial stress-associated alterations of gene expression and indicated fluctuations of transcriptional levels over time. Additionally, agreement with the quantitative results obtained by SAGE was observed only for genes up-regulated in HCMV-infected cells. This finding pointed to various technical and statistical parameters that all may be critical for quantitative transcriptome studies using global approaches, especially when exploring biological systems in a critical phase of cellular physiology.otherM,,Kenzelmann; K MuhlemannName: Marc Kenzelmann; Email: m.kenzelmann@dkfz.de; Phone: +41 31 632 3251; Fax: +41 31 632 3550; Department: Molecular Genome Analysis; Institute: Institute of Medical Microbiology, University of Bern; Address: Friedbuhlstrasse 51; City: Bern; Zip/postal_code: 3010; Country: Switzerland  T/7!!AMFibroblast cells immediate-early after human cytomegalovirus infectionGSE506Public on Jul 16 20032003-07-022005-05-297Human cytomegalovirus (HCMV) has been shown to have the potential to alter cellular gene expression early after infection. However, one-gene approaches and the use of closed system gene expression technologies have identified only few cellular genes whose activity changed immediate-early. We therefore used serial analysis of gene expression (SAGE) to investigate the transcriptional program of human fibroblasts in response to HCMV in the immediate-early phase of infection. Differential expression of various cellular genes was monitored. Transcriptional expression changes of genes coding for ribosomal proteins reflected a general cellular response to starvation and stress. But differential regulation of genes coding for transcription factors and proteins associated with cellular metabolism, homeostasis and cell structure may reprn in the ZR75-1 estrogen dependent breast cancer cell line. In this manner we have identified several genes that were regulated by estrogen or tamoxifen. Here we report the identification and initial characterization of EIT-6 (Estrogen Induced Tag-6), a novel nuclear protein and a new member of the evolutionarily conserved SM-20 family of growth regulatory immediate-early genes. EIT-6 appears to be a direct transcriptional target of the estrogen receptor and constitutive expression of EIT-6 promotes colony growth in human breast cancer cells. These data indicate that EIT-6 may play a role in estrogen induced cell growth.otherPankaj,,Seth; Ian Krop; Dale Porter; Kornelia PolyakName: Kornelia Polyak; Email: kornelia_polyak@dfci.harvard.edu; Phone: 617-632-2106; Fax: 617-632-3775; Laboratory: Polyak; Department: Adult Oncology; Institute: Dana-Farber Cancer Institute; Address: 44 Binney Street; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA; Web_link: http://research.dfci.harvard.edu/polyaklab P0a7!!5u+Novel estrogen and tamoxifen induced genesGSE507Public on Jul 16 20032003-07-022005-06-15;The breast cancer promoting effects of estrogen and the chemopreventive effects of tamoxifen are thought to be mediated by the estrogen receptor, a ligand-dependent transcription factor. Therefore, comprehensive analysis of gene expression profiles following estrogen or tamoxifen treatment may help us better understand the role estrogen plays in tumorigenesis. We utilized SAGE (Serial Analysis of Gene Expression) technology to identify genes regulated by estrogen and tamoxife ated from control and PC3-JNK2AS libraries, corresponding to 15,999 and 20,698 unique transcripts, respectively. Transcripts corresponding to transcription factors, stress-induced genes, and apoptosis-related genes were up-regulated in the PC3-JNK2AS library, revealing a significant stress response after the inhibition of JNK2 expression. Genes involved in DNA repair, mRNA turnover, and drug resistance were found to be down-regulated by inhibition of JNK2 expression, further highlighting the importance of JNK2 signaling in regulating cell homeostasis and tumor cell growth.otherOlga,U,Potapova; Sergey,V,Anisimov; Myriam Gorospe; Ryan,H,Dougherty; William,A,Gaarde; Kenneth,R,Boheler; Nikki,J,HolbrookName: Nikki,J.,Holbrook; Email: nikki.holbrook@yale.edu; Phone: 203-737-5847; Fax: 203-737-1801; Laboratory: Geriatrics Section; Department: Department of Internal Medicine; Institute: Yale University School of Medicine; Address: 333 Cedar Street; City: New Heaven; State: CT; Zip/postal_code: 06520; Country: USA &&N17!! Targets of c-Jun NH(2)-terminal kinase 2-mediated tumor growth regulationGSE508Public on Jul 16 20032003-07-022005-06-15NAlthough the c-Jun NH(2)-terminal kinase (JNK) pathway has been implicated in mediating cell growth and transformation, its downstream effectors remain to be identified. Using JNK2 antisense oligonucleotides (JNK2AS), we uncovered previously a role for JNK2 in regulating cell cycle progression and survival of human PC3 prostate carcinoma cells. Here, to identify genes involved in implementing JNK2-mediated effects, we have analyzed global gene expression changes in JNK2-deprived PC3 cells using Serial Analysis of Gene Expression. More than 40,000 tags each were gener"%to a large degree by the glycoprotein hormone FSH, which is required for the testis to acquire full size and spermatogenic capacity. Signaling events initiated by the binding of FSH to its receptor lead to an alteration of Sertoli cell gene expression. To characterize the changes in gene expression in FSH-treated Sertoli cells, we used the mRNA from these cells to screen Affymetrix U34A rat GeneChip oligonucleotide microarrays. Sertoli cells from 20-d-old rats were cultured in the presence of 25 ng/ml ovine FSH. At 0, 2, 4, 8, and 24 h after the addition of FSH, total RNA was purified and used to prepare biotinylated target, which was hybridized to the U34A rat microarray containing approximately 9000 rat genes. Analysis identified 100-300 transcripts at each time point that were up-regulated or down-regulated by 2-fold or greater. Genes previously reported to be FSH or cAMP regulated in rat Sertoli cells were identified, in addition to numerous genes not reported to be expressed or FSH regulated in Sertoli cells. The expression patterns of five of these genes, encoding nerve growth factor inducible gene B, PRL-1, PC3 nerve growth factor-inducible antiproliferative putative secreted protein, diacylglycerol acyltransferase, and an expressed sequence tag, in FSH- and N,O'-dibutyryl cAMP-treated rat Sertoli cells were confirmed and characterized by Northern blot analysis. Thus, we have begun to define the transcriptome induced and repressed by FSH in rat Sertoli cells, and we have generated datasets of genes available for further analysis in regard to spermatogenesis and Sertoli cell signaling.otherDerek,J,McLean; Patrick,J,Friel; Derek,J,Pouchnik; Michael,D,Griswoldwww.wsu.edu/~griswold/microarray; www.wsu.edu/~griswold/microarray/Name: Derek,J,McLean; Email: dmclean@wsu.edu; Phone: 509-335-2240; Fax: 509-335-9688; Laboratory: Griswold; Department: School of Molecular Biosciences; Institute: Washington State University; Address: Box 644660; City: Pullman; State: WA; Zip/postal_code: 99164-4660; Country: USA ^m3-7!!'a7Sepsis gene expression profiling: murine splenic compared with hepatic responsesGSE510Public on Jul 16 20032003-07-022005-06-15yThe aim of this series of experiments was to gain experience in sepsis gene expression profiling in a well-accepted model of murine polymicrobial abdominal sepsis and begin characterizing (in the parlance of genomics)'27!!9?Gene expression in follicle-stimulating hormone-treated rat Sertoli cellsGSE509Public on Jul 16 20032003-07-022005-06-15_Spermatogenesis requires the presence of functional somatic Sertoli cells in the seminiferous tubules of the testis. Sertoli cells provide support and factors necessary for the successful progression of germ cells into spermatozoa. Sertoli cells are regulated $( the sepsis "transcriptome." DESIGN: Prospective animal study. SETTING: University-based animal research facility.SUBJECTS C57BL/6 mice. INTERVENTIONS: After induction of general anesthesia, cecal ligation and puncture were performed to induce peritonitis and polymicrobial sepsis. The control group had sham laparotomy only. Three samples of spleen and liver were collected from septic and sham animals at 24 hrs after laparotomy. Changes in expression were measured for 588 annotated mouse genes by using a commercially available complementary DNA microarray kit. MEASUREMENTS AND MAIN RESULTS: Broad-scale gene expression profiles were characterized for septic liver and spleen and compared with sham controls. The analytical tools used included commercially available software packages and a novel analysis program. Very little overlap was observed in the septic gene expression profiles of these two organs. Most of the genes identified have previously been linked to regulation of the inflammatory response; importantly, however, some have not. In addition, hierarchical cluster analysis showed that cecal ligation and puncture at 24 hrs induced coordinate expression of genes that alter cell signaling and survival pathways in spleen, consistent with previously published reports of sepsis-induced splenocyte apoptosis. The current limitations of microarray analysis as reflected in these studies are also discussed. CONCLUSIONS: Microarray technology provides a powerful new tool for rapidly analyzing tissue-specific changes in gene expression induced by sepsis in animal models.otherJ,P,Cobb; J,M,Laramie; G,D,Stormo; J,J,Morrissey; W,D,Shannon; Y Qiu; I,E,Karl; T,G,Buchman; R,S,HotchkissName: Jason,Matthew,Laramie; Email: laramiej@msnotes.wustl.edu; Phone: 314-747-0054; Fax: 314-362-7474; Laboratory: Cellular Injury and Adaptation Laboratory; Department: Surgery; Institute: Washington University; Address: 660 South Euclid Avenue; City: St. Louis; State: MO; Zip/postal_code: 63110; Country: USA; Web_link: www.cia.wustl.edu proteins associated with immune cell function and with transcription and translation, exhibited increased expression subsequent to viral infection. Gene families exhibiting a decline in gene expression were confined to the 72 hr time point and included genes associated with catabolism and a subset of genes involved with cell signaling and synthetic pathways. Self-organizing map (SOM) cluster analysis identified temporal patterns of coordinated gene expression in infected PBMCs including genes associated with the immune response, the cytoskeleton, and ribosomal subunit structural proteins required for protein synthesis.otherM,T,Vahey; M,E,Nau; L,L,Jagodzinski; J Yalley-Ogunro; M Taubman; N,L,Michael; M,G,LewisName: Maryanne Vahey; Email: mvahey@hivresearch.org; Phone: 301-251-5058; Fax: 301-762-7460; Laboratory: Laboratory of Functional Genomics; Department: ; Institute: Walter Reed Army Institute of Research; Address: 1600 East Gude Drive; City: Rockville; State: MD; Zip/postal_code: 20850; Country: USA ii 4?7!!G;gProliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RFGSE511Public on Jul 16 20032003-07-022005-05-29Exploiting the power of high-density gene arrays, the simultaneous expression analysis of 5600 cellular genes was executed on proliferating peripheral blood mononuclear cells (PBMCs) from three normal human donors that were infected in vitro with the T cell tropic laboratory strain of HIV-1, RF. Profiles of expressed genes were assessed at 1, 12, 24, 48, and 72 hr postinfection and compared with those of matched uninfected PBMCs. Viral infection resulted in an overall increase in the number of genes expressed with peaks of expression at 1, 12, and 48 hr postinfection. Functional clustering of genes whose expression level in infected PBMCs varied by 2-fold or greater from levels in the controls indicated that cellular activation markers,),SE512Public on Jul 16 20032003-07-022005-05-29_Using the Affymetrix HuGeneFL GeneChip, the global expression patterns of genes in the peripheral blood mononuclear cells (PBMCs) of rhesus macaques, infected with SIVmac251 and exhibiting rapid, typical, or slow rates of disease progression, were examined. Assessments of the change in gene expression (fold change), the temporal coordination of gene expression (self-organizing map analysis), and the similarities and significant differences in gene expression across the groups were performed on samples taken before infection and 3 and 7 weeks postinfection. An upregulation of the p27 interferon-inducible gene and of genes associated with cellular activation and immune response was observed in all three groups. Rapidly progressing animals exhibited a modest number of genes with a change in expression of 3-fold or greater, typically progressing animals exhibited the greatest number, and slowly progressing animals exhibited the fewest. Self-organizing map cluster analysis indicated that rapidly progressing animals exhibited the least coordinated gene expression over the three study time points, typically progressing animals exhibited a moderate degree, and animals with slow progression exhibited the most coordinated gene expression. Mann-Whitney U analysis indicated that differences in gene expression were most pronounced between the rapidly and slowly progressing groups and least pronounced between the rapidly and typically progressing animals. These observations elucidate distinct features of gene expression in animals with different rates of disease progression.otherM,T,Vahey; M,E,Nau; M Taubman; J Yalley-Ogunro; P Silvera; M,G,LewisName: Maryanne Vahey; Email: mvahey@hivresearch.org; Phone: 301-251-5058; Fax: 301-762-7460; Laboratory: Laboratory of Functional Genomics; Department: ; Institute: Walter Reed Army Institute of Research; Address: 1600 East Gude Drive; City: Rockville; State: MD; Zip/postal_code: 20850; Country: USA S;SX7G7!!S AIDS-related Kaposi's sarcomaGSE514Public on Jul 16 20032003-07-022007-10-22Kaposi's Sarcoma (KS) is a proliferation of aberrant vascular structures lined by spindle cells, and is caused by a gammaherpes virus (HHV8/KSHV). Its course is aggravated by co-infection with HIV-1, where the timing of infection with HIV-1 and HHV8 is important for the clinical outcome. METHODS: In order to better understand the pathogenesis of KS, we have analysed tissue 0F67!!/+iQCynomolgus monkey testicular cDNAs for discovery of novel human genesGSE513Public on Jul 16 20032003-07-022005-06-15BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and.B5'7!!sgPeripheral Blood Mononuclear Cells of Rhesus Macaques Infected with SIVmac251G+/ attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl.We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were shown to be expressed very highly in the cynomolgus monkey testis, but not ubiquitously. CONCLUSIONS: In this report, we determined 302 full-insert sequences of cynomolgus monkey cDNAs with enough length of open reading frames to discover novel transcripts as human homologues. Among 302 cDNA sequences, human homologues of 89 cDNAs have not been predicted in the annotated human genome sequence in the Ensembl. Additionally, we identified 75 dominantly expressed genes in testis among the full-sequenced clones by using a DNA microarray. Our cDNA clones and analytical results will be valuable resources for future functional genomic studies.otherNaoki,,Osada; Munetomo Hida; Jun Kusuda; Reiko Tanuma; Makoto Hirata; Yumiko Suto; Momoki Hirai; Keiji Terao; Sumko Sugano; Katsuyuki Hasihmotohttp://www.nih.go.jp/yoken/genebank/index.htmlName: Naoki Osada; Email: osada@nih.go.jp; Phone: +81-3-5285-1111; Fax: +81-3-5285-1181; Laboratory: Division of genetic resources; Institute: National Institute of Infectious Diseases; Address: 1-23-1, Toyama-cho, Shinjuku-ku; City: Tokyo; State: Tokyo; Zip/postal_code: 162-8640; Country: Japan; Web_link: http://www.nih.go.jp/yoken/genebank/index.html1from two AIDS-KS lesions, and from normal skin by serial analysis of gene expression (SAGE). Semi-quantitative RT-PCR was then used to validate the results. RESULTS: The expression profile of AIDS-related KS (AIDS-KS) reflects an active process in the skin. Transcripts of HHV8 were found to be very low, and HIV-1 mRNA was not detected by SAGE, although it could be found using RT-PCR. Comparing the expression profile of AIDS-KS tissue with publicly available SAGE libraries suggested that AIDS-KS mRNA levels are most similar to those in an artificially mixed library of endothelial cells and leukocytes, in line with the description of KS lesions as containing spindle cells with endothelial characteristics, and an inflammatory infiltrate. At least 64 transcripts were found to be significantly elevated, and 28 were statistically downregulated in AIDS-KS compared to normal skin. Five of the upregulated mRNAs, including Tie 1 and sialoadhesin/CD169, were confirmed by semi-quantitative PCR to be elevated in additional AIDS-KS biopsies. Antibodies to sialoadhesin/CD169, a known marker of activated macrophages, were shown to specifically label tumour macrophages. CONCLUSION: The expression profile of AIDS-KS showed 64 genes to be significantly upregulated, and 28 genes downregulated, compared with normal skin. One of the genes with increased expression was sialoadhesin (CD169). Antibodies to sialoadhesin/CD169 specifically labelled tumour-associated macrophages, suggesting that macrophages present in AIDS-KS lesions belong to a subset of human CD169+ macrophages.otherMarion,,Cornelissen; Antoinette,C,van der Kuyl; Remco van den Burg; Audrey van der Schoot; John,T,Dekker; Jolanda Maas; Fokla Zorgdrager; Bert Tigges; Carel,J,van Noesel; Jaap Goudsmit; Celeste LebbéName: Antoinette van der Kuyl; Email: a.c.vanderkuyl@amc.uva.nl; Phone: 31 20 5666778; Department: Human Retrovirology; Institute: Academic Medical Centre, University of Amsterdam; Address: ; City: Amsterdam; Zip/postal_code: 1105 AZ; Country: Netherlands  8?7!!ouEndothelial cell profilesGSE515Public on Jul 16 20032003-07-022005-05-29Umbilical vein, lung microvascular, aortic and coronary artery endothelial cell profiles generated. Further characterization gained by comparison with other selected cell types.otherName: Jennifer King; Email: jyking@stanford.edu; Phone: 650-736-0640; Laboratory: Quertermous Lab; Department: Cardiovascular Medicine; Institute: Stanford University; Address: ; City: Palo Alto; State: CA; Zip/postal_code: 94305; Country: USA t9=7!!#;gTNF treated SynoviocytesGSE516Public on Jul 03 20032003-07-032005-05-29LTime series of human arthritic synoviocytes treated with TNFalpha.time-courseJoanne,,Gallagher; Jillian Howlin; Conor Mc Carthy; Evelyn,P,Murphy; Barry Bresnihan; Oliver Fitzgearald; Catherine Godson; Hugh,R,Brady; Finian MartinName: Jill Howlin; Email: jillian.howlin@ucd.ie; Phone: +353 1 7162815; Laboratory: Mammary Gland Biology; Department: Pharmacology; Institute: The Conway Institute of Biomedical and Biomolecular Research; Address: University College Dublin Belfield; City: Dublin; Zip/postal_code: 4; Country: Ireland }:W7!!K}qActivation-tagged jaw-d mutant plantsGSE518Public on Jul 09 20032003-07-082005-05-29PHAnalysis of gene expression in activation-tagged jaw-d mutant plants. Total RNA was extracted from the aerial parts of two weeks old jaw-d and control plants.otherJ,F,Palatnik; D Weigel; Javier,F,Palatnik; Detlef WeigelName: Javier,Fernando,Palatnik; Email: javier.palatnik@tuebingen.mpg.de; Phone: +49-7071- 601 1406; Fax: +49-7071- 601 1412; Laboratory: Detlef Weigel; Department: Molecular Biology; Institute: Max Planck Institute; Address: 37-39 Spemannstrasse; City: Tuebingen; Zip/postal_code: D-72076; Country: Germany Y;97!!A'-V1 vs V1 FliA knockoutGSE521Public on Mar 03 20042003-07-102005-05-29Competive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which fliA gene encoding sigma 28 has been disruptedrepeat sampleCatherine,D,Carrillo; Eduardo,N,Taboada; Wendy,A,Findlay; John,H,NashName: John Nash; Email: John.Nash@nrc-cnrc.gc.ca; Phone: (613) 990-0990; Laboratory: Nash Lab; Department: Institute for Biological Sciences; Institute: National Research Council; Address: 100 Sussex Drive; City: Ottawa; State: ON; Zip/postal_code: K1A0R6; Country: Canada <7!!#qX-radiation (XR) sensitive HCT116-CloneK: XR at 0 and 4 GyGSE522Public on Dec 08 20032003-07-112005-05-29cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells without XR, 10 minutes, 6 hours, or 24 hours after XR at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywordstime-courseFelix,M,Mesak; Cheng,E,Ng; Wei,L,Tan; Sami,S,QutobName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada KK1=M7!!1'[Unirradiated HCT116-CloneK cellsGSE523Public on Dec 08 20032003-07-112005-05-29cDNA microarray study of unirradiated X-radiation (XR) sensitive HCT116-CloneK cells versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Sami,S,QutobName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada _>7!!a'UHCT116-CloneK cells 10 minutes after XR treatment at 4 GyGSE524Public on Dec 08 20032003-07-112005-05-29cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells 10 minutes after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada !![?y7!!_'UHCT116-CloneK cells 6 hours after XR treatment at 4 GyGSE525Public on Dec 08 20032003-07-112005-05-29cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells six hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada !![@{7!!]'UHCT116-CloneK cells 24 hours after XR treatment at 4 GyGSE526Public on Dec 08 20032003-07-112005-05-29cDNA microarray study of X-radiation (XR) sensitive HCT116-CloneK cells 24 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada $A+7!!{)Cervical CancerGSE527Public on Sep 12 20032003-07-112005-05-29ߜ?Expression profiles in normal and cancerous cervix tissue samplesotherZachariah,E,Selvanayagam; Ragini Vittal; Khew-Voon ChinName: Khew-Voon Chin; Email: chinkv@rci.rutgers.edu; Phone: 732-445-3400 x253; Fax: 732-445-0687; Laboratory: Laboratory for Cancer Research; Department: Chemical Biology; Institute: Ernest Mario School of Pharmacy, Rutgers University; Address: 164 Frelinghuysen Road; City: Piscataway; State: NJ; Zip/postal_code: 08854; Country: USA=y, and the NK2-specific domain (NK2-SD) of yet unknown function. One of the best characterized members of this group is the early cardiogenic marker Nkx2.5. Loss of function of Nkx2.5 leads to embryonic lethality around E10.5 due to an arrest of heart development at the looping stage. We have further dissected the function of Nkx2.5 in vivo by creating a knockout mouse line harboring an in frame deletion of the NK2-SD by Cre/loxP mediated excision. Homozygous mutant mice die at E14.5 due to severe cardiac malformations, e.g. common AV canal, DORV, and VSD. Lack of the NK2-SD leads to downregulation of the ventricular markers MLC-2v and Irx4 specifically in the right ventricle, and is accompanied with reduced right ventricular function. This function of Nkx2.5 seems to be independent of its ability to bind target DNA, since lack of the NK2-SD does not alter the DNA binding activity of Csx/Nkx2.5 in vitro. Heterozygous mutant mice show a spectrum of cardiac defects related to cardiac septation and valve morphogenesis, but lack conduction system defects as reported for heterozygous Nkx2.5 mice. The phenotype observed in NK2-SD mutant mice shows that Nkx2.5 is not only crucial during early steps of cardiogenesis but also plays an important role at later developmental stages.; ; Embryos were isolated at embryonic day 12.5. The entire embryo heart was taken and isolated in ice-cold PBS and immediately frozen on dry-ice. Total RNA was extracted from pooled samples of wildtype, heterozygous and mutant embryos.; KeywordsotherMartina,,Schinke; Lauren,E,Riggi; Iuan-Bor Chen; Seigo Izumohttp://cardiogenomics.med.harvard.edu/groups/proj1/pages/; http://cardiogenomics.med.harvard.edu/groups/proj1/pages/nk2-sd_home.htmlName: Martina Schinke; Email: mschinke@cgr.harvard.edu; Phone: 617-495-0676; Laboratory: Cardiogenomics; Department: Bauer Center for Genomic Research; Institute: Harvard University; Address: 7 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: www.cardiogenomics.org   eBW7!!qNK2 model of congenital heart diseaseGSE528Public on Jul 13 20032003-07-112005-06-15Lack of the conserved NK2-domain of the cardiac transcription factor Nkx2.5 causes multiple heart defects .; ; The NK2 family of homeobox genes constitutes a family of transcription factors that play an important role in different developmental processes. Members of this group are characterized by two highly conserved protein domains: the homeodomain, conferring DNA binding activit< mmC7!!{New targets of Drosophila adenosine deaminase acting on RNA (dADAR)GSE529Public on Jul 14 20032003-07-142005-06-15܆The aim of this experiment is to identify new targets of Drosophila adenosine deaminase acting on RNA (dADAR) by enriching Inosine-containing mRNA (I-mRNA) from wild type (C-S) and dADAR mutant flies and then hybridization with Drosophila cDNA arrays.otherShuli,,Xia; Jinghua Yang; Yingjun Su; Jiang Qian; Enbo Ma; Gabriel HaddadName: Shuli Xia; Email: xia@kennedykrieger.org; Phone: 443-923-2683; Institute: Kennedy-Krieger Institute; Address: ; City: Baltimore; State: MD; Zip/postal_code: 21205; Country: USA 8D97!!#'u-V1 vs V1 FlhA knockoutGSE530Public on Mar 03 20042003-07-142005-05-29Competitive hybridization of V1 variant of genome sequenced C. jejuni strain 11168 versus V1 variant in which flhA gene has been disrupted.repeat sampleCatherine,D,Carrillo; Eduardo,N,Taboada; John,H,NashName: John Nash; Email: John.Nash@nrc-cnrc.gc.ca; Phone: (613) 990-0990; Laboratory: Nash Lab; Department: Institute for Biological Sciences; Institute: National Research Council; Address: 100 Sussex Drive; City: Ottawa; State: ON; Zip/postal_code: K1A0R6; Country: Canada EA7!!W'u-V1 variant vs. V26 variantGSE531Public on Mar 03 20042003-07-142005-05-29Competitive hybridization of V1 variant versus V26 variant of genome sequenced C. jejuni strain 11168repeat sampleCatherine,D,Carrillo; Eduardo,N,Taboada; John,H,NashName: John Nash; Email: John.Nash@nrc-cnrc.gc.ca; Phone: (613) 990-0990; Laboratory: Nash Lab; Department: Institute for Biological Sciences; Institute: National Research Council; Address: 100 Sussex Drive; City: Ottawa; State: ON; Zip/postal_code: K1A0R6; Country: Canada @@DJPV\bhntz "(.4:@FLRX^djpv|4:5;6<7=8>9?:@;A>B?C@DAEBFCHDJ4:5;6<7=8>9?:@;A>B?C@DAEBFCHDJFKGLHMINJPLQMROSQTSUTXW[[]\_`aabccedfegfhhjikjlkmlnmonpoqprqtrwsxtyuzv{w|x}z|}     !"#$'()*+,-./„0Ä1Ą2ń3Ƅ4DŽ5Ȅ6Ʉ7ʄ8˄9̄:΄;τ<Є=ф>tolerizing allografts. In the tolerizing allografts there were induced marked expressions of a number of genes for proinflammatory factors, including interferon-gamma inducible cytokines and chemokines, as well as apoptosis-related genes which were also upregulated in the rejecting allografts. Moreover, these gene expression patterns continued to be upregulated more than 70 days post transplant. These results provide evidence that immunological tolerance can be induced and maintained in the presence of prominent proinflammatory gene expression in vivo.otherY,,Matsui; A Saiura; Y Sugawara; M Sata; K Naruse; H Yagita; T Kohro; C Mataki; A Izumi; T Yamaguchi; T Minami; T Sakihama; S Ihara; H Aburatani; T Hamakubo; T Kodama; M MakuuchiName: Yuichi Matsui; Email: ymatsui-tky@umin.ac.jp; Phone: 81-3-5452-5230; Laboratory: Laboratory for System Biology and Medicine; Department: Biology; Institute: University of Tokyo; Address: Komaba 4-6-1; City: Meguro-ku; State: Tokyo; Zip/postal_code: 153-8904; Country: Japan ((LsY7!!'q;Gene expression of transplanted heartsGSE582Public on Oct 14 20032003-08-082005-06-15C57/BL6 to C57/BL6; Balb/c to C57/BL6; Balb/c to C57/BL6 with anti CD80/86 mAb; ; Identificaton of gene expression profile in tolerizing murine cardiac allograft by co-stimulatory blockade.; ; The induction of specific tolerance would be the ultimate achievement in transplant immunology, but the precise mechanisms of immunological tolerance remain largely unknown. Here, we investigated global gene expression analysis in tolerizing murine cardiac allografts by means of oligonucleotide microarrays. Tolerance induction was achieved in cardiac allografts from BALB/c to C57BL/6 mice by daily intraperitoneal injection of anti-CD80 and CD86 mAbs. Comparative analysis revealed 64 genes to be induced more extensively in the tolerizing than in the syngeneic isografts, and 16 genes than in the rejecting allografts. Two genes were specifically upregulated in the v 77EtQ7!!S'oLoblolly pine - Juvenile vs MatureGSE583Public on Aug 11 20032003-08-082005-06-15Phase transition in wood formation.repeat sampleWalter,W,Lorenz; Jeffrey,F,Dean; W. Walter LorenzName: Jeffrey,F.D.,Dean; Email: jeffdean@uga.edu; Phone: 1-706-542-1710; Fax: 1-706-583-0881; Department: Warnell School of Forest Resources; Institute: University of Georgia; Address: ; City: Athens; State: GA; Zip/postal_code: 30602; Country: USA zu 7!!]'DNA methylation and histone deacetylation in neural stem cellsGSE587Public on Jan 04 20042003-08-122005-10-28Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA; histone deacetylase inhibitor), 500 nM 5-Aza-2’-deoxycytidine (AzaC; demethylating agent) or both compounds, or left untreated. Two independent experiments were performed.otherMartin,,ZenkeName: Martin Zenke; Email: Martin.Zenke@rwth-aachen.de; Phone: +49-241-80 80760; Fax: +49-241-80 82008; Department: Cell Biology; Institute: Institute for Biomedical Engineering; Address: Universitatsklinikum Aachen, RWTH; City: Aachen; State: NRW; Zip/postal_code: 52057; Country: Germany; Web_link: www.molcell.de ;v{7!!u#G#1Effect of Age on Fracture Healing in the Rat: Series 1GSE589Public on Feb 01 20042003-08-122007-06-18V:mRNA gene expression was measured in rats at 6 (young), 26 (adult) and 52 (older) weeks of age at the time of fracture. Samples were collected at 0, 0.4, 1, 2, 4, and 6 weeks after fracture. RNA from two rats were pooled for each Affymetrix Rat U34A array.; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseRalph,A,Meyer; Martha,H,MeyerName: Ralph,A.,Meyer; Email: ralpham@aol.com; Laboratory: Cannon Research Center, Rm. 304; Department: Orthopaedic Research Laboratory; Institute: Carolinas Medical Center; Address: P.O. Box 32861; City: Charlotte; State: NC; Zip/postal_code: 28232-2861; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE589/GSE589_RAW.tar cw?7!!e3USF1 haplotype comparisonGSE590Public on Feb 29 20042003-08-132005-10-28Comparison of gene expression for individuals affected with FCHL exhibiting the USF1 susceptibility haplotype and FCHL affected indiviuals carrying the protective haplotypeorderedPäivi,,Pajukanta; Heidi,E,Lilja; Janet,S,Sinsheimer; Rita,M,Cantor; Aldons,J,Lusis; Massimiliano Gentile; Leena PeltonenName: Massimiliano Gentile; Email: massimiliano.gentile@helsinki.FI; Phone: +358-9-47448726; Laboratory: Biomedicum Bioinformatics Unit; Department: Biomedicum Bioinformatics Unit; Institute: Biomedicum Helsinki; Address: Haartmaninkatu 8; City: Helsinki; Zip/postal_code: 000 14; Country: Finland; Web_link: http://www.bioinfo.helsinki.fi &xa7!![w7Heart failure in TNF-alpha transgenic miceGSE591Public on Nov 09 20032003-08-132005-05-29Cardiac-specific TNF-alpha transgenic mice are an excellent model to study the pathologenesis of heart failure. Affymetrix U74V2A was used to analyze the gene expression profile of male and female wildtype FVB and TNF-alpha transgenic mice at the time point of compensated hypertrophy and dilated heart failure. 3 week, 13 week and 40 week samples examined.otherZ,H,Tang; A,M,Feldman; Zhong,H,Tang; Arthur,M,FeldmanName: Zhong Tang; Email: zhong.tang@jefferson.edu; Phone: 215-955-3399; Laboratory: Center for Translational Medicine; Department: Medicine; Institute: Thomas Jefferson University; Address: 1025 Walnut Street; City: Philadelphia; State: PA; Zip/postal_code: 19107; Country: USA 001z7!!  OUterine Fibroid and Normal Myometrial Expression Profiles- U133 ArraysGSE593Public on Oct 17 20032003-08-132005-05-29Our study seeks to identify genes diffe~y{7!!#G#1Effect of Age on Fracture Healing in the Rat: Series 2GSE592Public on Feb 01 20042003-08-132007-06-18V:Study of rat femur fracture healing in young (6 weeks old), adult (26 weeks old), and older (52 weeks old) rats with samples collected at 0 time (no fracture) and at 0.4, 1, 2, 4, and 6 weeks after fracture. RNA from two rats were pooled for each array.; Keywordstime-courseRalph,A,Meyer; Martha,H,MeyerName: Ralph,A.,Meyer; Email: ralpham@aol.com; Laboratory: Cannon Research Center, Rm. 304; Department: Orthopaedic Research Laboratory; Institute: Carolinas Medical Center; Address: P.O. Box 32861; City: Charlotte; State: NC; Zip/postal_code: 28232-2861; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE592/GSE592_RAW.tarrentially expressed between uterine leiomyomas and normal myometrial tissue. This series consists of samples derived from normal myometrium and uterine leiomyomas obtained from fibroid afflicted patients.Total RNA was extracted from samples, converted to biotin-labeled cRNA, hybridized to oligonucleotide arrays, and followed by model based expression analysis.; ; In order to select differentially expressed genes of interest, dChip model-based expression analysis was employed. Significant genes were identified, utilizing the dChip software, as having an average fold change of > +1.5 or < -1.5 between leiomyoma and normal myometrium and p < 0.05. Under these conditions the 226 genes in the following list were identified.otherPaul,J,Hoffman; Dawn,B,Milliken; Ryan,R,Davis; Jeffrey,P,GreggName: Jeffrey Gregg; Email: jpgregg@ucdavis.edu; Phone: 916-703-0360; Department: ; Institute: University of California, Davis School of Medicine; Address: ; City: Sacramento; State: CA; Zip/postal_code: 95817; Country: USAin intact female Sprague-Dawley rats at 6 (young), 26 (adult) and 52 (older) weeks of age at the time of fracture. Samples were collected at 0, 0.4, 1, 2, 4, and 6 weeks after fracture. RNA from two rats were pooled for each Affymetrix Rat U34A array. Mid-shaft, simple, transverse left femoral fractures were induced after retrograde intramedullary rod fixation with a Bonnarens and Einhorn device. Samples were collected from one third of the femoral length, centered on the fracture site, including the external callus, cortical bone, and marrow elements.; Keywords; Keywords; Keywords; Keywords; KeywordsotherRalph,A,Meyer; Martha,H,Meyerwww.carolinashealthcare.orgName: Ralph,A.,Meyer; Email: ralpham@aol.com; Laboratory: Cannon Research Center, Rm. 304; Department: Orthopaedic Research Laboratory; Institute: Carolinas Medical Center; Address: P.O. Box 32861; City: Charlotte; State: NC; Zip/postal_code: 28232-2861; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE594/GSE594_RAW.tar $_$7|77!!w-=Human skeletal muscleGSE595Public on Dec 10 20032003-08-142005-06-15*aStandard Affymetrix procedure, RNA from frozen tissueequivalent probeDespina,,Sanoudou; Peter,B,Kang; Judith,N,Haslett; Mei Han; Louis,M,Kunkel; Alan,H,BeggsName: Despina Sanoudou; Email: dsanoudo@enders.tch.harvard.edu; Phone: +30-210-6597453; Fax: +30-210-6597545; Laboratory: Sanoudou Lab; Department: Molecular Biology; Institute: Foundation for Biomedical Research, Academy of Athens; Address: Soranou Efesiou 4; City: Athens; Zip/postal_code: 115 27; Country: Greece{e7!!GC#1Effect of Age on Fracture Healing in the RatGSE594Public on Jan 10 20042003-08-142007-06-18V:mRNA gene expression was measured  D}G7!!U/QInflammatory bladder responseGSE597Public on Aug 15 20032003-08-152005-06-15Bladders examined at 1, 4 and 24 hours after lipopolysaccharide, substance P or ovalbumin challenge.otherIgor,,Dozmorov; Marcia,R,Saban; Nicholas Knowlton; Michael Centola; Ricardo SabanName: Ricardo Saban; Email: ricardo-saban@ouhsc.edu; Phone: 405-271-3700 xt 1; Fax: 405-271-5440; Department: ; Institute: University of Oklahoma Health Sciences Center; Address: ; City: Oklahoma City; State: OK; Zip/postal_code: 73104; Country: USA; Web_link: http://www.ouhscphysio.org/ XK7!!]i5Dietary salt and renal functionGSE599Public on Feb 14 20042003-08-182005-06-15Serum and glucocorticoid-induced kinase 1 (SGK1) activates the epithelial sodium channel (eNaC) in tubules. We examined renal SGK1 abundance in salt-adaptation and in salt-sensitive hypertension. Sprague-Dawley and Dahl salt-sensitive rats wer~~57!!u-[Phopshate starvationGSE598Public on Aug 22 20032003-08-152005-05-29Two arrays of phopshate starvation. PHO5 spot was not good with some arrays, and so was quantitated on other arraysequivalent probeDennis,,Wykoff; Mike Springer; Erin O'Shea; Nicole MillerName: Dennis Wykoff; Email: dennis.wykoff@villanova.edu; Phone: 415-476-2166; Laboratory: O'Shea; Department: Biochemistry; Institute: UCSF; Address: 600 16th St; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USAe placed on either 8% or 0.3% NaCl diets for 10 days. Plasma aldosterone levels were approximately 2.5-fold greater on 0.3% versus 8% NaCl diets in both rat strains. Both serum and glucocorticoid-induced kinase 1 transcript and protein abundance were less (P<0.01) in Sprague-Dawley rats and greater (P<0.01) in Dahl salt-sensitive rats on 8% versus 0.3% NaCl diets. The cDNA sequences of serum and glucocorticoid-induced kinase 1 in both strains of rat were the same. The present results provide evidence that the abundance of serum and glucocorticoid-induced kinase 1 in rat kidney may play a role in salt adaptation and the pathogenesis of hypertension and suggests that aldosterone is not the primary inducer of SGK1 in the Sprague-Dawley rat.; KeywordsotherM,,Farjah; B,P,Roxas; D,L,Geenen; R,S,DanzigerName: Bryan Angelo,P,Roxas; Email: baproxas@uic.edu; Phone: 312-590-3742; Institute: University of Illinois at Chicago; Address: 900 S. Ashland Ave.; City: Chicago; State: IL; Zip/postal_code: 60607; Country: USA 7!! %oqS. cerevisiae mutant with a constitutively activated Ras/cAMP pathwayGSE600Public on Aug 19 20032003-08-192005-06-15UComparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28.; Keywords; KeywordsotherDawn,L,Joneshttp://www.cogeme.man.ac.uk/DawnsData/default.htmName: Dawn Jones; Email: d.jones@umist.ac.uk; Phone: 01612004179; Department: ; Institute: UMIST; Address: ; City: Manchester; Zip/postal_code: M60 1QD; Country: United Kingdom b7!! +Identification of new and unpredicted full length Arabidopsis genesGSE601Public on Oct 30 20032003-08-202005-06-15ެExamination of cRNA from Arabidopsis flowers, roots and suspension cell culture using custom high-density Affymetrix genome tiling arrays in order to identify new and unpredicted genes.otherJun,,Lim; Huaming Chen; Paul Shinn; Christopher Kim; Rosa Cheuk; Joseph,M,Dale; Curtis,J,Palm; Audrey Southwick; Kayoko Yamada; Hank,C,Yu; Ronald,W,Davis; Athanasios Theologis; Joseph,R,Eckersignal.salk.eduName: Jun Lim; Email: jlim@salk.edu; Phone: 858-453-4100 ext.1533; Fax: 858-558-6379; Laboratory: Genomic Analysis Laboratory; Department: PBIO-E; Institute: The Salk Institute for Biological Studies; Address: 10010 N. Torrey Pines Rd.; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA; Web_link: signal.salk.edun column. After 48 hours of growth with 70% confluency, cells were exposed to either T3, DITPA or CGS for another 48 hours before harvesting. Final concentrations of T3, DITPA and CGS in the medium were 6nM, 218nM and 1nM respectively.; ; RNA was prepared from cells with Triazol. Twenty micrograms of total RNA was reverse transcribed and labeled with Alexa Fluor 546 and 647. Labeled probes were hybridized with Qiagen's rat unigene oligo library. After 2 low and 1 high stringency washes Prolong antifade was added to the slides to prevent bleaching effect. Slides were scanned in Array Worx scanner with dual wave length.; ; The data ratio was normalized using a location and intensity dependent Lowess formula.equivalent probeName: Niranjan Maitra; Email: nmaitra@email.arizona.edu; Phone: 520-626-4966; Fax: 520-626-8408; Laboratory: Eugene Morkin; Department: Sarver Heart Center; Institute: University of Arizona; Address: 1501 North Campbell Avenue; City: Tucson; State: AZ; Zip/postal_code: 85724; Country: USA RR\m7!![Phosphate metabolism in Saccharomyces cerevisiaeGSE603Public on Aug 29 20032003-08-202005-05-29%Investigation of Saccharomyces cerevisiae phosphate metabolism. Cells starved for phosphate, cells grown with intermediate and high phosphate concentrations, and PHO4 mutant cells examined.otherDennis,,Wykoff; Mike Springer; Erin O'Shea; Nicole MillerName: Dennis Wykoff; Email: dennis.wykoff@villanova.edu; Phone: 415-476-2166; Laboratory: O'Shea; Department: Biochemistry; Institute: UCSF; Address: 600 16th St; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USAB-7!!{-OT3,DITPA and CGSGSE602Public on Aug 23 20032003-08-202005-05-29%:Rat ventricular cardiomyocytes were prepared from 18 day old fetus. Approximately 6 million cells were plated on 100 mm culture plate. The serum used in the medium was depleted from thyroid hormone by passing through anion exchange resi4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays.; ; Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions.otherKayoko,,Yamada; Joseph,M,Dale; Hank,C,Wu; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Curtis,J,Palm; Paul Shinn; Audrey,M,Southwick; Ronald,W,Davis; Joseph,R,Ecker; Athanasios TheologisName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/ g7!!mSIdentification of new full length Arabidopsis genes - pilot arraysGSE604Public on Oct 30 20032003-08-212005-06-15ެIdentification of new and unpredicted full length Arabidopsis genes.; ; Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at  O7!!/SIdentification of new full length Arabidopsis genes - whole genome arraysGSE605Public on Oct 30 20032003-08-212005-06-15ެIdentification of new and unpredicted full length Arabidopsis genes.; ; Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings using whole genome tiling arrays.otherKayoko,,Yamada; Audrey,M,Southwick; Joseph,M,Dale; Curtis,J,Palm; Hank,C,Wu; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Paul Shinn; Joseph,R,Ecker; Ronald,W,Davis; Athanasios TheologisName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/ .A7!!+Control vs. AngII InfusionGSE606Public on Oct 20 20032003-08-252005-10-28UThe genetic background of mice used in this study is mainly C57BL/6J with a small contribution from 129/Sv and DBA/2J strains. Male littermates were received continuous administration of AngII for 7 days at 0.9ug/hour. On day 7 of AngII infusion, the blood pressure of infused mice was (mmHg, mean ± SD) 156 ± 1, while the control littermates remained normotensive (106 ± 9).otherFaina,,SchwartzName: Faina Schwartz; Email: fschw@bu.edu; Phone: 617-638-4049; Fax: 617-638-4027; Laboratory: Faina Schwartz/Haralambos Gavras; Department: Medicine, Hypertension Section; Institute: Boston University School of Medicine; Address: 700 Albany Street,W508; City: Boston; State: MA; Zip/postal_code: 02118; Country: USAotal RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. (2002) Mol. Plant Pathol. 3: 301) and purified with a silica membrane column (Qiagen, RNeasy). Twenty micrograms biotinylated complementary RNA (cRNA) was prepared as described (Hernan et al. (2003) Cancer Res. 63, 140) from the purified total RNA. The resulting cRNA was used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the manufacturer's protocols. The array images were analyzed with the Affymetrix Microarray Suite 5.0 software with the target intensity set to 500. Normalized signal intensities were generated by multiplying signal intensities by ratio figure which set GapC (ID_REFotherErin,,Osborne; Chris SomervilleName: Erin,A,Osborne; Email: eosborne@Andrew2.stanford.edu; Phone: 650-325-1521 x439; Laboratory: Chris Somerville; Department: Department of Plant Biology; Institute: Carnegie Institute of Washington; Address: 260 Panama Dr.; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA sss7!! KQArabidopsis thaliana leaf, stem and flower tissues.GSE607Public on Aug 27 20032003-08-262005-06-150Analysis of gene expression in Arabidopsis thaliana leaf, stem and flower tissues.; ; Columbia (Col-0) Arabidopsis thaliana plants were grown at a density of 4 plants per 5 inch square pot either in a growth chamber or a green house set to 25*C by day, 20*C by night. Days were set to a 16hr photoperiod with 125 micro mol m-2s-1 fluorescent irradiation.; Expanding leaves were harvested 15 days post germination in the middle of the photoperiod (3 replicates).; Expanding upper 2" of the stem with siliques and pedicels removed were harvested 29 days post germination in the middle of the photoperiod (4 replicates).; Developed flowers and unopened buds were harvested 29 days post germination in the middle of the photoperiod (4 replicates).; ; RNA and Microarray Methods: T   qA7!!/Human embryonic stem cellsGSE608Public on Jan 19 20042003-08-262005-05-29 Undifferentiated human embryonic stem cells grown on mouse embryonic fibroblast feeder layers. HES3 and HES4 are proprietary human ES cell lines of ES Cell International Pte Ltd. Singapore.otherWoon-Khiong,,ChanName: Mark Richards; Email: obgmarkr@nus.edu.sg; Phone: 65-68744381; Institute: National University of Singapore; Address: ; City: Singapore; Zip/postal_code: 117543; Country: Singapore B U7!!Ge SCID vs Normal Thymocyte ComparisonsGSE609Public on Oct 10 20032003-08-272005-05-29ҀGene expression data from thymocytes of a 6 month old infant and thymocytes of a SCID patientotherHarjit,K,Dadi; Amos,J,Simon; Chaim,M,RoifmanName: Harjit,Kaur,Dadi; Email: hdadi@sickkids.on.ca; Phone: 416 813 8623; Fax: 416 813 8624; Laboratory: Dr. C.M. Roifman; Department: Infection, Immunity, Injury & Repair Research; Institute: Hospital for Sick Children; Address: 555 University Avenue,; City: Toronto; State: Ontario; Zip/postal_code: M5G 1X8; Country: Canada  =7!!'5 Allylamine Dose ResponseGSE610Public on Sep 02 20032003-08-272005-05-29Response to Oxidative Stress via administration of Allylaminedose responseCharles,R,Partridge; Mahalet,G,Tadesse; Charles,D,Johnson; Kim,P,Lu; Kenneth,S,RamosName: Kenneth,S.,Ramos; Email: kenneth.ramos@louisville.edu; Phone: 502-852-5217; Department: Biochemistry and Molecular Biology; Institute: University of Louisville School of Medicine; Address: ; City: Louisville; State: KY; Zip/postal_code: 40292; Country: USA V K7!!=+WM Neurospheres of WT and BMI-1 KOGSE611Public on Oct 14 20032003-08-272005-05-29cThe cRNA derived from Brain and Gut neurospheres of wild type and BMI-1 knockout mice were hybridized to Affymetrix mouse ver 2 Chips A, B and C. In case of brain neurospheres, the cRNA were generated by one round RNA amplification (conventional method). In contrast, the cRNA of Gut neurospheres were generated by two round RNA amplifications.parallel sampleAnna,V,Molofsky; Ricardo Pardal; Toshihide Iwashita; In-Kyung Park; Michael,F,Clarke; Sean,J,MorrisonName: Toshihide Iwashita; Email: iwashita@umich.edu; Phone: 734-615-3588; Fax: 734-615-8133; Laboratory: Morrison lab; Department: Internal Medicine; Institute: University of Michigan; Address: 1500 E. Medical Center Drive; City: Ann Arbor; State: MI; Zip/postal_code: 48109; Country: USAls were purified by using the commercial available anti-mCD8 microbeads. Microarray experiments based on prepared neuroectodermal cells from wild-type embryos verse glide/gcm overexpressed embryos at stage 11 have revealed 76 gene differentially regulated by overexpression of glide/gcm.; Among them, there are 11 genes have already been shown to be regulated by glide/gcm in the previous publications. Additionally, we have identified 4 more new glide/gcm-regulated genes by in situ hybridization or immunohistochemical staining. It is very convincing that reduction of the tissue complexity by cell purification leads to low false positives in microarray experiment.repeat sampleName: Haiqiong Montalta-He; Email: haiqiong.he@stud.unibas; Phone: +41 61 2671616; Fax: +41 61 2671613; Laboratory: Heinrich Reichert; Department: Developmental Neurobiology; Institute: Institute of Zoology; Address: Klingelbergstrasse 50/70; City: Basel; Zip/postal_code: CH 4056; Country: Switzerland; Web_link: http://www.zoo.unibas.ch/  7!!?'3 Drosophila gliogenesis during early embryogenesis - sorted experimentGSE612Public on Oct 28 20032003-08-282005-05-29We report here the application of magnetic cell separation in microarray experiment to understand Drosophila gliogenesis during early embryogenesis. At stage 11, neuroectodermal cells were labeled by a fusion transmembrane protein, mCD8-GFP, in the wild-type embryos as wells as in the embryos where glide/gcm was overexpressed. Following the cell dissociation, neuroectodermal cells were purified by using the commercial available anti-mCD8 microbeads. Microarray experiments based on prepared neuroectodermal cells from wild-type embryos verse glide/gcm overexpressed embryos at stage 11 have revealed 76 gene differentially regulated by overexpression of glide/gcm.; Among them, there are 11 genes have already been shown to be regulated by glide/gcm in the previous publications. Additionally, we have identified 4 more new glide/gcm-regulated genes by in situ hybridization or immunohistochemical staining. It is very convincing that reduction of the tissue complexity by cell purification leads to low false positives in microarray experiment.repeat sampleName: Haiqiong Montalta-He; Email: haiqiong.he@stud.unibas; Phone: +41 61 2671616; Fax: +41 61 2671613; Laboratory: Heinrich Reichert; Department: Developmental Neurobiology; Institute: Institute of Zoology; Address: Klingelbergstrasse 50/70; City: Basel; Zip/postal_code: CH 4056; Country: Switzerland; Web_link: http://www.zoo.unibas.ch/ _S7!!S)effect of +/- mutations in ES cellsGSE614Public on Sep 28 20032003-08-282006-07-27effect of +/- mutations in ES cellsotherDerek,J,SymulaName: Derek Symula; Email: symula@wadsworth.org; Phone: 518-880-1317; Institute: Wadsworth Center Genomics Institute; Address: ; City: Troy; State: NY; Zip/postal_code: 12180; Country: USA !7!!?'3 Drosophila gliogenesis during early embryogenesis - wholemount experimentsGSE613Public on Oct 28 20032003-08-282005-05-29We report here the application of magnetic cell separation in microarray experiment to understand Drosophila gliogenesis during early embryogenesis. At stage 11, neuroectodermal cells were labeled by a fusion transmembrane protein, mCD8-GFP, in the wild-type embryos as wells as in the embryos where glide/gcm was overexpressed. Following the cell dissociation, neuroectodermal celentation analysis and TUNEL assay showed that in aged vessels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (microarray, real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.repeat sampleAnna,,Csiszar; Zoltan UngvariName: Anna Csiszar; Email: anna_csiszar@nymc.edu; Phone: 914-309-4735; Fax: 914-594-4018; Department: Physiology; Institute: New York Medical College; Address: ; City: Valhalla; State: NY; Zip/postal_code: 10595; Country: USA uG7!!'GQAged F344 rat coronary arteryGSE615Public on Oct 28 20032003-08-302005-05-29Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmssels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. Vascular expression and activity of TNFa convertase enzyme were preserved in aging. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.repeat sampleAnna,,CsiszarName: Anna Csiszar; Email: anna_csiszar@nymc.edu; Phone: 914-309-4735; Fax: 914-594-4018; Department: Physiology; Institute: New York Medical College; Address: ; City: Valhalla; State: NY; Zip/postal_code: 10595; Country: USA xxB7!!7GTrans-acting regulatory variation in Saccharomyces cerevisiaeGSE617Public on Sep 03 20032003-09-022005-05-29Natural genetic variation can cause significant differences in gene expression, but little is known about the polymorphisms that affect gene regulation. We analyzed regulatory variation in .I7!!!''QYoung F344 rat coronary arteryGSE616Public on Oct 28 20032003-08-302005-05-29Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmentation analysis and TUNEL assay showed that in aged vea cross between laboratory and wild strains of Saccharomyces cerevisiae. Clustering and linkage analysis defined groups of coregulated genes and the loci involved in their regulation. Most expression differences mapped to trans-acting loci. Positional cloning and functional assays showed that polymorphisms in GPA1 and AMN1 affect expression of genes involved in pheromone response and daughter cell separation, respectively. We also asked whether particular classes of genes were more likely to contain trans-regulatory polymorphisms. Notably, transcription factors showed no enrichment, and trans-regulatory variation seems to be broadly dispersed across classes of genes with different molecular functionsotherG,,Yvert; R,B,Brem; J Whittle; J,M,Akey; E Foss; E,N,Smith; R Mackelprang; L KruglyakName: Gael Yvert; Email: yvert@insa-tlse.fr; Phone: 011-33-5-61-55-94-25; Laboratory: Kruglyak; Institute: Fred Hutchinson Cancer Research Center; Address: ; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USArmal cells were purified by using the commercial available anti-mCD8 microbeads. Microarray experiments based on prepared neuroectodermal cells from wild-type embryos verse glide/gcm overexpressed embryos at stage 11 have revealed 76 gene differentially regulated by overexpression of glide/gcm.; Among them, there are 11 genes have already been shown to be regulated by glide/gcm in the previous publications. Additionally, we have identified 4 more new glide/gcm-regulated genes by in situ hybridization or immunohistochemical staining. It is very convincing that reduction of the tissue complexity by cell purification leads to low false positives in microarray experiment.otherName: Haiqiong Montalta-He; Email: haiqiong.he@stud.unibas; Phone: +41 61 2671616; Fax: +41 61 2671613; Laboratory: Heinrich Reichert; Department: Developmental Neurobiology; Institute: Institute of Zoology; Address: Klingelbergstrasse 50/70; City: Basel; Zip/postal_code: CH 4056; Country: Switzerland; Web_link: http://www.zoo.unibas.ch/   ho7!!?3Drosophila gliogenesis during early embryogenesisGSE618Public on Oct 27 20032003-09-022005-05-29We report here the application of magnetic cell separation in microarray experiment to understand Drosophila gliogenesis during early embryogenesis. At stage 11, neuroectodermal cells were labeled by a fusion transmembrane protein, mCD8-GFP, in the wild-type embryos as wells as in the embryos where glide/gcm was overexpressed. Following the cell dissociation, neuroectode aged vessels there was a ~4 fold increase in the number of apoptotic endothelial cells. Analysis of the expression of apoptosis-related genes (real-time PCR) showed that in aged coronary arteries there was an increased expression of TNFa, TNFb, caspase 9 and an increased presence of cleaved caspase 3 and caspase 9 (Western blotting), whereas expression of TNFR1 and that of TRADD, Bcl-2, Bcl-X(L), Bid, Bax, caspase 8 and caspase 3 were unchanged. Vascular expression and activity of TNFa convertase enzyme were preserved in aging. We propose that aging-induced up-regulation of TNFa and decreased bioavailability of NO promote endothelial apoptosis in coronary arteries that may lead to the development of endothelial dysfunction and ischemic heart disease in the elderly.otherAnna,,CsiszarName: Anna Csiszar; Email: anna_csiszar@nymc.edu; Phone: 914-309-4735; Fax: 914-594-4018; Department: Physiology; Institute: New York Medical College; Address: ; City: Valhalla; State: NY; Zip/postal_code: 10595; Country: USA HHY7!! #=sY1Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronc=w7!!!'QComparison of young and aged F344 rat coronary arteryGSE619Public on Oct 28 20032003-09-022005-06-15Previous studies showed that aging in coronary arteries is associated with pro-inflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by inducing endothelial apoptosis. To test this hypothesis we characterized pro-apoptotic alterations in the phenotype of coronary arteries of aged (26 month old) and young (3 month old) F344 rats. DNA fragmentation analysis and TUNEL assay showed that inhial epithelial cell lineGSE620Public on Oct 29 20032003-09-032005-10-28އ,Most individuals with cystic fibrosis (CF) carry one or two mutations that result in a maturation defect of the full-length CFTR protein. The deltaF508 mutation results in a mutant protein that is degraded by the proteasome instead of progressing to the apical membrane where it functions as a cyclic AMP-regulated chloride channel. 4 phenylbutyrate modulates heat shock protein expression and promotes trafficking of deltaF508 thus permitting maturation and membrane insertion. The goal of this study was to gain insight into the genetic mechanism of PBA action through a large-scale analysis of gene expression. The Affymetrix genome spanning U133 microarray set was used to compare mRNA expression in untreated IB3-1 cell line cultures with cultures treated with 1mM 4-phenylbuyterate for 12 and 24 hr. IB3-1 deltaF508/W1282X) bronchial epithelial cells were cultured in T75 flasks with gentamicin-free LHC-8 medium. Cells were fed with 10 ml of media every 2 to 3 days. After reaching 80% confluence cells were treated with 1 mM PBA. A T75 flask of confluent IB3-1 cells was rinsed twice with ice cold Hank’s buffer then scraped into 3ml of ice cold TRIzol (Gibco BRL) then rinsed with 3 ml ice cold TRIzol and the mRNA was isolated according to the TRIzol protocol. A total of 5 control cultures, 3 cultures with 12 hr BPA application and 3 cultures with 24 hr PBA application were processedtime-courseJerry,M,Wright; Pamela,L,Zeitlin; Liudmila Cebotaru; Sandra,E,Guggino; William,B,Gugginohttp://www.hopkins-genomics.org/cf/cf_research.htmlName: Jerry,M.,Wright; Email: jwright@jhmi.edu; Phone: 410-614-5010; Department: Physiology; Institute: Johns Hopkins Medical Institutions; Address: 725 N. Wolfe St; City: Baltimore; State: MD; Zip/postal_code: 21205; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE620/GSE620_RAW.tarcystitis (IC) have been shown to differ from explanted control cells in several ways, including production of an antiproliferative factor (APF), altered production of certain epithelial growth factors, and rate of proliferation. To better understand the role of the APF in abnormal bladder epithelial cell proliferation in IC, we studied gene expression patterns in normal bladder epithelial cells treated with APF vs. mock APF and compared them to expression patterns in IC vs. normal cells using microarray analysis. Oligo-dT-primed total cellular RNA was labeled with [33P]dCTP and hybridized to GeneFilter GF211 microarray membranes (Research Genetics) containing cDNA for 3,964 human genes. Thirteen genes that function in epithelial cell proliferation or differentiation were consistently differentially expressed in both IC (compared with control) and APF-treated (compared with mock APF-treated) normal bladder epithelial cells. The general pattern of gene expression in IC and APF-treated cells suggested a less proliferative phenotype, with increased expression of E-cadherin, phosphoribosylpyrophosphate synthetase-associated protein 39, and SWI/SNF complex 170-kDa subunit, and decreased expression of vimentin, {alpha}2-integrin, {alpha}1-catenin, cyclin D1, and jun N-terminal kinase 1; these findings were confirmed for the structural gene products (E-cadherin, vimentin, {alpha}2-integrin, and {alpha}-catenin) by immunohistochemistry. These results are compatible with the previously noted decreased proliferation rate of IC and APF-treated normal cells, and indicate that the mechanism whereby APF inhibits cell proliferation may involve both downregulation of genes that stimulate cell proliferation along with upregulation of genes that inhibit cell growth.otherS,,Keay; F Seillier-Moiseiwitsch; C Zhang; T,C,Chai; J ZhangName: Susan Keay; Email: skeay@umaryland.edu; Phone: 410-605-7000 ext 6450; Institute: University of Maryland, Baltimore; Address: ; City: Baltimore; State: MD; Zip/postal_code: 21201; Country: USA !?7!!O#1 LT2_MitomycinC_2ug/ml_RNAGSE622Public on May 10 20042003-09-032005-06-15^-Gene expression of Salmonella enterica sv Typhimurium LT2 post treatment with 2ug/ml mitomycin C.time-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USAL7!!Interstitial cystitis and antiproliferative factor treatmentGSE621Public on Sep 03 20032003-09-032005-05-29(Changes in human bladder epithelial cell gene expression associated with interstitial cystitis or antiproliferative factor treatment.; ; Explanted bladder epithelial cells from patients with interstitial  )M7!!Y#1 14028s_hydrogen_peroxide_2mM_RNAGSE623Public on May 10 20042003-09-032005-05-29Gene expression in Salmonella enterica sv Typhimurium 14028s post treatment with 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA G7!!G#1 LT2_hydrogen_peroxide_2mM_DNAGSE624Public on May 10 20042003-09-032005-05-29Gene content Salmonella enterica sv Typhimurium LT2 post treatment with 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA .M7!!S+1 SL1344_hydrogen_peroxide_2mM_DNAGSE625Public on May 10 20042003-09-032005-05-29^-Gene content in Salmonella enterica sv Typhimurium SL1344 post treatment with 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA nn7!!+U1Auxin mediated gene expression in WT, arf7, arf19 and arf7 arf19 mutantsGSE627Public on Oct 19 20052003-09-042005-10-28oRNA samples were extracted from liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h.; ; Lines used for this study:; Columbia wild-type; nph4-1(arf7) single mutant; arf19-1 single mutant; nph4-1 arf19-1 double mutant; ; Treatment:; Control (EtOH); Auxin treated (5µM IAA); Keywords; Keywordsparallel sampleYoko,,Okushima; Athanasios TheologisName: Yoko Okushima; Email: okushima@bs.naist.jp; Phone: 510-559-5921; Fax: 510-559-5678; Laboratory: Athanasios Theologis Lab.; Department: Plant and Microbial Biology; Institute: Plant Gene Expression Center, U. C. Berkeley; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE627/GSE627_RAW.tare contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol receptor ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage.; Keywords; Keywords; Keywordstime-courseJohn,J,Welch; Lewis,A,Chodosh; Mitchell,J,WeissName: John,J.,Welch; Email: welchjo@email.chop.edu; Phone: 215-590-0558; Fax: 215-590-4834; Laboratory: Weiss Laboratory; Department: Division of Hematology; Institute: Children's Hospital of Philadelphia; Address: 34th & Civic Center Blvd.; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE628/GSE628_RAW.tar #7!!c+U1Auxin-mediated gene expression in WT, iaa17, axr3 and iaa5iaa6iaa19 mutantsGSEsU7!!#kw1Erythroid Differentiation: G1E ModelGSE628Public on Feb 01 20042003-09-042005-05-29kG1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclon629Public on Dec 01 20052003-09-042005-12-20zGlobal gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5�M IAA) for 2 h. Columbia (WT), IAA17 loss of function mutant allele (iaa17-2), IAA17 gain of function mutant allele (axr3-1) and iaa5 iaa6 iaa19 triple loss of function mutant allele (i5i6i19) were used for this study. Each experimental condition has three true replicates for a total of 24 hybridizations. Dataparallel sampleYoko,,Okushima; Athanasios TheologisName: Yoko Okushima; Email: okushima@bs.naist.jp; Phone: 510-559-5921; Fax: 510-559-5678; Laboratory: Athanasios Theologis Lab.; Department: Plant and Microbial Biology; Institute: Plant Gene Expression Center, U. C. Berkeley; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE629/GSE629_RAW.tar EE7I7!!1Auxin-mediated gene expressionGSE630Public on Dec 01 20052003-09-042005-10-28Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h.otherY,,Okushima; A Theologis; Yoko Okushima; Athanasios TheologisName: Yoko Okushima; Email: okushima@bs.naist.jp; Phone: 510-559-5921; Fax: 510-559-5678; Laboratory: Athanasios Theologis Lab.; Department: Plant and Microbial Biology; Institute: Plant Gene Expression Center, U. C. Berkeley; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE630/GSE630_RAW.tar for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The “R” environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis.; ; Keywords; KeywordsotherYoko,,Okushima; Athanasios TheologisName: Yoko Okushima; Email: okushima@bs.naist.jp; Phone: 510-559-5921; Fax: 510-559-5678; Laboratory: Athanasios Theologis Lab.; Department: Plant and Microbial Biology; Institute: Plant Gene Expression Center, U. C. Berkeley; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE631/GSE631_RAW.tar ``y7!!GU1Auxin mediated gene expression in WT and arf2-6 mutantGSE631Public on Oct 19 20052003-09-042005-10-28&Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations.; ; Data analysis:; Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used ''UU7!!OControl and Congestive Heart FailureGSE632Public on Sep 08 20032003-09-052005-05-29Congestive heart failure was done by artificial myocardial infarction. After extracting total RNA from control and infarcted ventricles with Triazol, messenger RNA was isolated with Qiagen mRNA isolation kit. About 1.5ug poly A+ RNA was taken for probe preparation. Probe was labeled with Alexa Fluor 546 and 657. Labeled probes were hybridized with Qiagen rat unigene oligo library. After 2 low and 1 high stringency washes Prolong Antifade was added to the slides to prevent bleaching effect. The data ratio was normalized using a location and intensity dependent Lowess formula.otherName: Niranjan Maitra; Email: nmaitra@email.arizona.edu; Phone: 520-626-4966; Fax: 520-626-8408; Laboratory: Eugene Morkin; Department: Sarver Heart Center; Institute: University of Arizona; Address: 1501 North Campbell Avenue; City: Tucson; State: AZ; Zip/postal_code: 85724; Country: USA ll Q7!!Ok7} Anti-inflammatory compounds in SCIGSE633Public on Oct 03 20032003-09-052005-05-29mA screen of 5 anti-inflammatory compounds for their effects in explanted, cultured rat spinal cord slices. All injured (explanted) cords are cultured for 4 hrs.orderedJonathan,Z,Pan; Rebecka Jornsten; Ronald,P,Harthttp://www.ngelab.orgName: Ronald Hart; Email: rhart@rci.rutgers.edu; Phone: 732-445-1783; Fax: 732-445-2063; Department: W.M. Keck Center for Collaborative Neuroscience; Institute: Rutgers University; Address: 604 Allison Rd Rm D251; City: Piscataway; State: NJ; Zip/postal_code: 08854; Country: USA; Web_link: http://www.ngelab.org J!g7!!/!Muscle - atypical diabetes protein expressionGSE634Public on Mar 01 20042003-09-052005-06-15 !Skeletal muscle biopsies from atypical diabetics at presentation and remission. Protein expression determined with antibody arraysotherDonald,B,Thomason; Aidar,R,Gosmanov; Guillermo,E,UmpierrezName: Donald,B.,Thomason; Email: thomason@physio1.utmem.edu; Phone: 901-448-7224; Fax: 901-448-7126; Department: Physiology; Institute: The University of Tennessee Health Science Center; Address: 894 Union Ave; City: Memphis; State: TN; Zip/postal_code: 38163; Country: USA and extracellular matrix genes for vincristine, ribosomal protein and translation-associated genes for asparaginase, and RAS signaling and nucleosome remodeling complex genes for daunorubicin. The identification of novel genomic determinants of cellular drug resistance provides new insights for overcoming drug resistance in acute lymphoblastic leukemia.; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4; http://www.stjuderesearch.org/data/ALL4/Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE635/GSE635_RAW.tar 55?"_7!!/K1"Identification of novel genomic determinants of cellular drug resistance in acute lymphoblastic leukemia.GSE635Public on Aug 06 20042003-09-082006-09-08bFCellular drug resistance is associated with an unfavorable prognosis in pediatric acute lymphoblastic leukemia (ALL). To identify genes conferring resistance to antileukemic agents, we analyzed the expression of >12,700 genes in sensitive and resistant ALL cells obtained at diagnosis from 174 patients. This revealed 42, 59, 54 and 22 genes (P≤0.001) that were differentially expressed in B-lineage ALL that was sensitive versus resistant to prednisolone, vincristine, asparaginase or daunorubicin, respectively, with prediction accuracies of 71-76%. Notably, 149 of the discriminating genes have not been previously associated with resistance to these anticancer agents. These included carbohydrate-metabolism and transcription-associated genes for prednisolone, cytoskeleton vv#G7!![ +S#Expression of Annotated GenesGSE636Public on Oct 30 20032003-09-082005-06-15ެContains a row for each annotated gene in each sample, indicating whether our analysis called the gene "present" or "absent" in the sample. Gene names and coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).otherJoseph,M,Dale; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Curtis,J,Palm; Paul Shinn; Audrey,M,Southwick; Hank,C,Wu; Kayoko Yamada; Ronald,W,Davis; Joseph,R,Ecker; Athanasios Theologissignal.salk.eduName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/ ??=$[7!!5 +S$Antisense Expression of Annotated GenesGSE637Public on Oct 30 20032003-09-082005-06-15ެContains a row for each annotated gene in each sample, indicating whether our analysis called the region antisense to the coding region of the gene "present" or "absent" in the sample. Gene names and coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).otherJoseph,M,Dale; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Curtis,J,Palm; Paul Shinn; Audrey,M,Southwick; Hank,C,Wu; Kayoko Yamada; Ronald,W,Davis; Joseph,R,Ecker; Athanasios Theologissignal.salk.eduName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/5ެContains a row for each intergenic cluster in each sample, indicating whether our analysis called the cluster "present" or "absent" in the sample. Intergenic clusters are novel (unannotated) genes detected by aligning Arabidopsis cDNAs/ESTs to the genome. Cluster coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).otherJoseph,M,Dale; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Curtis,J,Palm; Paul Shinn; Audrey,M,Southwick; Hank,C,Wu; Kayoko Yamada; Ronald,W,Davis; Joseph,R,Ecker; Athanasios Theologissignal.salk.eduName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/ ,",f'+7!!_1'SpermatogenesisGSE640Public on Oct 02 20032003-09-092005-05-29ݦA multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets.; ; Understanding mammq&M7!!+ +S&Expression in Intergenic RegionsGSE639Public on Oct 30 20032003-09-082005-06-15w%O7!!5 +S%Expression of Intergenic ClustersGSE638Public on Oct 30 20032003-09-082005-06-1ެContains a row for each intergenic region in each sample, indicating whether our analysis called a window within the region "present" or "absent" in the sample. Intergenic regions are regions containing neither annotated genes nor intergenic clusters. Region coordinates refer to version 3 of the TIGR annotation as submitted to GenBank (GI numbers 22330780, 22326553, 22331929, 22329272, 22328163).otherJoseph,M,Dale; Huaming Chen; Rosa Cheuk; Christopher Kim; Jun Lim; Curtis,J,Palm; Paul Shinn; Audrey,M,Southwick; Hank,C,Wu; Kayoko Yamada; Ronald,W,Davis; Joseph,R,Ecker; Athanasios Theologissignal.salk.eduName: Guixia Yu; Email: gyu@berkeley.edu; Phone: 510-559-5924; Department: Plant Gene Expression Center; Institute: University of California, Berkeley / USDA; Address: 800 Buchanan St.; City: Albany; State: CA; Zip/postal_code: 94710; Country: USA; Web_link: http://pgec-genome.ars.usda.gov/alian spermatozoan development and the events surrounding fertilization has grown slowly, in part because of uncertainty about the number and identity of the cellular components involved. Determination of those transcripts expressed specifically by germ cells should provide an inclusive list of probable critical proteins. Here, total mouse testis transcript profiles were trimmed of transcripts found in cultures enriched in Sertoli or interstitial cells to yield a germ cell-enriched transcript profile. Monitoring of changes of this profile in the developing testis identified 1,652 genes whose transcript abundance increased markedly coincident with the onset of meiosis. Remarkably, 351 of these genes ( approximately 20%) appear to be expressed only in the male germline. Germ cell-specific transcripts are much less common earlier in testis development. Further analysis of the UniGene EST database coupled with quantitative PCR indicates that approximately 4% of the mouse genome is dedicated to expression in postmeiotic male germ cells. Most or many of the protein products of these transcripts are probably retained in mature spermatozoa. Targeted disruption of 19 of these genes has indicated that a majority have roles critical for normal fertility. Thus, we find an astonishing number of genes expressed specifically by male germ cells late in development. This extensive group provides a plethora of potential targets for germ cell-directed contraception and a staggering number of candidate proteins that could be critical for fertilization.otherN,,Schultz; F,K,Hamra; D,L,Garbers; Nikolaus Schultz; David,L,GarbersName: Nikolaus Schultz; Email: schultz@cbio.mskcc.org; Phone: 646-888-2604; Laboratory: David Garbers; Department: Green Center for Reproductive Biology Sciences; Institute: The University of Texas Southwestern Medical Center; Address: 5323 Harry Hines Blvd.; City: Dallas; State: TX; Zip/postal_code: 75390-9051; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE640/GSE640_RAW.tar p(?7!!;k(Control vs. 35S:AtRALF1-1GSE641Public on Feb 06 20042003-09-092005-05-29This series (two repeats) compares the transcriptional changes caused by the overexpression of the AtRALF1-1 cDNA. AtRALF1-1 is one of the nine Arabidopsis isoforms of the polypeptide hormone RALF (PNAS 98, 12843).otherDaniel,S,Moura; Gregory Pearce; Clarence,A,RyanName: Daniel,Scherer de,Moura; Email: daniel_moura54@hotmail.com; Phone: 509-3351890; Fax: 509-3353412; Laboratory: Clarence "Bud" Ryan; Institute: Institute of Biological Chemistry; Address: ; City: Pullman; State: WA; Zip/postal_code: 99164-6340; Country: USA >)/7!!+Se)Kidney expressionGSE642Public on Sep 09 20032003-09-092005-05-29sRNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA.otherMichael,S,Simonson; Rangnath MishraName: Michael,S,Simonson; Email: mss5@po.cwru.edu; Phone: 2163681251; Fax: 2163681249; Department: Medicine- Nephrology; Institute: Case Western Reserve University; Address: 2109 Adelbert Rd; City: Cleveland; State: OH; Zip/postal_code: 44106; Country: USA; Web_link: http://www.cwru.edu/med/simonson 5*77!!m1*ASP sensitive all ALLGSE643Public on Aug 06 20042003-09-092005-05-29bFprimary ALL cells (B- and T-lineage) sensitive to L-asparaginase by the MTT in vitro sensitivity assay; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE643/GSE643_RAW.tar 5+77!!m1+ASP resistant all ALLGSE645Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) resistant to L-asparaginase by the MTT in vitro sensitivity assay; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE645/GSE645_RAW.tar 6,97!!m1,PRED sensitive all ALLGSE646Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE646/GSE646_RAW.tar 4-97!!i1-PRED resistant all ALLGSE647Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) resistant to prednisolone by the MTT in vitro sensitivity assay; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE647/GSE647_RAW.tar .77!!k_[K1.VCR sensitive all ALLGSE648Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaubhttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE648/GSE648_RAW.tar /77!!k_[K1/VCR resistant all ALLGSE649Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) resistant to vincristine by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaubhttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE649/GSE649_RAW.tar 4077!!k10DNR sensitive all ALLGSE650Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) sensitive to daunorubicinby the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE650/GSE650_RAW.tar 7177!!q11DNR resistant all ALLGSE651Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B- and T-lineage) resistant to daunorubicin by the MTT in vitro sensitivity assay; ; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE651/GSE651_RAW.tar U2G7!!#E2Chondrogenesis in ATDC5 cellsGSE652Public on Sep 10 20032003-09-102007-12-14 SAGE analysis of early chondrogenesis in ATDC5 cells induced by BMP4time-courseMatthias,B,Wahl; Chisa Shukunami; Ulrich Heinzmann; Kumiko Hamajima; Yuji Hiraki; Kenji ImaiName: Matthias Wahl; Email: mbw@stowers-institute.org; Phone: ++49 89 3187 4117; Fax: ++49 89 3187 3099; Department: Institute of Developmental Genetics; Institute: GSF - National Research Center for Environment and Health; Address: Ingolstaedter Landstrasse 1; City: Neuherberg; Zip/postal_code: D-85764; Country: Germany .337!!c13ASP sensitive B-ALLGSE653Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) sensitive to L-asparaginase by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE653/GSE653_RAW.tar .437!!c14ASP resistant B-ALLGSE654Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) resistant to L-asparaginase by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE654/GSE654_RAW.tar P557!!_K15PRED sensitive B-ALLGSE655Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4; www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE655/GSE655_RAW.tar -657!!_16PRED resistant B-ALLGSE656Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) resistant to prednisolone by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE656/GSE656_RAW.tar +737!!]17VCR sensitive B-ALLGSE657Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE657/GSE657_RAW.tar +837!!]18VCR resistant B-ALLGSE658Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) resistant to vincristine by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE658/GSE658_RAW.tar *937!![19DNR sensitive B-ALLGSE659Public on Aug 06 20042003-09-102005-05-29bFprimary ALL cells (B-lineage) sensitive to daunorubicin by the MTT in vitro sensitivity assay; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE659/GSE659_RAW.tar .:37!!c1:DNR resistant B-ALLGSE660Public on Aug 06 20042003-09-102005-05-29bF; primary ALL cells (B-lineage) resistant to daunorubicin by the MTT in vitro sensitivity assay; ; KeywordsotherAmy,,Holleman; Meyling,H,Cheok; Monique,L,Den Boer; Wenjian Yang; Karin,M,Kazemier; Gritta,E,Janka-Schaub; Rob Pieters; William,E,Evanshttp://www.stjuderesearch.org/data/ALL4Name: William,E,Evans; Email: william.evans@stjude.org; Phone: 901-495-4995; Fax: 901-495-6869; Laboratory: Evans; Department: Pharmaceutical Sciences; Institute: St.Jude Children's Research Hospital; Address: 332 N. Lauderdale St.; City: Memphis; State: TN; Zip/postal_code: 38105; Country: USA; Web_link: http://www.stjude.org/leukemia/bio_evans.htmftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE660/GSE660_RAW.tardium containing either ABA or GA (Gibberellin) plant hormones and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer.otherJunshi,,Yazaki; Zenpei Shimatani; Akiko Hashimoto; Yuko Nagata; Fumiko Fujii; Kanako Shimbo; Shoshi KikuchiName: Junshi Yazaki; Email: yaz@nias.affrc.go.jp; Phone: 81-29-838-7007; Fax: 81-29-838-7007; Laboratory: Gene Expression; Department: Molecular Genetics; Institute: National Institute of Agrobiological Sciences; Address: 2-1-2 Kan-nondai; City: Tsukuba; State: Ibaraki; Zip/postal_code: 305-8602; Country: Japan; Web_link: http://cdna01.dna.affrc.go.jp/RMOS/index.html ++I;?7!!co;ABA or GA calli treatmentGSE661Public on Mar 05 20042003-09-102005-05-29Y7!!# O>indole-3-acetic acid (IAA) time courseGSE664Public on Oct 12 20032003-09-122007-12-14߃Approximately 500 surface sterilized seeds of Arabidopsis seeds (ecotype: Col-0) were sterilely sown on filter disks overlaying solid ½ MS media 1% sucrose, stratified at 4C for 48 h and grown in darkness at 25C for 4 d. Seedlings were gently submerged by application to the plates of the different auxin solutions (made in ethanol carrier; 0.1% final concentration) and at the indicated times (20 min, 40 min, 60 min), the seedlings were lifted from the plate en mass and flash frozen in liquid nitrogen.time-courseJohn,,Pufky; Yang Qiu; Rao Mulpuri; Patrick Hurban; Alan JonesName: Yang Qiu; Email: yqiu@paragen.com; Phone: 919-425-3720; Department: Investigational Genomics; Institute: Paradigm Genetics, Inc; Address: 108 TW Alexander Dr.; City: RTP,; State: NC; Zip/postal_code: 27709; Country: USA CC9?[7!!#}?Orotic acid induced fatty liver diseaseGSE665Public on Sep 16 20042003-09-152005-06-15 A time course of orotic acid induced fatty liver disease. Kyoto and Wistar strain rats were exposed to orotic acid for days 1, 3 and 14. Controls are also included.; Keywords; Keywords; Keywordstime-courseJulian,L,Griffin; Stephanie Bonney; Chris Mann; Abdul Hebbachi; Geoff Gibbons; Carol Shoulders; James Scott; J NicholsonName: Julian Griffin; Email: jlg40@mole.bio.cam.ac.uk; Phone: +44(0)1223 333626; Laboratory: Griffin; Department: Biochemistry; Institute: University of Cambridge; Address: Tennis Court Road; City: Cambridge; Zip/postal_code: CB2 1QW; Country: United Kingdom WA7!!3'9=AC14GSE667Public on Dec 16 20032003-09-162005-10-2814 days age controlrepeat sampleMartin,,Flück; Silvia Schmutz; Matthias Wittwer; Hans Hoppeler; Dominique DesplanchesName: Martin Flück; Email: flueck@ana.unibe.ch; Phone: +41 31 631 4619; Fax: +41 31 631 3807; Laboratory: Hoppeler; Department: Department of Anatomy; Institute: University of Berne; Address: Bühlstrase 26; City: Berne 9; State: Bern; Zip/postal_code: 3000; Country: Switzerland @G7!!sm@RNA degradation and apoptosisGSE666Public on Sep 17 20032003-09-162005-05-29RNA degradation and apoptosis studies in PMBCs and NB 4 cellsotherHerbert,,Auer; Sandya Lyianarachchi; David Newsom; Marko,I,Klisovic; Guido Marcucci; Karl Kornacker; David,L,NewsomName: Herbert Auer; Email: auer-2@medctr.osu.edu; Phone: 614 247 7116; Department: ; Institute: Human Cancer Genetics; Address: 420 West 12th Ave; City: Columbus; State: OH; Zip/postal_code: 43210; Country: USA; Web_link: www.dnaarrays.org ;&;gC7!!O'9=CHS-R1GSE669Public on Dec 16 20032003-09-162005-10-2814 days suspended, 1 day reloadedrepeat sampleMartin,,Flück; Silvia Schmutz; Matthias Wittwer; Hans Hoppeler; Dominique DesplanchesName: Martin Flück; Email: flueck@ana.unibe.ch; Phone: +41 31 631 4619; Fax: +41 31 631 3807; Laboratory: Hoppeler; Department: Department of Anatomy; Institute: University of Berne; Address: Bühlstrase 26; City: Berne 9; State: Bern; Zip/postal_code: 3000; Country: SwitzerlandVB7!!/'9=BHS14GSE668Public on Dec 16 20032003-09-162005-10-2814 days suspendedrepeat sampleMartin,,Flück; Silvia Schmutz; Matthias Wittwer; Hans Hoppeler; Dominique DesplanchesName: Martin Flück; Email: flueck@ana.unibe.ch; Phone: +41 31 631 4619; Fax: +41 31 631 3807; Laboratory: Hoppeler; Department: Department of Anatomy; Institute: University of Berne; Address: Bühlstrase 26; City: Berne 9; State: Bern; Zip/postal_code: 3000; Country: Switzerland Heart FailureGSE670Public on Nov 02 20032003-09-172005-06-15ONumerous murine models of heart failure (HF) have been described, many of which develop progressive deterioration of cardiac function. We have recently demonstrated that several of these can be "rescued" or prevented by transgenic cardiac expression of a peptide inhibitor of the beta-adrenergic receptor kinase (betaARKct). To uncover genomic changes associated with cardiomyopathy and/or its phenotypic rescue by the betaARKct, oligonucleotide microarray analysis of left ventricular (LV) gene expression was performed in a total of 53 samples, including 12 each of Normal, HF, and Rescue. Multiple statistical analyses demonstrated significant differences between all groups, and further demonstrated that betaARKct Rescue returned gene expression toward that of Normal. In our statistical analyses, we found that the HF phenotype is blindly predictable based solely on gene expression profile. To investigate the progression of HF, LV gene expression was determined in young mice with mildly diminished cardiac function and in older mice with severely impaired cardiac function. Interestingly, mild and advanced HF mice shared similar gene expression profiles and, importantly, the mild HF mice were predicted as having a HF phenotype when blindly subjected to our predictive model described above. These data not only validate our predictive model, but further demonstrate that, in these mice, the HF gene expression profile appears to already be set in the early stages of HF progression. Thus, we have identified methodologies that have the potential to be used for predictive genomic profiling of cardiac phenotype, including cardiovascular disease.otherB,C,Blaxall; R Spang; H,A,Rockman; W,J,KochName: Burns Blaxall; Email: burns.blaxall@duke.edu; Phone: 919-684-6361; Institute: Duke University Medical Center; Address: ; City: Durham; State: NC; Zip/postal_code: 27710; Country: USA DG7!!cDDifferential Myocardial Gene Expression in the Development and Rescue of Murine signal(s) must be transmitted from irradiated to shielded tissues. The time course of transcript abundance changes monitored by RNA blot hybridization and real time RT-PCR indicated that the response kinetics to UV-B are very rapid as some transcript levels are altered within 1 h exposure, in both exposed and shielded tissues. As the same total UV-B irradiation dose applied at three intensities elicited different transcript profiles, transcriptome changes do not show reciprocity. Confirming and extending prior microarray hybridization results, supplemental UV-B increased expression of stress response and ribosomal protein genes, while photosynthesis-associated genes were down regulated in adult leaves.otherPaula,,Casati; Virginia WalbotName: Paula Casati; Email: pcasati@fbioyf.unr.edu.ar; Phone: 54-341-4371955; Laboratory: Casati; Department: Biological Sciences; Institute: Universidad Nacional de Rosario; Address: Suipacha 531; City: Rosario; State: Santa Fe; Zip/postal_code: 2000; Country: Argentina VE]7!!qI)ERapid molecular responses of maize to UV-B: gene expression profiling in irradiated and shielded tissuesGSE671Public on Oct 29 20032003-09-182005-05-29Microarray hybridization was used to assess UV-B responses in both directly exposed and shielded tissues of a maize line deficient in anthocyanin accumulation. Among 347 transcripts found to be regulated after 8 h of high UV-B irradiation, 285 were increased significantly in at least one organ but only 80 were down-regulated by UV-B. Although some genes were regulated by UV-B in more than one sample, most UV-B regulated genes were organ-specific. A larger number of transcript changes occurred in directly exposed than in shielded organs, and more transcripts levels were changed in adult than in seedling tissues. Because shielded tissues including roots, immature ears, and leaves covered with a plastic that absorbs UV-B exhibited altered transcriptome profiles after plant exposure to UV-B, somelts, supplemented with 2 mM glutamine and 10% heat-inactivated FCS. Cells were grown in an incubator with a humidified atmosphere of 5% CO2 in air at 37oC for several days to reach confluence.; HCMV strain AD169 (American Type Culture Collection, Manassas, VA) was used in these studies. A continually replenished stock of HCMV was cultured in confluent MRC-5 cells. At the appropriate time, the infected cells were lysed and the infectivity of the resultant viral stock was assayed by plaque assay. For the studies reported here, HCMV infection was carried out by exposing the confluent MRC-5 cells to a virus stock at a multiplicity of infection (MOI) of ~3-5 plaque-forming units (PFU) per cell for 1 h at 370C. To control for non-specific effects of the cell lysate portion of the viral stock, a parallel set of MRC-5 cells were always mock infected by a 1h exposure to a lysate of uninfected MRC-5 cells. After the infectious period of exposure, both mock- and virus-treated cells were rinsed with phosphate buffered saline (PBS) followed by fresh culture medium and returned to cell culture for various post-exposure (PE) times.; Mock- or HCMV-infected cells were homogenized in guanidinium isothiocyanate, followed by the isolation of total RNA following the method of Chirgwin et al. (PubMed ID 518835). Purity and integrity of the RNA were checked spectroscopically and by gel electrophoresis prior to use. Two successive oligo (dT) cellulose columns were then used to isolate poly A+ RNA for microarray analysis, yielding 600 ng of mRNA per channel (mock-infected or HCMV-infected cells). These were labeled with Cy3 and Cy5 dyes respectively prior to hybridization with a UniGEM V cDNA microarray (Incyte Genomics, St Louis, MO).otherW,E,Crowe; L,M,Maglova; P Ponka; J,M,RussellName: Lilia Maglova-Crowe; Email: lmmaglov@syr.edu; Phone: 315-443-1809; Fax: 315-443-2012; Department: Biology; Institute: Syracuse University; Address: 130 College Place, BRL; City: Syracuse, New York; State: NY; Zip/postal_code: 13244; Country: USA <<GI7!!/=GMuscle unloading and reloadingGSE673Public on Dec 16 20032003-09-192006-09-08{Examination of effect of mechanical loading induced by hindlimb suspension, and subsequent reloading, in soleus muscle in 14 day old female pathogen–free Wistar rats.; Keywords; KeywordsotherM,,Flück; Silvia Schmutz; Matthias Wittwer; Hans Hoppeler; Dominique DesplanchesName: Martin Flück; Email: flueck@ana.unibe.ch; Phone: +41 31 631 4619; Fax: +41 31 631 3807; Laboratory: Hoppeler; Department: Department of Anatomy; Institute: University of Berne; Address: Bühlstrase 26; City: Berne 9; State: Bern; Zip/postal_code: 3000; Country: SwitzerlandF7!!UeFIron chelation on human cytomegalovirus infected MRC-5 fibroblastsGSE672Public on Sep 20 20032003-09-192005-10-28MRC-5 cells (American Type Culture Collection, Manassas, VA) derived from human lung fibroblasts (passages 19-25) were cultured in MEM with Earle’s sa   qHY7!!#sHNormal Muscle - Female , Effect of AgeGSE674Public on Sep 22 20032003-09-192005-05-29Healthy younger (20-29 yr) and older (65-71 yr) women donated vastus lateralis muscle under standard conditions.; Keywords; Keywordstime-courseStephen,,Welle; Charles,A,Thornton; Andrew,I,BrooksName: Stephen Welle; Email: stephen_welle@urmc.rochester.edu; Phone: 585-273-3117; Institute: University of Rochester; Address: ; City: Rochester; State: NY; Zip/postal_code: 14642; Country: USA -Iq7!!#{[ITime course analysis of response to HCMV infectionGSE675Public on Sep 25 20032003-09-192005-05-29The effect of human cytomegalovirus infection; on cellular mRNA accumulation was analyzed by gene chip technology over a 48h time coursetime-courseEdward,P,Browne; Bret Wing; David Coleman; Thomas ShenkName: Thomas Shenk; Email: tshenk@molbio.princeton.edu; Phone: 609-258-1704; Department: Department of Molecular Biology; Institute: Princeton University; Address: ; City: Princeton; State: NJ; Zip/postal_code: 08544; Country: USA ..%K?7!!AQKToward a functional annotation of the human genome using artificial transcription factorsGSE677Public on Dec 12 20032003-09-222005-05-29ߥToward a functional annotation of the human genome using artificial transcription factors.otherName: Jin-Soo Kim; Email: toolgen@toolgen.com; Phone: 82-42-863-8166; Institute: ToolGen, Inc.; Address: ; City: Daejon; Zip/postal_code: 305-390; Country: Korea%J7!!gsJEffect of c-fos expression in osteoclastogenic splenocytesGSE676Public on Sep 19 20042003-09-222005-06-15Effect of c-fos expression in osteoclastogenic splenocytes.otherKoichi,,Matsuo; Chen Zhao; Hiroyuki AburataniName: Koichi Matsuo; Email: matsuo@sc.itc.keio.ac.jp; Phone: +81-3-3353-1211 ext. 61223; Fax: +81-3-5360-1508; Department: Department of Microbiology and Immunology; Institute: School of Medicine, Keio University; Address: 35 Shinanomachi, Shinjuku-ku; City: Tokyo; Zip/postal_code: 160-8582; Country: Japan aldosterone and vasopressinGSE678Public on Sep 24 20032003-09-242005-10-28LIn this study, we analyzed the transcriptome of a highly differentiated mouse clonal CCD principal cell line (mpkCCD(cl4)) and the changes in the transcriptome induced by aldosterone and vasopressin. Serial analysis of gene expression (SAGE) was performed on untreated cells and on cells treated with either aldosterone or vasopressin for 4 h. The transcriptomes in these three experimental conditions were determined by sequencing 169,721 transcript tags from the corresponding SAGE libraries. Limiting the analysis to tags that occurred twice or more in the data set, 14,654 different transcripts were identified, 3,642 of which do not match known mouse sequences. Statistical comparison (at P < 0.05 level) of the three SAGE libraries revealed 34 AITs (aldosterone-induced transcripts), 29 ARTs (aldosterone-repressed transcripts), 48 VITs (vasopressin-induced transcripts) and 11 VRTs (vasopressin-repressed transcripts). A selection of the differentially-expressed, hormone-specific transcripts (5 VITs, 2 AITs and 1 ART) has been validated in the mpkCCD(cl4) cell line either by Northern blot hybridization or reverse transcription-PCR. The hepatocyte nuclear transcription factor HNF-3-alpha (VIT39), the receptor activity modifying protein RAMP3 (VIT48), and the glucocorticoid-induced leucine zipper protein (GILZ) (AIT28) are candidate proteins playing a role in physiological responses of this cell line to vasopressin and aldosterone.otherMaya,,Robert-Nicoud; Marjorie Flahaut; Jean-Marc Elalouf; Marie Nicod; Miguel Salinas; Marcelle Bens; Alain Doucet; Patrick Wincker; François Artiguenave; Jean-Daniel Horisberger; Alain Vandewalle; Bernard,C,Rossier; Dmitri FirsovName: Jean-Marc Elalouf; Email: jean-marc.elalouf@cea.fr; Phone: (33) 1 69088022; Fax: (33) 1 69084712; Laboratory: Laboratoire de PhysioGénomique; Department: IBITEC-S; Institute: CEA Saclay; Address: ; City: 91191 Gif/ Yvette Cedex; Zip/postal_code: 91191; Country: France  aNu7!!%cA1NTranscript Profiling of Arabidopsis Plant Life CycleGSE680Public on Jan 01 200MG7!!{#=Myeast filamentous-form growthGSE679Public on Feb 02 20042003-09-252005-05-294Wild-type diploid cells were shifted from yeast-form growth in SHAD liquid (plentiful glucose and ammonium) to filamentous-form growth on SLAD agar (low ammonium). Samples of filamentous-form cells were collected hourly for 10 hours. Filamentous-form and yeast-form exponential-phase targets were co-hybridized.time-courseName: Timothy Galitski; Email: tgalitski@systemsbiology.org; Phone: 206-732-1206; Institute: Institute for Systems Biology; Address: 1441 N. 34th Street; City: Seattle; State: WA; Zip/postal_code: 98103; Country: USA\La7!!Y[5LTranscriptome of a mouse kidney cortical collecting duct cell line: effects of52003-09-252006-12-01This series contain all stages Arabidopsis plant development. Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedBrandon,H,Le; Anhthu,Q,Bui; Julie Pelletier; Linda,W,Kwong; Jack,K,Okamuro; Robert,L,Fischer; Gary,N,Drews; John,J,Harada; Robert,B,Goldberghttp://estdb.biology.ucla.edu/genechip/pubsName: Brandon Le; Email: ble@ucla.edu; Phone: 310-825-3270; Fax: 310-825-8201; Department: Molecular, Cell and Developmental Biology; Institute: University of California, Los Angeles; Address: 621 Charles E Young Drive South; City: Los Angeles; State: CA; Zip/postal_code: 90095; Country: USA; Web_link: http://www.mcdb.ucla.edu/Research/Goldbergftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE680/GSE680_RAW.tar  O17!!{=?OPKR overexpressionGSE682Public on Sep 22 20042003-09-252005-10-28#Global analysis of gene expression in NIH3T3 cells over-expressing RNA-dependent serine/threonine protein kinase (PKR).otherOlivier,,Donzé; Jing Deng; Joseph Curran; Robert Sladek; Didier Picard; Nahum SonenbergName: Rob Sladek; Email: rob.sladek@mail.mcgill.ca; Phone: 514-398-3311; Institute: Montreal Genome Centre; Address: 740 avenue du Docteur Penfield; City: Montreal; State: PQ; Zip/postal_code: H3A 1A4; Country: Canada ;;AP+7!!9{5PGene expression profiles in normal and Otx2-/- early gastrulating mouse embryosGSE683Public on Sep 25 20032003-09-252005-06-15We compared gene expression profiles in wild-type and Otx2(-/-) 6.5 days postcoitum embryos by using a serial analysis of gene expression assay adapted to microdissected structures. Among a broader list, the study of six genes found to be differentially expressed allows defining a role for Otx2 in the orchestration of cell movements leading to the adequate organization of the embryo before gastrulation.otherLise,,Zakin; Bruno Reversade; Berangere Virlon; Christophe Rusniok; Philippe Glaser; Jean-Marc Elalouf; Philippe BruletName: Jean-Marc Elalouf; Email: jean-marc.elalouf@cea.fr; Phone: (33) 1 69088022; Fax: (33) 1 69084712; Laboratory: Laboratoire de PhysioGénomique; Department: IBITEC-S; Institute: CEA Saclay; Address: ; City: 91191 Gif/ Yvette Cedex; Zip/postal_code: 91191; Country: France0032003-09-262005-06-15ݦThe vertebrate homologues of Drosophila dachsund, DACH1 and DACH2, have been implicated as important regulatory genes in development. DACH1 plays a role in retinal and pituitary precursor cell proliferation and DACH2 plays a specific role in myogenesis. DACH proteins contain a domain (DS-domain) that is conserved with the proto-oncogenes Ski and Sno. Since the Ski/Sno proto-oncogenes repress AP-1 and SMAD signaling, we hypothesized that DACH1 might play a similar cellular function. Herein, DACH1 was found to be expressed in breast cancer cell lines and to inhibit TGF-beta induced apoptosis. DACH1 repressed TGF-beta induction of AP-1 and Smad signaling in gene reporter assays and repressed endogenous TGF-beta responsive genes by microarray analyses. DACH1 bound to endogenous NCoR and Smad4 in cultured cells and DACH1 co-localized with NCoR in nuclear dot-like structures. NCoR enhanced DACH1 repression and the repression of TGF-beta-induced AP-1 or Smad-signaling by DACH1 required the DACH1 DS domain. The DS-domain of DACH was sufficient for NCoR-binding at a Smad4-binding site. Smad4 was required for DACH1 repression of Smad signaling. In Smad4 null HTB-134 cells, DACH1 inhibited the activation of SBE-4 reporter activity induced by Smad2 or Smad3 only in the presence of Smad4. DACH1 participates in the negative regulation of TGF-beta signaling by interacting with NCoR and Smad4.otherKongming,,Wu; Ying Yang; Chenguang Wang; Maria,A,Davoli; Mark D'Amico; Anping Li; Kveta Cveklova; Zbynek Kozmik; Michael,P,Lisanti; Robert,G,Russell; Ales Cvekl; Richard,G,PestellName: Kongming Wu; Email: kw58@georgetown.edu; Phone: 202-687-3008; Fax: 202-687-4638; Laboratory: Richard Pestell's Lab; Department: Lombardi Cancer Center & Department of Oncology; Institute: Georgetown University; Address: 3970 Reservoir Rd, NW; City: Georgetown; State: DC; Zip/postal_code: 20057; Country: USA ~~NS7!!_AmSPrim_FibsGSE687Public on Mar 01 20042003-09-302006-10-02cTo determine changeR=7!!+;!RGene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumorsGSE686Public on Mar 24 20042003-09-262005-10-2860 fresh frozen HNSCC from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. 55 tumor samples were collected from the primary tumor and five tumor samples were collected from a local recurrence at the primary site; one tumor also had a sample of the primary tumor and an associated lymph node metastasis . In addition, we profiled three normal tonsillar epithelium samples that were collected from three pediatriclQ{7!!}sQDACH1 inhibits TGF-beta signaling through binding Smad4GSE685Public on Oct 15 2 patients following routine tonsillectomy and four HNSCC tumor derived cell lines (UNC7, UMSCCA1, CAL27 and JHU022). Each experimental sample (tumor, normal or cell line) was assayed versus a “common reference” sample that was a pool of total RNA derived from 30 of the HNSCC samples. This tumor pool reference strategy has been successfully used in another profiling study. In total, 78 experiments were performed, which utilized three separate preparations of the common reference pool.; ; Keywords; Keywords; Keywordsparallel sampleChristine,H,Chung; Joel,S,Parker; Gamze Karaca; Junyuan Wu; William,K,Funkhouser; Dominic Moore; Dong Xiang; William,W,Shockley; Mark,C,Weissler; Lynn,G,Dressler; Carol,G,Shores; Wendell,G,Yarbrough; Charles,M,PerouName: Charles Perou; Email: cperou@med.unc.edu; Phone: 919-843-5740; Fax: 919-843-5718; Department: CB#7295; Institute: University of North Carolina at Chapel Hill; Address: 102 Mason Farm Road; City: Chapel Hill; State: NC; Zip/postal_code: 27599-7295; Country: USAs in gene expression in primary fibroblasts undergoing replicative senescence, a direct comparison between early passage proliferating cells and senescent cells was performed. Frozen stocks of the primary fibroblasts (HMF3) from which the lines HMF3A and HMF3Dwt were derived (O'Hare, PNAS:98, 2001) were serially passaged twice through to senescence to yield 2 independent sets of RNA. A third set of RNA was from a different female donor (F1068). The three different sets of RNA were put on 4 arrays each. Data is also provided for F1068 fibroblasts at late passage.; Keywords; Keywords; KeywordsorderedKristine,,Hardy; Louise Mansfield; Alan Mackay; Silvia Benvenuti; Mike O'Hare; Parmjit JatName: Kristine Hardy; Email: u4096741@anu.edu.au; Phone: 61 2 6125 4545; Fax: 61 2 6125 0415; Laboratory: Cytokine Gene Expression; Department: ; Institute: John Curtin School of Medical Research, ANU; Address: Building 54, Mills Road ; City: Acton; State: ACT; Zip/postal_code: 0200; Country: Australiacreated from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen. HMF3A cells cease proliferating by 4 days at 39°C. We directly compared the gene expression profiles of cells at 33.5°C and after shift up to 39.5°C for 7 days (10 arrays, 3 biological replicates). To eliminate genes that change in response to the temperature shift, we compared the profiles of HMF3Dwt cells at 33°C and those shifted up to 39°C for 7 days (4 arrays, 2 biological replicates). Since HMF3Dwt cells were immortalised with wild type U19 LT antigen, they proliferate at both temperatures.; To break up the list of genes obtained with the 7 day shift, we performed several further comparisons on the arrays. HMF3A cells at 33°C were compared to the primary donor fibroblasts (HMF3 passage 8, 4 arrays), HMF3A cells shifted to 39°C for 2 days (4 arrays, 2 biological repeats), HMF3A cells shifted to 39°C for 7 days and then shifted back to 33°C for 3 days (8 arrays, 4 biological repeats) or 7 days (4 arrays, 2 biological repeats). As a comparison to the irreversible process of senescence, we sought to identify genes that changed upon reversible growth arrest, quiescence. Thus changes that occurred when the cells were grown to confluency and starved were also determined (2 biological replicate, 6 arrays).; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedKristine,,Hardy; Louise Mansfield; Alan Mackay; Silvia Benvenuti; Mike O'Hare; Parmjit JatName: Kristine Hardy; Email: u4096741@anu.edu.au; Phone: 61 2 6125 4545; Fax: 61 2 6125 0415; Laboratory: Cytokine Gene Expression; Department: ; Institute: John Curtin School of Medical Research, ANU; Address: Building 54, Mills Road ; City: Acton; State: ACT; Zip/postal_code: 0200; Country: Australia QdV!7!! AmVHMF3A_RNAiGSE690Public on Mar 01 20042003-09-302006-10-02cHMF3A cells, create4U%7!!1AmUGSEp53_v_ConGSE689Public on Mar 01 20042003-09-302005-10-28HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inac}T+7!!1AmTHMF3A_with_3DwtGSE688Public on Mar 01 20042003-09-302006-10-02cHMF3A cells, tivation of T antigen. Given the importance of p53, we sought to determine what gene changes were affected if its activation was inhibited. To do this we used the Genetic Suppressor Element (GSE)56 which inhibits the transcriptional activity of p53 (Ossovskaya, 1996). The presence of the GSEp53 delayed the arrest of the HMF3A cells when LT was inactivated. However the cells did arrest. We thus examined the array profiles for 3A-GSEp53 cells after 2 and 7 days of LT inactivation (against 3A-GSEp53 cells at 33°C) and compared these to the profiles for 3A-puro cells.; Keywords; Keywords; Keywords; Keywords; KeywordsotherKristine,,Hardy; Louise Mansfield; Alan Mackay; Silvia Benvenuti; Mike O'Hare; Parmjit JatName: Kristine Hardy; Email: u4096741@anu.edu.au; Phone: 61 2 6125 4545; Fax: 61 2 6125 0415; Laboratory: Cytokine Gene Expression; Department: ; Institute: John Curtin School of Medical Research, ANU; Address: Building 54, Mills Road ; City: Acton; State: ACT; Zip/postal_code: 0200; Country: Australiad from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen.; The pSUPER-retro vector system (Brummelkamp, 2002) was used to selectively target genes for mRNA degradation in an attempt to determine if they had a role, in the changes to the transcriptome upon LT inactivation. The genes chosen for targeting were BTG2, NR4A3, DUSP1, PHLDA1 and STACb.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsotherKristine,,Hardy; Louise Mansfield; Alan Mackay; Silvia Benvenuti; Mike O'Hare; Parmjit JatName: Kristine Hardy; Email: u4096741@anu.edu.au; Phone: 61 2 6125 4545; Fax: 61 2 6125 0415; Laboratory: Cytokine Gene Expression; Department: ; Institute: John Curtin School of Medical Research, ANU; Address: Building 54, Mills Road ; City: Acton; State: ACT; Zip/postal_code: 0200; Country: Australia ##YWs7!!1]CWExpression Profiles of Rats Treated with Clofibric Acid: Comparison of Whole and Laser Capture Microdissected LiverGSE691Public on Dec 03 20032003-10-012005-06-15JzThis is an evaluation of the impact of the successive steps of LCM procedure on gene expression profiling by comparing profiles from LCM samples to those obtained with non-microdissected liver samples collected after a one month CLO treatment in the rat. We showed that the H&E staining used for identifying PP-foci and the laser microdissection itself do not impact on RNA quality.; Keywords; KeywordsotherCecile,,Michel; Chantal Desdouet; Beatrice Sacre-Salem; Jean-Charles Gautier; Ruth Roberts; Eric BoitierName: Cecile Michel; Email: Cecile.Michel@sanofi-aventis.com; Phone: 0(0 33)1 58 93 35 76; Laboratory: Toxicogenomic; Department: Drug Safety Evaluation; Institute: Aventis Pharma France; Address: 13, quai Jules Guesdes; City: Vitry sur Seine; Zip/postal_code: 94403; Country: France iXc7!!A'1)gXFLT3+/CD11b+ Dendritic cell (DC) progenitorGSE692Public on Sep 30 20042003-10-012005-09-07MFLT3+/CD11b+ Dendritic cell (DC) progenitor was amplified in vitro from mouse bone marrow.repeat sampleThomas,,Hieronymuswww.molcell.deName: Thomas Hieronymus; Email: thomas.hieronymus@rwth-aachen.de; Phone: +49 241 80 85 249; Fax: +49 241 80 82 008; Laboratory: AG Hieronymus; Department: Institute for Biomedical Engineering - Cell Biology; Institute: University Medical School, RWTH Aachen ; Address: Pauwelsstr. 30; City: Aachen; Zip/postal_code: 52074; Country: Germany; Web_link: www.molcell.de ""kZY7!! ]5ZSADE analysis of microdissected kidneyGSE694Public on Nov 14 20032003-10-01200kY[7!!1'M)gYLin-c-kit+Sca1+ hematopoetic stem cellsGSE693Public on Sep 30 20042003-10-012005-09-07Msorted hematopoetic stem cells from bone marrow;; with two rounds of amplificationrepeat sampleRalf,D,Kirsch; Thomas Hieronymuswww.molcell.deName: Thomas Hieronymus; Email: thomas.hieronymus@rwth-aachen.de; Phone: +49 241 80 85 249; Fax: +49 241 80 82 008; Laboratory: AG Hieronymus; Department: Institute for Biomedical Engineering - Cell Biology; Institute: University Medical School, RWTH Aachen ; Address: Pauwelsstr. 30; City: Aachen; Zip/postal_code: 52074; Country: Germany; Web_link: www.molcell.de5-10-28޳Libraries generated from microdissected kidney samples from the healthy pole of cancerous kidneys. Donors were from either sex. Libraries were generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences.otherDanielle,,Chabardès-Garonne; Arnaud Méjean; Jean-Christophe Aude; Lydie Cheval; Antonio Di Stefano; Marie-Claude Gaillard; Martine Imbert-Teboul; Monika Wittner; Chanth Balian; Véronique Anthouard; Catherine Robert; Béatrice Ségurens; Patrick Winckerhttp://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14595018&dopt=AbstractName: Jean-Marc Elalouf; Email: jean-marc.elalouf@cea.fr; Phone: (33) 1 69088022; Fax: (33) 1 69084712; Laboratory: Laboratoire de PhysioGénomique; Department: IBITEC-S; Institute: CEA Saclay; Address: ; City: 91191 Gif/ Yvette Cedex; Zip/postal_code: 91191; Country: France \E7!!#KAi\Gene expression in germ lineGSE696Public on Dec 24 20032003-10-022006-04-24{Identification of genes expressed in the germ line of C. elegans.; This SuperSeries is composed of the following subset Series:; GSE715: glp-4 adults; GSE716: glp-4 L2; GSE717W[m7!!!#+[Drosophila melanogaster transcriptome life cycleGSE695Public on Dec 31 20032003-10-022005-05-29qTime course analysis series in Development of the transcriptome from Drosophila melanogaster using the Heidelberg FlyArray. All stages were hybridized against embryonic stage 0-4 h as reference control.time-courseBoris,,BeckmannName: Boris Beckmann; Email: b.beckmann@dkfz.de; Phone: +49-6221-424679; Department: Funktionelle Genomanalyse; Institute: Deutsches Krebsforschungszentrum; Address: Im Neuenheimer Feld 580; City: Heidelberg; Zip/postal_code: 69121; Country: Germany: glp-4 L3; GSE718: glp-4 L4; GSE719: wt L2; GSE720: wt L3; GSE721: wt L4; GSE722: wt adults; GSE723: adult males vs reference; GSE724: no germline males vs reference; GSE725: oocytes vs sperm; GSE726: TP01 mid-L3; GSE727: TP02 late-L3; GSE728: TP03 late L3/early L4; GSE729: TP04 early L4; GSE730: TP05 late L4; GSE731: TP06 late L4/young adult; GSE732: TP07 early young adult; GSE733: TP08 late young adult; GSE734: TP09 adult; GSE735: TP10 adult with embs 1; GSE736: TP11 adult with emb 2; GSE737: TP12 adult with emb 3SuperSerieshttp://genome.med.yale.edu/Germbase; http://yam.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgi; http://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiRefer to individual SeriesName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbaseerum starved and either preincubated with DMSO (vehicle), preincubated with U0126 (10µM in DMSO) and infected with CVB3 (MOI 10), or preincubated with DMSO (vehicle) and infected with CVB3. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 0, 30 minutes, 3 and 9 hours following CVB3 infection (N=3 plates per time point), RNA was isolated, processed and hybridized to GeneChip®s (N=3 per sample)time-courseBobby,,Yanagawa; Honglin Luo; Nana Rezai; Zsuzsanna Hollander; Raymond,T,Ng; Ji Yuan; Jingchun Zhang; Decheng Yang; Timothy,J,Triche; Bruce,M,McManusName: Bruce,Maxwell,McManus; Email: bmcmanus@mrl.ubc.ca; Phone: 604-806-8586; Fax: 604-806-9274; Laboratory: Cardiovascular Research Laboratory; Department: Department of Pathology and Laboratory Medicine; Institute: iCAPTURE CENTRE Room 166, St. Paul's Hospital; Address: 1081 Burrard Street; City: Vancouver; State: BC; Zip/postal_code: V6Z 1Y6; Country: Canada K^A7!!iIY^Integrated stress responseGSE700Public on Oct 07 20032003-10-032005-05-29]Comparison of genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules.otherP,D,Lu; C Jousse; S,J,Marciniak; Y Zhang; I Novoa; D Scheuner; R,J,Kaufman; D Ron; H,P,HardingName: Heather,P.,Harding; Email: harding@saturn.med.nyu.edu; Phone: 212-263-7837; Department: Pharmacology; Institute: NYU School of Medicine; Address: 540 First Ave; City: New York; State: NY; Zip/postal_code: 10016; Country: USA)]57!!#7c]CVB3-infected HeLa cells (multiple time points and triplicate sample per time point)GSE697Public on Oct 07 20032003-10-032005-10-28HeLa cells were s /_7!!M#I7_Transcriptional response of lymphoblastoid cells to ionizing radiationGSE701Public on Oct 08 20032003-10-032005-05-29!Time series for gene expression changes following 3 Gy and 10 Gy of ionizing radiation exposure.time-courseKuang-Yu,,Jen; Vivian,G,CheungName: Kuang-Yu Jen; Email: kuang@mail.med.upenn.edu; Phone: 215-590-2664; Laboratory: Vivian G. Cheung Lab; Department: Department of Pediatrics and Genetics; Institute: University of Pennsylvania; Address: ; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USA x`Q7!!)Ocg`Antigen Presenting Dendritic CellsGSE702Public on Sep 30 20042003-10-032005-05-29MAssessing the gene expression repertoire of antigen presenting dendritic cellsotherThomas,,Hieronymus; Ralf,D,Kirschhttp://www.mdc-berlin.de/~zenke/index.shtmlName: Thomas Hieronymus; Email: thomas.hieronymus@rwth-aachen.de; Phone: +49 241 80 85 249; Fax: +49 241 80 82 008; Laboratory: AG Hieronymus; Department: Institute for Biomedical Engineering - Cell Biology; Institute: University Medical School, RWTH Aachen ; Address: Pauwelsstr. 30; City: Aachen; Zip/postal_code: 52074; Country: Germany; Web_link: www.molcell.de HH4aW7!!9syaBlood pulmonary arterial hypertensionGSE703Public on Nov 15 20032003-10-032005-05-29*4Microarray analysis of peripheral blood mononuclear (PBMC) cells in pulmonary arterial hypertension.; Keywords; Keywords; Keywords; Keywords; KeywordsotherTodd,M,Bull; Christopher,D,Coldren; Mark Moore; Sylk Sotto-Santiago; David,V,Pham; Norbert,F,Voelkel; Mark,W,GeraciName: Christopher,D,Coldren; Email: Chris.Coldren@uchsc.edu; Phone: 303 315 1918; Laboratory: Pulmonary Sciences and Critical Care Medicine; Department: Medicine; Institute: University of Colorado Health Sciences Center; Address: 4200 East 9th Ave; City: Denver; State: CO; Zip/postal_code: 80262; Country: USA jcW7!!'IucLung EC and non-EC comparison array AGSE705Public on Oct 08 20032003-10-032005-06-15Four sets of lung EC and non-EC comparisons and the calculated mean.repeat sampleJih-tung,,Pai; Erkki RuoslahtiName: Jih-tung Pai; Email: pai@burnham.org; Phone: 858-646-3100 x3692; Institute: The Burnham Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USAb[7!!'IubKidney EC and non-EC comparison array AGSE704Public on Oct 08 20032003-10-032005-05-29Four sets of kidney EC and non-EC comparisons and the calculated mean.repeat sampleJih-tung,,Pai; Erkki RuoslahtiName: Jih-tung Pai; Email: pai@burnham.org; Phone: 858-646-3100 x3692; Institute: The Burnham Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA jeW7!!'IueLung EC and non-EC comparison array BGSE707Public on Oct 08 20032003-10-032005-05-29Six sets of kidney EC and non-EC comparisons and the calculated mean.repeat sampleJih-tung,,Pai; Erkki RuoslahtiName: Jih-tung Pai; Email: pai@burnham.org; Phone: 858-646-3100 x3692; Institute: The Burnham Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USAd[7!!'IudKidney EC and non-EC comparison array BGSE706Public on Oct 08 20032003-10-032005-05-29Four sets of kidney EC and non-EC comparisons and the calculated mean.repeat sampleJih-tung,,Pai; Erkki RuoslahtiName: Jih-tung Pai; Email: pai@burnham.org; Phone: 858-646-3100 x3692; Institute: The Burnham Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USAlence properties including colonization of poultry, invasion of Caco-2 cells, and motility. Transcript profiles obtained from whole genome DNA microarrays and proteome analyses demonstrated that these differences are reflected in late flagellar structural components and in virulence factors including those involved in flagellar glycosylation, and cytolethal distending toxin production. We identified putative s28 and s54 promoters for many of the affected genes, and found that greater differences in expression were observed for s28-controlled genes. Inactivation of the gene encoding s28, fliA, resulted in an unexpected increase in transcripts with s54 promoters, as well as decreased transcription of s28-regulated genes. This was unlike the transcription profile observed for the attenuated C. jejuni variant, suggesting that the reduced virulence of this organism was not entirely due to impaired function of s28. However, inactivation of flhA, an important component of the flagellar export apparatus, resulted in expression patterns similar to that of the attenuated variant. These findings indicate that the flagellar regulatory system plays an important role in campylobacter pathogenesis and that flhA is a key element involved in the coordinate regulation of late flagellar genes and of virulence factors in C. jejuni. Furthermore, we provide a model for flagellar regulation, which forms a foundation for the study of the unique regulatory networks in this important human pathogen.parallel sampleCatherine,D,Carrillo; Eduardo Taboada; John,H,Nash; Patricia Lanthier; John Kelly; Peter Lau; Rachel Verhulp; Oksana Mykytczuk; Jonathan Sy; Wendy,A,Findlay; Kingsley Amoako; Susantha Gomis; Philip Willson; John,W,Austin; Andy Potter; Lorne Babiuk; BrendaName: John Nash; Email: John.Nash@nrc-cnrc.gc.ca; Phone: (613) 990-0990; Laboratory: Nash Lab; Department: Institute for Biological Sciences; Institute: National Research Council; Address: 100 Sussex Drive; City: Ottawa; State: ON; Zip/postal_code: K1A0R6; Country: Canada 3g17!!G?CgMalaria resistanceGSE709Public on Oct 06 20032003-10-062005-10-28޵pExamination of molecular basis of malaria resistance. Spleens from malaria resistant AcB55 and AcB61strains compared with A/J mice.; ; Animals were sacrificed and spleens were rapidly frozen in liquid nitrogen, and subsequently stored at 80oC. Tissues were mechanically homogenized with a polytron and total cellular RNA was extracted using a commercially available reagent (TMTRIzol; Invitrogen). The poly-(A)+ fraction of the RNA was isolated by chromatography with oligo d(T f7!!I+ -fGenome-wide expression analyses of Campylobacter jejuni NCTC11168 ...GSE708Public on Mar 03 20042003-10-062005-05-29We examined two variants of the genome-sequenced strain, Campylobacter jejuni NCTC11168, which show marked differences in their viru) cellulose beads. For cDNA labeling, either 25 mg of total RNA or 2.5 mg of poly-(A) RNA was converted into cDNA using reverse transcriptase (RT; Super Script II, Invitrogen) and alternatively Cy5 or Cy3-labeled dCTP (1mM, Perkin Elmer-Cetus/NEN, Boston) in a reaction mixture containing 1.5 mL oligo (dT) (100pmol/ mL), 3 mL dNTP-dCTP (6.67mM each), 1 mL dCTP (2mM), 4 mL DTT (100mM), 8 mL 5 X RT Buffer (Invitrogen, California). The reactions were carried out at 42¼C for 3 hrs, after which the RNA was degraded by the addition of 0.5 mL RNase A (1 mg/mL) and 1.5 mL RNaseH 5 units/mL). Labeled cDNA was separated from unincorporated nucleotides (Qiagen column) and further concentrated by evaporation under vacuum.; The arrays were pre-hybridized for 1-2hrs with DIGEasy hybridization buffer (Roche) containing 10ug/ml denatured salmon sperm DNA, and 10ug/ml yeast tRNA. The Cy5 and Cy3 labelled cDNAs were combined and hybridized in the same medium and incubated with the arrays for 16-18hrs at 37Co. Finally, the arrays were washed 3 x 10 mins in 0.1 x SSC (20 X SSC is 3M sodium chloride, 0.3 M sodium citrate, pH 7.0), 0.1%SDS at 50Co, and 4 x 3min in 0.1 x SSC at room temperature, and dried by centrifugation.; Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray fluorescent scanner and image intensity data were extracted and analyzed with QuantArray 3.0 analysis software. Quantification data was imported in GeneSpring (Silicon Genetics). The import format was modified to maintain information relevant to user-contributed flagging as well as QC parameter furnished by the array manufacturer. Dye swap and Intensity-based normalization (Lowess) were performed using the default settings.otherGundula,,Min-Oo; Anny Fortin; Mi-Fong Tang; Andre Nantel; Mary,M,Stevenson; Philippe GrosName: Gundula Min-Oo; Email: gundula.min-oo@mail.mcgill.ca; Phone: 5143982542; Department: Biochemistry; Institute: McGill University; Address: ; City: Montreal; State: Quebec; Zip/postal_code: H3G 1Y6; Country: Canada pp h_7!!'hdiabetic_nephropathy_streptozotocin_db_dbGSE710Public on Jan 20 20042003-10-072005-10-28diabetes, mouse models, diabetic nephropathy, streptozotocin db/dbotherKatalin,,Susztak; Erwin Böttinger1; Akiva Novetsky; Dan Liang; Yanqing Zhu; Emilio Ciccone; Dona Wu; Stephen Dunn; Peter McCue; Kumar SharmaName: Weijia Zhang; Email: weijia.zhang@mssm.edu; Phone: 718-430-3616; Fax: 718-430-2732; Laboratory: Nephrology; Department: Medicine; Institute: Albert Einstein College of Medicine; Address: 1300 Morris Park Ave; City: Bronx; State: NY; Zip/postal_code: 10461; Country: USA; Web_link: http://www.aecom.yu.edu/BottingerLab/ _ijk7!!a#3cjCVB3-infected HeLa cells (multiple time points)GSE712Public on Oct 09 20032003-iy7!!!IuiComparison between EC and non-EC after EC purificationGSE711Public on Oct 08 20032003-10-082005-06-15Comparison between EC and non-EC after EC purification in kidney and lung.otherJih-tung,,Pai; Erkki RuoslahtiName: Jih-tung Pai; Email: pai@burnham.org; Phone: 858-646-3100 x3692; Institute: The Burnham Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA10-082005-10-28HeLa cells were serum starved and preincubated with DMSO (vehicle) and infected with CVB3. Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process. At 0, 30 minutes, 1, 3, 5, 7 and 9 hours following CVB3 infection, RNA was isolated, processed and hybridized to GeneChip®s.time-courseBobby,,Yanagawa; Honglin Luo; Nana Rezai; Zsuzsanna Hollander; Raymond,T,Ng; Ji Yuan; Jingchun Zhang; Decheng Yang; Timothy,J,Triche; Bruce McManusName: Bruce,Maxwell,McManus; Email: bmcmanus@mrl.ubc.ca; Phone: 604-806-8586; Fax: 604-806-9274; Laboratory: Cardiovascular Research Laboratory; Department: Department of Pathology and Laboratory Medicine; Institute: iCAPTURE CENTRE Room 166, St. Paul's Hospital; Address: 1081 Burrard Street; City: Vancouver; State: BC; Zip/postal_code: V6Z 1Y6; Country: Canadaf the targets implied regulation of biologically divergent responses and suggested involvement of transcriptional and translational machinery, inflammatory, anti-proliferative and anti-angiogenic responses. The data support the notion that UVC radiation induces prominent, dose-dependent downregulation of transcription. However, the data strongly suggest that transcriptional repression is also target gene selective. Furthermore, the results demonstrate that dose-dependent induction of cell cycle arrest and apoptosis by UVC radiation are transcriptionally highly distinct responses.otherMassimiliano,,Gentile; Leena Latonen; Marikki LaihoName: Massimiliano Gentile; Email: massimiliano.gentile@helsinki.fi; Phone: +358-9-47448726; Fax: +358-9-1912 5554; Laboratory: Biomedicum Bioinformatics Unit; Department: Biomedicum Bioinformatics Unit; Institute: Biomedicum Helsinki; Address: Haartmaninkatu 8; City: Helsinki; State: Finland; Zip/postal_code: 000 14; Country: Finland; Web_link: http://www.bioinfo.helsinki.fi VkK7!!skUV radiation-induced DNA damageGSE713Public on Oct 08 20032003-10-082005-06-15DNA damage caused by UV radiation initiates cellular recovery mechanisms, which involve activation of DNA damage response pathways, cell cycle arrest and apoptosis. To assess cellular transcriptional responses to UVC-induced DNA damage we compared time course responses of human skin fibroblasts to low and high doses of UVC radiation known to induce a transient cellular replicative arrest or apoptosis, respectively. UVC radiation elicited >3-fold changes in 460 out of 12,000 transcripts and 89% of these represented downregulated transcripts. Only 5% of the regulated genes were common to both low and high doses of radiation. Cells inflicted with a low dose of UVC exhibited transcription profiles demonstrating transient regulation followed by recovery, whereas the responses were persistent after the high dose. A detailed clustering analysis and functional classification o yvyym%7!!W+imglp-4 adultsGSE715Public on Dec 31 20032003-10-102005-05-29{glp-4 adults vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbasel'7!!elPorcine liverGSE714Public on Nov 15 20032003-10-092005-07-20FFasting, fed, and Clofibric Acid comparisonsotherYewon,,Cheon; Mark Band; Jonathan,E,Beever; Manabu,T,NakamuraName: Yewon Cheon; Email: yecheon@uiuc.edu; Phone: 217-333-7371; Institute: University of Illinois at Urbana Champaign; Address: ; City: Urbana; State: IL; Zip/postal_code: 61801; Country: USA  qo7!!O+ioglp-4 L3GSE717Public on Dec 31 20032003-10-102005-05-29{glp-4 L3 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbaseqn7!!O+inglp-4 L2GSE716Public on Dec 31 20032003-10-102005-05-29{glp-4 L2 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase  rq7!!W+iqwt L2GSE719Public on Dec 31 20032003-10-102005-05-29{wild type L2 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbaseqp7!!O+ipglp-4 L4GSE718Public on Dec 31 20032003-10-102005-05-29{glp-4 L4 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase  rs7!!W+iswt L4GSE721Public on Dec 31 20032003-10-102005-05-29{wild type L4 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbaserr7!!W+irwt L3GSE720Public on Dec 31 20032003-10-102005-05-29{wild type L3 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase yt7!!]+itwt adultsGSE722Public on Dec 31 20032003-10-102005-05-29{wild type adult vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase u=7!!i+iuadult males vs referenceGSE723Public on Dec 31 20032003-10-102005-05-29{wild type adult males vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase vI7!!y+ivno germline males vs referenceGSE724Public on Dec 31 20032003-10-102005-05-29{no germline glp-4 adult males vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase w-7!!i+iwoocytes vs spermGSE725Public on Dec 31 20032003-10-102005-05-29{fem-1(lf) oocytes only vs fem-3(gf) sperm onlyotherValerie,,Reinkehttp://yam.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase x#7!!+ixTP01 mid-L3GSE726Public on Dec 31 20032003-10-102005-05-29{Timepoint 01 wild type mid-L3 larvae vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase y%7!! +iyTP02 late-L3GSE727Public on Dec 31 20032003-10-102005-05-29{Timepoint 02 wild type late-L3 larvae vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase %z77!!+izTP03 late L3/early L4GSE728Public on Dec 31 20032003-10-102005-05-29{Timepoint 03 wild type late-L3/early L4 larvae vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase {'7!! +i{TP04 early L4GSE729Public on Dec 31 20032003-10-102005-05-29{Timepoint 04 wild type early L4 larvae vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase |%7!! +i|TP05 late L4GSE730Public on Dec 31 20032003-10-102005-05-29{Timepoint 05 wild type late-L4 larvae vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase %}=7!!+i}TP06 late L4/young adultGSE731Public on Dec 31 20032003-10-102005-05-29{Timepoint 06 wild type late L4/young adults vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase  ~97!!+i~TP07 early young adultGSE732Public on Dec 31 20032003-10-102005-05-29{Timepoint 07 wild type early young adult vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase 77!! +iTP08 late young adultGSE733Public on Dec 31 20032003-10-102005-05-29{Timepoint 08 wild type late young adult vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase !7!!w+iTP09 adultGSE734Public on Dec 31 20032003-10-102005-05-29{Timepoint 09 wild type adult vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase !97!!+iTP10 adult with embs 1GSE735Public on Dec 31 20032003-10-102005-05-29{Timepoint 10 wild type adults with embs 1 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase 77!! +iTP11 adult with emb 2GSE736Public on Dec 31 20032003-10-102005-05-29{Timepoint 11 wild type adult with emb 2 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbaseofflrx~ &,28>DJPV\bhntz "(.4:@FLRX^djpv|ӄAԄCׄDلE܄G݄HބI߄KNOPSVWXӄAԄCׄDلE܄G݄HބI߄KNOPSVWXZ\^_`aceghjkmo q s t u vwxyz{|}~!" # $ % & '(),04789;=>@ B!D#F%I(N)O*R,S.V0W1X2Y3Z4[5\8_9`:a;b=i>j?k@lAmBnCoDpEqFrGsHtIuJvKwLxMyNzO{P|Q}R~SU 77!! +iTP12 adult with emb 3GSE737Public on Dec 31 20032003-10-102005-05-29{Timepoint 12 wild type adult with emb 3 vs mixed stage referenceotherValerie,,Reinkehttp://ymd.med.yale.edu/ymd_prod/cgi-bin/ymd_public_data.cgiName: Valerie Reinke; Email: valerie.reinke@yale.edu; Phone: 203-785-5228; Laboratory: Reinke lab; Department: Genetics; Institute: Yale University School of Medicine; Address: 333 Cedar St; City: New Haven; State: CT; Zip/postal_code: 06520; Country: USA; Web_link: http://genome.med.yale.edu/Germbase ;;AO7!!+)}Rat models of cardiac hypertrophyGSE738Public on Mar 12 20042003-10-122005-10-28Cardiac hypertrophy was induced by aortic banding (6, 12, 16, and 30 weeks), myocardial infarction (3 and 9 weeks), an av-fistula (aorta abd. to v. cava inf.. 3 and 8 weeks), or hormone infusion (two weeks either angiotensin 2 or a thyroxin analogue). Sham operated or saline infused animals served as controls. Gene expression was determined by Affymetrix RGU34A GeneChip's to identify genes with common regulation in the different models of cardiac hypertrophy.otherClaes,C,StrømName: Claes,C,Strøm; Email: ccs@dadlnet.dk; Phone: +45 35456734; Fax: +45 35456500; Laboratory: CHARC (Copenhagen Heart Arrhythmia Research Center); Department: Department of Medicine B; Institute: H:S Rigshospitalet, University of Copenhagen Medical School; Address: 20, Juliane Mariesvej; City: Copenhagen; Zip/postal_code: 2100; Country: Denmark; Web_link: www.molheart.dk   oU7!!y)}Exercise induced cardiac hypertrophyGSE739Public on Jul 12 20042003-10-132005-10-28H{Cardiac hypertrophy was induced by treadmill running. Sedentary animals served as controls. Gene expression was determined by Affymetrix RGU34A GeneChip's to identify genes with differential expression in an adaptive model of cardiac hypertrophy.otherClaes,C,StrømName: Claes,C,Strøm; Email: ccs@dadlnet.dk; Phone: +45 35456734; Fax: +45 35456500; Laboratory: CHARC (Copenhagen Heart Arrhythmia Research Center); Department: Department of Medicine B; Institute: H:S Rigshospitalet, University of Copenhagen Medical School; Address: 20, Juliane Mariesvej; City: Copenhagen; Zip/postal_code: 2100; Country: Denmark; Web_link: www.molheart.dk FF6O7!!C+e1QRosetta_Merck_Splicing_ExperimentGSE740Public on Dec 19 20032003-10-142005-05-29This series represents 52 tissues hybridized across 5 different chip patterns. Probes were placed at every exon-exon junction in each transcript.; Keywordsparallel sampleJason,M,Johnson; John Castle; Philip Garrett-Engele; Patrick,M,Loerch; Zhengyan Kan; Christopher,D,Armour; Ralph Santos; Eric,E,Schadt; Roland Stoughton; Daniel,D,Shoemakerhttp://www.rii.comName: John Castle; Email: john_castle@merck.com; Phone: 425-636-6337; Laboratory: Rosetta; Department: Informatics; Institute: Merck; Address: 12040 115th Ave NE; City: Kirkland; State: WA; Zip/postal_code: 98034; Country: USA ons: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (plastic, Matrigel, collagen I, collagen IV, laminin, and fibronectin).; 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer’s instructions.; 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP.; 5. No external controls were added.; ; III. Hybridization procedures and parameters; 1. Sample, array type, batch and serial # used; 2. Hybridization protocol: Hybridization was carried out using the manufacturer’s recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS.; IV. Measurement data and specifications of data processing; 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis.; 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.otherJ,T,HandaName: James,T,Handa; Email: jthanda@jhmi.edu; Phone: 410 614-5481; Fax: 410 614-5471; Laboratory: Michael Panitch Macular Degeneration Laboratory; Department: Wilmer Eye Institute; Institute: Johns Hopkins Medical Institutes; Address: 600 N. Wolfe St.; City: Baltimore; State: MD; Zip/postal_code: 21287; Country: USA &{7!!ANative versus cultured retinal pigment epithelium cellsGSE741Public on Oct 15 20032003-10-142005-10-28;I. Exp Design; 1. Type of experiment: Comparison of native versus cultured RPE cells; 2. Experimental factors: Native RPE versus ARPE-19 cells grown on different matrices; 3. How many hybridizations in exp: 21; 4. If a common reference used for all the hybs: no; 5. Quality control steps: three independent arrays for each condition; 6. Description: The expression profile of ARPE-19 cells grown on different matrices were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 3 donors.; ; II. Samples used, extract prep, and labeling; 1. Biosource: Human donor globes from NDRI (63, 71, 74 years old) and ARPE-19 cells.; 2. Manipulati q )7!Y retired GSE743GSE743Public on Mar 05 20072007-03-06Accession "GSE743" has been retired, and the following accession has been created in its place: GSE358http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE358Name: GEO Admin; Institute: NCBI; Address: 8600 Rockville Pike; City: Bethesda; State: MD; Zip/postal_code: 20894; Country: USAq)7!Y retired GSE742GSE742Public on Mar 05 20072007-03-06Accession "GSE742" has been retired, and the following accession has been created in its place: GSE357http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE357Name: GEO Admin; Institute: NCBI; Address: 8600 Rockville Pike; City: Bethesda; State: MD; Zip/postal_code: 20894; Country: USA pp ;7!!%!+HEVEC dedifferentiationGSE751Public on Oct 18 20032003-10-162005-10-28:A double screen has been carried out by comparing freshly isolated HEVEC (D0-Hevec) from human tonsils to freshly purified HUVEC (D0-Huvec), and to dedifferentiated HEVEC (D2-Hevec) grown ex vivo for two days, using three Clontech commercial nucleotide arrays (Atlas Human Cardiovascular, 1.2 I and 1.2II Arrays); Keywords; KeywordsotherDelphine-Armelle,,Lacorre; Espen,S,Baekkevold; Ignacio Garrido; Per Brandtzaeg; Guttorm Haraldsen; François Amalric; Jean-Philippe GirardName: Delphine-Armelle Lacorre; Email: delphine-armelle.lacorre@ipbs.fr; Phone: 05 61 17 59 49; Fax: 05 61 17 59 94; Laboratory: Laboratoire de Biologie Vasculaire; Department: Protéome et Cibles Thérapeutiques; Institute: IPBS - CNRS UMR 5089; Address: 205, route de Narbonne; City: Toulouse; Zip/postal_code: 31077; Country: France z _7!!kEHalothane/Isoflurane Repetitive ExposuresGSE752Public on Oct 20 20032003-10-162005-06-15Rats were exposed to 90 minutes of 0.8% halothane or 1.0% isoflurane twice a day for a total of 5 or 10 exposures. Animals did not require intubation. All exposures and hybridizations were performed at the Univ. of Pennsylvania.; KeywordsotherRoderic,G,Eckenhoff; Maryellen,F,Eckenhoff; James,G,HeckerName: Roderic Eckenhoff; Email: roderic.eckenhoff@uphs.upenn.edu; Phone: 215-662-3705; Department: ; Institute: University of Pennsylvania; Address: ; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USA 0 37!!S[A_MRI-no-lytic-lesionGSE753Public on Jan 01 20042003-10-162005-05-29;This series represents samples of multiple myeloma patients without bone lytic lesion by MRI.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsotherErming,,Tian; Fenghuang Zhan; Ronald Walker; Erik Rasmussen; Yupo Ma; Bart Barlogie; John,D,Shaughnessyhttp://lambertlab.uams.eduName: John,D.,Shaughnessy; Email: jshaughnessy@uams.edu; Phone: 1-501-296-1503, X1457; Fax: 1-501-686-6442; Laboratory: Donna D. and Donald M. Lambert Laboratory of Myeloma Genetics; Department: Division of Basic Sciences; Institute: Myeloma Institute for Research and Therapy; Address: 4301 West Markham St., Slot 776; City: Little Rock; State: AR; Zip/postal_code: 72205; Country: USA; Web_link: http://lambertlab.uams.edu/ * -7!!M[A_MRI-lytic-lesionGSE754Public on Jan 01 20042003-10-162005-05-29;This series represents samples of multiple myeloma patients with bone lytic lesion by MRI.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsotherErming,,Tian; Fenghuang Zhan; Ronald Walker; Erik Rasmussen; Yupo Ma; Bart Barlogie; John,D,Shaughnessyhttp://lambertlab.uams.eduName: John,D.,Shaughnessy; Email: jshaughnessy@uams.edu; Phone: 1-501-296-1503, X1457; Fax: 1-501-686-6442; Laboratory: Donna D. and Donald M. Lambert Laboratory of Myeloma Genetics; Department: Division of Basic Sciences; Institute: Myeloma Institute for Research and Therapy; Address: 4301 West Markham St., Slot 776; City: Little Rock; State: AR; Zip/postal_code: 72205; Country: USA; Web_link: http://lambertlab.uams.edu/ DI7!!e[A_MRI lytic and no lytic lesionsGSE755Public on Jan 01 20042003-10-162005-05-29;This series represents samples of multiple myeloma patients with and without bone lytic lesion by MRI.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsotherErming,,Tian; Fenghuang Zhan; Ronald Walker; Erik Rasmussen; Yupo Ma; Bart Barlogie; John,D,Shaughnessyhttp://lambertlab.uams.eduName: John,D.,Shaughnessy; Email: jshaughnessy@uams.edu; Phone: 1-501-296-1503, X1457; Fax: 1-501-686-6442; Laboratory: Donna D. and Donald M. Lambert Laboratory of Myeloma Genetics; Department: Division of Basic Sciences; Institute: Myeloma Institute for Research and Therapy; Address: 4301 West Markham St., Slot 776; City: Little Rock; State: AR; Zip/postal_code: 72205; Country: USA; Web_link: http://lambertlab.uams.edu/ (37!!'GKEffect of bovine viral diarrhoea virus infection in Madin-Darby bovine kidney cellsGSE756Public on May 31 20042003-10-172005-06-15Analysis of gene expression induced in Madin-Darby bovine kidney cells (MDBK) infected with Bovine viral diarrhoea virus BVDV2 strain 1373.otherJohn,D,Neill; Julia,F,RidpathName: John,D.,Neill; Email: john.neill@ars.usda.gov; Phone: 515-663-7730; Laboratory: VPDLRU; Institute: National Animal Disease Center; Address: 2300 Dayton Ave.; City: Ames; State: IA; Zip/postal_code: 50010; Country: USA _7!!}M{Drosophila melanogaster strain comparisonGSE757Public on Dec 02 20032003-10-172005-10-28Comparison of gene expression in wild type, Oregon[R], Antennapedia[73b], Apterous[56f] Drosophila melanogaster strains.otherRick,,Johnston; Rachel Nutall; Michael Doctolero; Pamela Edwards; Jining Lü; Bruce Wang; Marina Vainer; Huibin Yue; Xinhao Wang; James Minor; Alex Lash; Cathy Chan; Thomas Goralski; Michael Parisi; Brian Oliver; Scott ScottName: Brian Oliver; Email: Brian_Oliver@nih.gov; Phone: 301-496-5495; Fax: 301-496-5239; Department: LCDB; Institute: National Institutes of Health, NIDDK; Address: 50 South Drive; City: Bethesda; State: MD; Zip/postal_code: 20892-8028; Country: USA; Web_link: http://www.niddk.nih.gov/intram/people/boliver.htm+ip microarrays to identify HP-responsive genes. Primary ONH astrocytes from two male Caucasian donors (passage 4) were grown to 75% confluence and were exposed for 6, 24 or 48 h to control ambient pressure (CP6, CP24, CP48) or hydrostatic pressure (HP6, HP24, HP48), or harvested at the beginning of the pressure experiment (CP0). Total RNA was extracted using Qiagen RNeasy columns and converted to biotin-labeled cRNA by standard Affymetrix protocols available at web site http://pathology.wustl.edu/~mgacore/genechip.htm#Preparing. Hybridization of the labeled cRNA to Human Genome U95Av2 chips (Affymetrix) was carried out by using Genechip Instrument System (Affymetrix) at Genechip Core Facility of Washington University. A total of 44 chips were generated and distributed as follows: seven for control pressure (CP) at time 0, four CP at 6 h, seven for hydrostatic pressure (HP) at 6 h, eight for CP at 24 h, eight for HP at 24 h, five for CP at 48 h and five for HP at 48h P. The arrays were washed and stained with streptavidin-phycoerythrin followed by scanning on an Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA), and then scanned by an Affymetrix GeneArray Scanner. Data was analyzed by Affymetrix Microarray Suite (version 5.0), linear regression analysis, and GeneSpring expression Analysis Software (version 6.0, Silicon Genetics). For analysis, the samples were scaled to the same target intensity (1500) to allow comparison of multiple samples, and raw data were normalized to median of each gene across all chips for fold change analysis using GeneSpring.time-courseOlga,,Agapova; Ping Yang; Amy Parker; William Shannon; Paula Pecen; Jill Duncan; Mercedes Salvador-Silva; M,R,Hernandez; M Rosario HernandezName: M Rosario Hernandez; Email: m-hernandez-neufeld@northwestern.edu; Phone: 312-503-1064; Fax: 312-503-1062; Laboratory: Hernandez; Department: Ophthalmology; Institute: Northwestern University; Address: 330 Chicago Avenue; City: Chicago; State: IL; Zip/postal_code: 60611; Country: USA B<+7!!Gq1Overexpression of dn-p21ras as a model system for severe dilated cardiomyopa.n7!!=+ECLong oligonucleotide arrays verse short oligonucleotide arrays-CTX066GSE759Public on Oct 22 20032003-10-202005-10-28:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from human neural stem cells treated with v-47!!u#%QGene expression in human optic nerve head (ONH) astrocytesGSE758Public on Jan 01 20042003-10-202006-12-15Gene expression in human optic nerve head (ONH) astrocytes exposed to either 60 mm Hg hydrostatic pressure (HP) or control ambient pressure (CP) was compared using Affymetrix GeneCh*ehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h.; For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11755, 11756, 11780, 11781, 11782, and 11783) which represent the RNA preps harvested at three different time (Jan 16, 2002, Jan 24, 2002, and Feb 20, 2002).; For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The same RNA preps used for Affymetrix array analysis were also used for Agilent array analysis. Finally, three replicates (GSM 11803, 11804 and 11809) were generated.parallel sampleJiang,,Li; Jeffrey,A,JohnsonName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USAthyGSE760Public on Oct 24 20032003-10-202005-06-15Mice heterozygous for dn-p21 littermates were sacrificed at 10 weeks of age. Ventricles were isolated and snap-frozen in liquid nitrogen. Use 3 month old FVB Females as controls. [GSM2334, GSM2335, GSM2336]; Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/ras_home.html; Keywords; KeywordsotherMartina,,Schinke; Tetsuo Shioi; Lauren Riggi; Seigo Izumo; Iuan Chenhttp://cardiogenomics.med.harvard.edu; http://cardiogenomics.med.harvard.edu/home; http://www.cardiogenomics.med.harvard.edu/groups/proj1/pages/fvb_home.htmlName: Martina Schinke; Email: mschinke@cgr.harvard.edu; Phone: 617-495-0676; Laboratory: Cardiogenomics; Department: Bauer Center for Genomic Research; Institute: Harvard University; Address: 7 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: www.cardiogenomics.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE760/GSE760_RAW.tar01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h.; For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11865, 11866, 11858, 11857, 11870, and 11871) which represent the RNA preps harvested at three different time (April 17, 2001, March 15, 2001, and Feb 21, 2001).; For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The RNA prep used for Agilent array analysis was not the same as the one used for Affymetrix array analysis. Finally, three replicates (GSM 11828, 11831 and 11835) were generated.parallel sampleJiang,,Li; Jeffrey,A,JohnsonName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USA r+7!![icCCFAlmasan_CaP1GSE762Public on Jun 01 20042003-10-202005-05-29The experiment design was multifold, consisting of a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 mixed gamma and beta source, with two additional samples, one exposed to radiation in four fractions instead of all at once, and one containing th1#7!!a+ECLong oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cellsGSE761Public on Oct 22 20032003-10-202005-10-28Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to measure differential gene expression in RNA samples generated from human neuroblastoma cells treated with vehicle (EtOH, 0./e parent LNCaP cell line. PolyA+ RNA was extracted, processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HGU-95 (Av1-E) chip sets, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedJeffrey,C,Buchsbaum; Bendi Gong; John,G,Hissong; Subrata Ray; Eric,A,Klein; Warren,E,Heston; Alexandru AlmasanName: John,Gilmary,Hissong; Email: hissonj@ccf.org; Phone: 216-445-7105; Fax: 216-445-6269; Laboratory: Almasan Lab NB40; Department: Cancer Biology; Institute: Lerner Research Institute Cleveland Clinic Foundation; Address: 9500 Euclid Ave.; City: Cleveland; State: OH; Zip/postal_code: 44195; Country: USA; Web_link: http://www.lerner.ccf.org/cancerbio/almasan/3outcomes in response to chemotherapy. Tumors derived from basal epithelium have a poorer prognosis than tumors derived from luminal epithelium. To gain insight into differences underlying this disparity, we treated cell lines derived from basal epithelium (immortalized human mammary epithelial cells) and those derived from luminal epithelium (MCF-7 and ZR-75-1) with two chemotherapeutics commonly used in the treatment of breast cancer. Treatment doses for doxorubicin (DOX) and 5-fluorouracil (5FU) were selected to cause comparable cytotoxicity across all four cell lines. The predominant gene expression in each of the four cell lines was a general stress response, but distinct gene expression patterns were observed depending upon cell type. Both cell types up-regulated DNA damage response genes such as p21waf1, but the response in the luminal cells was much more dramatic and included many p53-regulated genes. Luminal cell lines down-regulated a large number of cell cycle regulators and other genes involved in cellular proliferation, while basal cell lines down-regulated a smaller set of genes, many of which are involved in cellular differentiation. These results were compared to gene expression data from tumor samples collected before and after treatment with DOX or 5FU/mitomycin C. Similarities between the in vitro and in vivo responses validate this model for studying gene expression responses to chemotherapy in these cell types. Understanding cell-type specific responses to chemotherapeutics will help in tailoring treatment to patients based upon tumor characteristics.; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseMelissa,A,Troester; Katherine,A,Hoadley; Theresa Sørlie; Brittney-Shea Herbert; Jerry Shay; Charles,M,PerouName: Charles Perou; Email: cperou@med.unc.edu; Phone: 919-843-5740; Fax: 919-843-5718; Department: CB#7295; Institute: University of North Carolina at Chapel Hill; Address: 102 Mason Farm Road; City: Chapel Hill; State: NC; Zip/postal_code: 27599-7295; Country: USA 7!!#qGComparison of Gene Expression in Uterine Smooth Muscle TumorsGSE764Public on J57!!o#e!Cell-type specific responses to chemotherapeutics in breast cancerGSE763Public on Apr 18 20042003-10-212005-10-28Recent studies have identified clinical subtypes of breast tumors that arise from different cell types and have different 2an 01 20042003-10-212005-08-09Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma. Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.otherBradley,J,Quade; George,L,Mutter; Cynthia,C,Mortonhttp://www.bwhpathology.org/gynpath/smooth_muscle_profiles/Name: Bradley,J,Quade; Email: bquade@partners.org; Phone: 617-732-5475; Fax: 617-738-6996; Laboratory: Division of Women's and Perinatal Pathology; Department: Pathology; Institute: Brigham and Women's Hospital; Address: 75 Francis Street; City: Boston; State: MA; Zip/postal_code: 02115; Country: USA; Web_link: http://www.bwhpathology.org/gynpath/9=@BDDFIIJINRPSV\\bcdefg }G7!!'+a1Control vs CF Small IntestineGSE765Public on Jan 26 20042003-10-212005-05-29Total RNA was prepared from the entire small intestines of 40 day old Control and CFTR null mice (2 males and 1 female of each genotype), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.parallel sampleOxana,,Norkina; Simran Kaur; Donna Ziemer; Robert,C,De LisleName: Robert,C,De Lisle; Email: rdelisle@kumc.edu; Phone: 913-588-2742; Department: Anatomy & Cell Biology; Institute: Univ Kansas Med Ctr; Address: 3901 Rainbow Blvd; City: Kansas City; State: KS; Zip/postal_code: 66160; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE765/GSE765_RAW.tar AA;;7!!c'cRASF + IKB/Adtet + TNFaGSE766Public on Oct 23 20032003-10-212005-05-29Rheumatoid arthritis synovial fibroblasts (RASF) were transected with an adenovirus (Ad) expressing a dominant negative (DN) form of Ik-B stimulated 18 hours later with TNF-a. Controls were RASF transfected with Adtet then treated with TNF-a 18 hours later. RNA was extracted 3 hours after TNF-a application. The same cell line was split into 6 lots grown up and then treated with the virus independent. Each of the Ik-B and Adtet has 3 replications. Data is Hu95Av2 processed with MAS 4.0.repeat sampleHuang-Ge,,Zhang; Karren Hyde; Hui-Chen Hsu; David Allison; Grier,P,Page; John,B,Mountz; Jacob Brand; Juling Zhou; Shaohua Yu; David,B,Allison; John,D,Mountz; Huang-Ge PageName: Grier Page; Email: gpage@uab.edu; Phone: 205-934-4930; Institute: University of Alabama at Birmingham; Address: ; City: Birmingham; State: AL; Zip/postal_code: 35294; Country: USA {{HS7!! #EACNeural stem and neuroblastoma cellsGSE768Public on Oct 22 20032003-10-222006-04-:37!!['7ktime 0.5 hr to 0 hrGSE767Public on Nov 26 20032003-10-222005-05-29Six dye swap replicates were performed with material derived 0.5 hour after stimulation of HUVECs with PMA and RMAC11 hybridised to material obtained at time 0 hours.repeat sampleJ,R,Gamble; M,A,Vadas; C,N,Hahn; C,J,Drogemuller; S,A,Waterman; A Tsykin; G,J,GoodallName: Anna Tsykin; Email: anna.tsykin@adelaide.edu.au; Phone: 61 8 83036388; Institute: Hanson Institute; Address: ; City: Adelaide; Zip/postal_code: 5000; Country: Australia25>Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from (1) human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h, and (2) neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h.; This SuperSeries is composed of the following subset Series:; GSE759: Long oligonucleotide arrays verse short oligonucleotide arrays-CTX066; GSE761: Long oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cellsSuperSeriesJiang,,Li; Jeffrey,A,JohnsonRefer to individual SeriesName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USA %97!!_++a1CF vs control PancreasGSE769Public on Mar 29 20042003-10-222005-06-15ܥTotal RNA was prepared using TRIzol reagent from the pancreata of eight week old male mice. The genotypes were Control: gastrin+/-, CFTR+/+; and CF: gastrin+/-, CFTR-/-. All mice were on 95% black6, 5% 129Sv background. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.parallel sampleSimran,,Kaur; Donna Ziemer; Oxana Norkina; Linda,C,Samuelson; Robert,C,De LisleName: Robert,C,De Lisle; Email: rdelisle@kumc.edu; Phone: 913-588-2742; Department: Anatomy & Cell Biology; Institute: Univ Kansas Med Ctr; Address: 3901 Rainbow Blvd; City: Kansas City; State: KS; Zip/postal_code: 66160; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE769/GSE769_RAW.tarells extracted at 24 hr. After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseJeffrey,C,Buchsbaum; Bendi Gong; John,G,Hissong; Subrata Ray; Eric,A,Klein; Warren,E,Heston; Alexandru AlmasanName: John,Gilmary,Hissong; Email: hissonj@ccf.org; Phone: 216-445-7105; Fax: 216-445-6269; Laboratory: Almasan Lab NB40; Department: Cancer Biology; Institute: Lerner Research Institute Cleveland Clinic Foundation; Address: 9500 Euclid Ave.; City: Cleveland; State: OH; Zip/postal_code: 44195; Country: USA; Web_link: http://www.lerner.ccf.org/cancerbio/almasan/ L:/7!!['ktime 3 hr to 0 hrGSE771Public on Nov 25 20032003-10-232005-05-29Four dye swap replicates were performed with material derived 3 hour after stimulation of HUVECs with PMA and RMAC11, hybridised to material obtained at time 0 hours.repeat sampleName: Anna Tsykin; Email: anna.tsykin@adelaide.edu.au; Phone: 61 8 83036388; Institute: Hanson Institute; Address: ; City: Adelaide; Zip/postal_code: 5000; Country: Australia(-7!!g#icCCF_Almasan_CaPKGSE770Public on Jun 01 20042003-10-222005-05-29The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source. Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation. The untreated control sample, labeled 0, was collected concurrently with the c< aM7!!75Abeta-activated Array ExperimentGSE772Public on Oct 29 20032003-10-232005-05-29This series represents the samples used to generate the associated gene listing. The samples contained belong to two Platform accessions GPL561 and GPL562. There is a slight redundancy in the gene list due to multiple strong hits for a given gene. Clone selection was based on a fold >= 1.2 with a p-value <= 0.1 in at least 2 probe samples.otherL,,Gan; S Ye; A Chu; K Anton; S Yi; V Vincent; D von Schack; D Chin; J Murray; S Lohr; L Patthy; M Gonzalez-Zulueta; K Nikolich; R UrferName: Scott,Curtis,Lohr; Email: slohr@agyinc.com; Phone: 650-228-1140; Fax: 650-228-1180; Department: Bioinformatics; Institute: AGY Therapeutics Inc.; Address: 290 Utah Ave.; City: South San Francisco; State: CA; Zip/postal_code: 94080; Country: USA; Web_link: www.agyinc.comransgenic thyroid, of +/- 13.000 genes. 360 genes or EST showed a strong modulation with background corrected values of fluorescence superior to 2 fold change. The modulated genes were classified according to their proposed gene ontology functions. Approximately half of them were upregulated. The function of the majority of these genes in thyroid physiology is still to be determined. Some of them, like IGF-I, IGF-BP3, IGF-BP5, may play an important role in the development of thyroid nodules through paracrine mechanisms.; Keywords; Keywordsparallel sampleJean-Christophe,,Goffard; Ling Jin; Hortensia Mirescu; Paul Van Hummelen; Catherine Ledent; Jaques Emile Dumont; Bernard Corvilainhttp://www.microarrays.beName: Paul Van Hummelen; Email: paul.vanhummelen@vib.be; Phone: +32(0)16 34 79 39; Fax: +32(0)16 34 79 40; Department: MicroArray Facility; Institute: Flanders Institute for Biotechnology; Address: Herestraat 49; City: Leuven; Zip/postal_code: B-3000; Country: Belgium; Web_link: http://www.microarrays.be G A7!!+?oThyroid RDC8 versus C57Bl6GSE773Public on Nov 25 20032003-10-232005-06-15:`Mutations of the thyrotropin receptor leading to constitutive activation of the cAMP cascade are responsible for the development of hot nodules, if arising in a somatic cell, and non-auto-immune hyperthyroidism, when occurring in a germinal cell. An animal model of constitutive activation of the thyroid cAMP cascade has been obtained by generating transgenic mice expressing the adenosine receptor (Tg-A2aR) under the control of the thyroglobulin promoter. These mice develop huge goiters and die prematurely due to hyperthyroidism induced cardiac failure. To identify new genes involved in the tumorigenic pathway of the thyroid, we designed a protocol using microarray technology to study the differential expression, between normal and t?ransgenic thyroid, of +/- 13.000 genes. 360 genes or EST showed a strong modulation with background corrected values of fluorescence superior to 2 fold change. The modulated genes were classified according to their proposed gene ontology functions. Approximately half of them were upregulated. The function of the majority of these genes in thyroid physiology is still to be determined. Some of them, like IGF-I, IGF-BP3, IGF-BP5, may play an important role in the development of thyroid nodules through paracrine mechanisms.; Keywords; Keywordsparallel sampleJean-Christophe,,Goffard; Ling Jin; Hortensia Mirescu; Paul Van Hummelen; Catherine Ledent; Jaques Emile Dumont; Bernard Corvilainhttp://www.microarrays.beName: Paul Van Hummelen; Email: paul.vanhummelen@vib.be; Phone: +32(0)16 34 79 39; Fax: +32(0)16 34 79 40; Department: MicroArray Facility; Institute: Flanders Institute for Biotechnology; Address: Herestraat 49; City: Leuven; Zip/postal_code: B-3000; Country: Belgium; Web_link: http://www.microarrays.be T![7!!+?oThyroid C57Bl6 versus RDC8 (Color Flip)GSE774Public on Nov 25 20032003-10-232005-05-29:`Mutations of the thyrotropin receptor leading to constitutive activation of the cAMP cascade are responsible for the development of hot nodules, if arising in a somatic cell, and non-auto-immune hyperthyroidism, when occurring in a germinal cell. An animal model of constitutive activation of the thyroid cAMP cascade has been obtained by generating transgenic mice expressing the adenosine receptor (Tg-A2aR) under the control of the thyroglobulin promoter. These mice develop huge goiters and die prematurely due to hyperthyroidism induced cardiac failure. To identify new genes involved in the tumorigenic pathway of the thyroid, we designed a protocol using microarray technology to study the differential expression, between normal and tActed left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.htmlotherMartina,,Schinke; Jeffrey Brown; Seigo Izumohttp://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.htmlName: Martina Schinke; Email: mschinke@cgr.harvard.edu; Phone: 617-495-0676; Laboratory: Cardiogenomics; Department: Bauer Center for Genomic Research; Institute: Harvard University; Address: 7 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: www.cardiogenomics.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE775/GSE775_RAW.tar \\_#K7!!{[/q1Physiologic cardiac hypertrophyGSE776Public on Oct 24 20032003-10-232005-06-15Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a; vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressivelyE-"U7!!eq1Mouse model of myocardial infarctionGSE775Public on Oct 24 20032003-10-232005-06-15This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarC strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow.; Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.htmlotherPeter,,Kang; Jeffrey Brown; Seigo Izumohttp://cardiogenomics.med.harvard.edu; http://cardiogenomics.med.harvard.edu/homeName: Martina Schinke; Email: mschinke@cgr.harvard.edu; Phone: 617-495-0676; Laboratory: Cardiogenomics; Department: Bauer Center for Genomic Research; Institute: Harvard University; Address: 7 Divinity Ave; City: Cambridge; State: MA; Zip/postal_code: 02138; Country: USA; Web_link: www.cardiogenomics.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE776/GSE776_RAW.tar m%17!!1'ktime 24 hr to 0 hrGSE778Public on Nov 25 20032003-10-242005-05-29Four dye swap replicates were performed with material derived 24 hours after stimulation of HUVECs with PMA and RMAC11 hybridised to material obtained aGi$/7!!+'ktime 6 hr to 0 hrGSE777Public on Nov 25 20032003-10-242005-05-29Four dye swap replicates were performed with material derived 6 hours after stimulation of HUVECs with PMA and RMAC11 hybridised to material obtained at time 0 hours.; Keywords; Keywords; Keywords; Keywordsrepeat sampleC,,HahnName: Anna Tsykin; Email: anna.tsykin@adelaide.edu.au; Phone: 61 8 83036388; Institute: Hanson Institute; Address: ; City: Adelaide; Zip/postal_code: 5000; Country: Australiat time 0 hours.; The cDNAs used in this microarray were identified as part of collaborative project between the IMVS and Bionomics Limited. The project aims were to identify genes up-regulated during in vitro capillary tube formation as targets for angiogenesis-based therapeutics.; ; Any requests for further information regarding the data generated from this collaboration should be directed to Bionomics Limited (www.bionomics.com.au) at the; following address:; ; Bionomics Limited; 31 Dalgleish Street; Thebarton, South Australia; Australia, 5031; Phone: 618 8354 6104; Fax: 618 8354 6199; Email: busdev@bionomics.com.au; Keywords; Keywords; Keywords; Keywordsrepeat sampleC,,HahnName: Anna Tsykin; Email: anna.tsykin@adelaide.edu.au; Phone: 61 8 83036388; Institute: Hanson Institute; Address: ; City: Adelaide; Zip/postal_code: 5000; Country: Australiaative project between the IMVS and Bionomics Limited. The project aims were to identify genes up-regulated during in vitro capillary tube formation as targets for angiogenesis-based therapeutics.; ; This SuperSeries is composed of the following subset Series:; GSE767: time 0.5 hr to 0 hr; GSE771: time 3 hr to 0 hr; GSE777: time 6 hr to 0 hr; GSE778: time 24 hr to 0 hr; ; Any requests for further information regarding the data generated from this collaboration should be directed to Bionomics Limited (www.bionomics.com.au) at the; following address:; ; Bionomics Limited; 31 Dalgleish Street; Thebarton, South Australia; Australia, 5031; Phone: 618 8354 6104; Fax: 618 8354 6199; Email: busdev@bionomics.com.autime-courseC,,Hahn; J,R,Gamble; M,A,Vadas; C,N,Hahn; C,J,Drogemuller; S,A,Waterman; A Tsykin; G,J,GoodallRefer to individual SeriesName: Anna Tsykin; Email: anna.tsykin@adelaide.edu.au; Phone: 61 8 83036388; Institute: Hanson Institute; Address: ; City: Adelaide; Zip/postal_code: 5000; Country: Australia ;(;r(u7!!+Y[1Normal and Renal Cell Carcinoma Kidney Tissue, HumanGSE781Public on Nov 25 20032003-10-242005L#'K7!![?oGene Expression Profile in thyroid of Transgenic Mice over-expressing the AdenJL&37!!#IAkangiogenesis courseGSE779Public on Nov 25 20032003-10-242006-04-25This is a time course experiment with 4 - 6 slides per time point where all samples were hybridised to time zero. The microarray slides were scanned using a GenePix 4000B Scanner (Axon Instruments, Foster City, CA, USA). The “SPOT” software package (CSIRO) was used to identify spots and subtract backgrounds. The extracted information was normalised using the “Statistics in Microarray Analysis" (SMA) open source R package. Scaled print tip group lowes normalisation was performed for each slide and replicate slides were scaled to each other.; ; The cDNAs used in this microarray were identified as part of collaborHKosine Receptor 2aGSE780Public on Nov 25 20032003-10-242005-06-15:`Mutations of the thyrotropin receptor leading to constitutive activation of the cAMP cascade are responsible for the development of hot nodules, if arising in a somatic cell, and non-auto-immune hyperthyroidism, when occurring in a germinal cell. An animal model of constitutive activation of the thyroid cAMP cascade has been obtained by generating transgenic mice expressing the adenosine receptor (Tg-A2aR) under the control of the thyroglobulin promoter. These mice develop huge goiters and die prematurely due to hyperthyroidism induced cardiac failure. To identify new genes involved in the tumorigenic pathway of the thyroid, we designed a protocol using microarray technology to study the differential expression, between normal and transgenic thyroid, of +/- 13.000 genes. 360 genes or EST showed a strong modulation with background corrected values of fluorescence superior to 2 fold change. The modulated genes were classified according to their proposed gene ontology functions. Approximately half of them were upregulated. The function of the majority of these genes in thyroid physiology is still to be determined. Some of them, like IGF-I, IGF-BP3, IGF-BP5, may play an important role in the development of thyroid nodules through paracrine mechanisms. This study demonstrates the feasibility of sequentially after the cascade of events leading to the formation of benign tumors such as hot thyroid nodule or hyperfunctional goitre.otherJean-Christophe,,Goffard; Ling Jin; Hortensia Mirescu; Paul Van Hummelen; Catherine Ledent; Jaques Emile Dumont; Bernard Corvilainhttp://www.microarrays.beName: Paul Van Hummelen; Email: paul.vanhummelen@vib.be; Phone: +32(0)16 34 79 39; Fax: +32(0)16 34 79 40; Department: MicroArray Facility; Institute: Flanders Institute for Biotechnology; Address: Herestraat 49; City: Leuven; Zip/postal_code: B-3000; Country: Belgium; Web_link: http://www.microarrays.be-05-29k Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97).; ; For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1.; ; For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032.; Keywords; Keywords; Keywords; Keywords; Keywordsparallel sampleMarc,E,Lenburg; Louis,S,Liou; Norman,P,Gerry; Garrett,M,Frampton; Herbert,T,Cohen; Michael,F,ChristmanName: Marc,E.,Lenburg; Email: mlenburg@bu.edu; Phone: 617-414-1375; Fax: 617-414-1646; Department: Genetics and Genomics; Institute: Boston University School of Medicine; Address: 715 Albany Street, E613B; City: Boston; State: MA; Zip/postal_code: 02130; Country: USA; Web_link: http://gg.bu.eduftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE781/GSE781_RAW.tarn. After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseJeffrey,C,Buchsbaum; Bendi Gong; John,G,Hissong; Subrata Ray; Eric,A,Klein; Warren,E,Heston; Alexandru AlmasanName: John,Gilmary,Hissong; Email: hissonj@ccf.org; Phone: 216-445-7105; Fax: 216-445-6269; Laboratory: Almasan Lab NB40; Department: Cancer Biology; Institute: Lerner Research Institute Cleveland Clinic Foundation; Address: 9500 Euclid Ave.; City: Cleveland; State: OH; Zip/postal_code: 44195; Country: USA; Web_link: http://www.lerner.ccf.org/cancerbio/almasan/ J)57!!##icCCF_Almasan_CaPGSE56GSE782Public on Jun 01 20042003-10-242005-05-29The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function. Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source. Total RNA was extracted from cells at 6 and 24 hours after irradiation. The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr. It was not irradiated and was transfected with the base pLXSN retrovirus, lacking the inserted GSE56 coding regioM {*e7!!q'1qDetection of genes in different carbohydrates isolated by NSH using single channel slide based hybrdizationsGSE783Public on Mar 14 20042003-10-272005-06-153Isolation of genes from Aspergillus nidulans grown in different complex carbohydrates by NSH and the NSH method was evaluated by using single channel non competitive slide based hybridizations; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleAnamika,,Ray; Sunita Macwana; Patricia Ayoubi; Leo Hall; Rolf Prade; Andrew,J,MortName: Patricia,J,Ayoubi; Email: ayoubi@biochem.okstate.edu; Phone: 405-744-6209; Fax: 405-744-7799; Laboratory: OSU Microarray Core Facility; Department: Biochemistry and Molecular Biology; Institute: Oklahoma State University; Address: 246 Noble Research Center; City: Stillwater; State: OK; Zip/postal_code: 74078; Country: USA; Web_link: http://microarray.okstate.eduQnsity oligonucleotide Affymetrix MG_U74Av2 arrays, using manufacturer protocol. We measured the relative expression level of >12000 genes and ESTs.; -----------------------------------------; Samples used in analysis:; * GSM12501: Normal intestine diet #1 sample C1_0112 Dnmt+/- Min/+; * GSM12502: Tumor diet #1 sample T1_0112 Dnmt+/- Min/+; * GSM12503: Normal intestine diet #1 sample C2_0112 Dnmt+/+ Min/+; * GSM12504: Tumor diet #1 sample T2_0112 Dnmt+/+ Min/+; * GSM12505: Normal intestine diet #2 sample C1_003 Dnmt+/- Min/+; * GSM12506: Tumor diet #2 sample T1_003 Dnmt+/- Min/+; * GSM12507: Normal intestine diet #2 sample C2_003 Dnmt+/+ Min/+; * GSM12508: Tumor diet #2 sample T2_003 Dnmt+/+ Min/+; * GSM12509: Normal intestine diet #3 sample C1_005 Dnmt+/- Min/+; * GSM12510: Tumor diet #3 sample T1_005 Dnmt+/- Min/+; * GSM12511: Normal intestine diet #3 sample C2_005 Dnmt+/+ Min/+; * GSM12512: Tumor diet #3 sample T2_005 Dnmt+/+ Min/+; - - - - - - - - - - - - - - - - - - - - -; Comparisons were performed as described in Chen Z, Ge B, Hudson TJ and Rozen R. Gene Expression Patterns 1, 89-93, 2002. Comparing Normal intestine vs Adenoma.; - - - - - - - - - - - - - - - - - - - - -; This resulted in the identification of differentially expressed transcripts. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx WEB portal (www.Affymetrix.com) and literature.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedDaniel,,Leclerc; Liyuan Deng; Jacquetta Trasler; Rima RozenName: Daniel Leclerc; Email: daniel.leclerc@mail.mcgill.ca; Phone: 514-412-4400 x23281; Fax: 514-412-4331; Laboratory: Rima Rozen Laboratory; Department: Medical Genetics, Room 242; Institute: Montreal Children's Hospital; Address: 4060 Ste-Catherine West; City: Montreal; State: Quebec; Zip/postal_code: H3Z 2Z3; Country: Canada :?:,+7!!!+uAepileptogenesisGSE785Public on Oct 31 20032003-10-302005-05-29qexperimental group and control group in rat post-status epilepticus model.parallel sampleErik,,Hendriksen; Nicole Datson; Wim Ghijsen; Erwin van Vliet; Fernando Lopes da Silva; Jan Gorter; Erno VreugdenhilName: Nicole Datson; Email: datson_n@lacdr.leidenuniv.nl; Phone: (+31)71-5276222; Department: Medical Pharmacology; Institute: Leiden University; Address: ; City: Leiden; Zip/postal_code: 2333 CC; Country: Netherlands1+U7!!yTranscriptional Profiling of the Transition from Normal Intestine to Adenoma in the APC(Min/+) MouseGSE784Public on Oct 18 20042003-10-292006-12-20PTranscriptional Profiling of the Transition from Normal Intestine to Adenoma in the APC(Min/+) Mouse.; Tissue was from male 91-days old APC(Min/+) mouse (an animal model for human colon cancer). RNA was purified using Trizol and labeled for hybridization to high deP ]].K7!!s+%ACorticosteroid responsive genesGSE787Public on Oct 31 20032003-10-302005-05-29XThree groups of Wistar rats with different mT-Q7!!-WAshort and long attack latency miceGSE786Public on Oct 31 20032003-10-302005-05-29bTwo wild house mice lines were genetically selected for short and long attack latency. Mice with an attack latency <50s or >600s were considered short attack latency mice (SAL) and long attack latency mice(LAL) respectively. RNA from the hippocampus of 14 SAL or 14 LAL mice was pooled and used as input material for the SAGE libraries.otherDorine,,Feldker; Nicole Datson; Alexa Veenema; Erik Meulmeester; E. Ronald de Kloet; Erno VreugdenhilName: Nicole Datson; Email: datson_n@lacdr.leidenuniv.nl; Phone: (+31)71-5276222; Department: Medical Pharmacology; Institute: Leiden University; Address: ; City: Leiden; Zip/postal_code: 2333 CC; Country: Netherlandsanipulated levels of corticosterone were used to identify corticosteroid-responsive genes in hippocampus:; 1. rats were adrenalectomised (ADX); 2. In addition to ADX these rats were implanted with a subcutaneous pellet containing 20 mg corticosterone and 80% cholesterol (ADX + low CORT); 3. In addition to ADX and implantation of a corticosterone pellet, these rats received a subcutaneous injection with corticosterone (1 mg/kg bodyweight) three hours prior to decapitation ((ADX + low CORT) + acute high CORT).; ; All 3 groups of rats were decapitated three days after ADX and their hippocampus was isolated. Hippocampal RNA from 6 rats per group was pooled and used as input material for the SAGE libraries.parallel sampleNicole,,Datson; Jeannette van der Perk; E. Ronald de Kloet; Erno VreugdenhilName: Nicole Datson; Email: datson_n@lacdr.leidenuniv.nl; Phone: (+31)71-5276222; Department: Medical Pharmacology; Institute: Leiden University; Address: ; City: Leiden; Zip/postal_code: 2333 CC; Country: Netherlands:mRNA used for the analysis of these microarrays were previously analyzed for 34 genes by reverse transcription - polymerase chain reaction in Desai BJ et al., J.Orthop.Trauma 17: 689-698, 2003. These two data sets were subsequently studied to compare the results from these two different methods for mRNA quantitation. The comparison was publised in "Comparison of mRNA gene expression by RT-PCR and DNA microarray" by W. Etienne, M.H. Meyer, J. Peppers, and R.A. Meyer, Jr., BioTechniques 36 (4): 618-626, April 2004.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseRalph,A,Meyer; Martha,H,Meyer; Wiguins Etienne; Bhaloo,J,Desai; Johnny PeppersName: Ralph,A.,Meyer; Email: ralpham@aol.com; Laboratory: Cannon Research Center, Rm. 304; Department: Orthopaedic Research Laboratory; Institute: Carolinas Medical Center; Address: P.O. Box 32861; City: Charlotte; State: NC; Zip/postal_code: 28232-2861; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE788/GSE788_RAW.tar ]]+037!!W'3effect of age liverGSE789Public on Jan 02 20042003-10-312005-10-28C@effect of aging in old male rat liverrepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Swedenh/Q7!!#)#1Comparison of microarray to RT-PCRGSE788Public on Feb 01 20042003-10-302005-05-29U :1G7!!a'3aging in male rat liver (1-7)GSE790Public on Jan 02 20042003-10-312005-10-28C@effect of increasing age in male rat liverrepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Sweden 8297!!k'3GH inj old liver (1-7)GSE791Public on Jan 02 20042003-10-312005-10-28C@effect of hGH injections in old male rat liversrepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Sweden I3S7!!s'3effect of age in male rat fat (1-3)GSE792Public on Jan 02 20042003-10-312005-10-28C@effect of increasing age in male rat adipose tissuerepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Sweden >457!!{'3GH inj old fat (1-3)GSE793Public on Jan 02 20042003-10-312005-10-28C@effect of hGH injections in old male rat adipose tissuerepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Sweden <5I7!!c'3aging in male rat muscle (1-3)GSE794Public on Jan 02 20042003-10-312005-10-28C@effect of aging in male rat skeletal musclerepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Sweden bb/87!!M#UAX-radiation (XR) resistant HCT116-Clone2: XR at 0 and 4 GyGSE797Public on Jun 0^T757!!u1iBladder cancer cellsGSE796Public on Nov 03 20032003-10-312005-08-30Examination of gene expression in several bladder cancer cell lines grown on either plastic, SIS (small intestine submucosa) ]K6M7!!}'3GH inj old male rat muscle (1-3)GSE795Public on Jan 02 20042003-10-312005-10-28C@effect of hGH injections in old male rat skeletal musclerepeat samplePetra,,Tollet-Egnell; Paolo Parini; Nina Ståhlberg; Ingrid Lönnstedt; Norman Lee; Mats Rudling; Amilcar Flores-Morales; Gunnar NorstedtName: Petra,Elisabeth,Tollet-Egnell; Email: petra.tollet.egnell@cmm.ki.se; Phone: 46-8-51776546; Laboratory: Gunnar Norstedt; Department: Dept of Molecular Medicine; Institute: Karolinska Institute; Address: CMM L8:01; City: Stockholm; Zip/postal_code: 17176; Country: Swedengel or matrigel.; A data table of normalized values is appended below. Data were normalized as described in detail by Knowlton N, Dozmorov IM, Centola M. Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics. 2004 Dec 12;20(18):3687-90.; In brief, the normalization method relies on a number of low expression genes to provide an estimate of non-specific binding. This information is then used to perform a Z transformation on the data. Once normalized the data are "unbiased" through robust linear regression to allow comparisons across different membranes.otherIgor,,Dozmorov; Kimberly,D,Kyker; Craig Cadwell; Michael,B,Centola; Robert,E,HurstName: Robert,Evan,Hurst; Email: robert-hurst@ouhsc.edu; Phone: 405-271-3930; Fax: 405-271-3289; Laboratory: Adult Urology Lab; Department: Urology; Institute: Oklahoma University Health Sciences Center; Address: 920 S. L. Young Blvd; City: Oklahoma City; State: OK; Zip/postal_code: 73112; Country: USA4 20042003-11-032006-04-25cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells without XR, 10 minutes, 6 hours, or 24 hours after XR at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; This SuperSeries is composed of the following subset Series:; GSE798: Unirradiated HCT116-Clone2 cells; GSE799: HCT116-Clone2 cells 10 min after XR treatment at 4 Gy; GSE800: HCT116-Clone2 cells 6 hours after XR treatment at 4 Gy; GSE801: HCT116-Clone2 cells 24 hours after XR treatment at 4 Gytime-courseFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanRefer to individual SeriesName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada XX$9M7!!'UUnirradiated HCT116-Clone2 cellsGSE798Public on Jun 04 20042003-11-032005-05-29cDNA microarray study of unirradiated X-radiation (XR) resistant HCT116-Clone2 cells versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.repeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada y:w7!!'UHCT116-Clone2 cells 10 min after XR treatment at 4 GyGSE799Public on Jun 04 20042003-11-032005-05-29cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 10 minutes after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywords; Keywords; Keywords; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada w;y7!!'UHCT116-Clone2 cells 6 hours after XR treatment at 4 GyGSE800Public on Jun 04 20042003-11-032005-05-29cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 6 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywords; Keywords; Keywords; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canada S=7!!%#%KBurn20GSE802Public on May 07 20042003-11-042006-09-08Type of experiment: Cocy<{7!!'UHCT116-Clone2 cells 24 hours after XR treatment at 4 GyGSE801Public on Jun 04 20042003-11-032005-05-29cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 24 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.; Keywords; Keywords; Keywords; Keywordsrepeat sampleFelix,M,Mesak; Cheng,E,Ng; Wei,L,TanName: Felix,M.,Mesak; Email: Felix.Mesak@orcc.on.ca; Phone: 1-613-737 7700 ext. 6940-42; Fax: 1-613-247 3524; Laboratory: Dr. Cheng E. Ng; Department: Centre for Cancer Therapeutics; Institute: Ottawa Regional Cancer Centre; Address: 503 Smyth Rd. 3rd Floor; City: Ottawa; State: ON; Zip/postal_code: K1H 1C4; Country: Canadadmparison of liver samples between sham (control) and 20% TBSA (total burn surface area) burn rats collected at 1h, 4h, 8h, and 24h.; ; Experimental factors: Burn injury and time; ; Experiment design: All experimental liver samples collected after 1h, 4h, 8h, and 24h after burn injury were compared to a common reference (sham control treated as 0h time point); ; Bio source: Sprague-Drawley male rats weighing 150-200 g supplied through Charles river laboratories, MA (www.criver.com); ; Bio material manipulations: Rats (n=3 for each scald-burn and sham-burn time point) were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment. Water and rat chow were provided ad libitum to the animals. On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned. The burn injury consisted of a full-skin-thickness scald burn of the dorsum, ecalculated to be ~ 20% of the rat’s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s [Yamaguchi, 1997 #416]. Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. At each time point, three animals belonging to each group was sacrificed, the serum collected, and stored at –80oC.; ; Hybridization extract: Total RNA was isolated from approximately 50 mg of pooled liver tissue using the Nucleospin II RNA isolation kit from Clontech (Palo Alto, CA), as per the manufacturer’s instructions.; ; Labeling protocol: Labeling was performed as instructed by Affymetrix, Inc (www.affymetrix.com). In brief, 10 μg of total RNA was used for the double-stranded cDNA synthesis using the T7-oligo (dT) promoter primer kit (Affymetrix Inc.) and superscript RT II enzyme (Invitrogen). 1 μg of cDNA was labeled through invitro transcription reaction using T7 DNA polymerase in the presencef of biotin labeled ribonucleotides. The cRNA was cleaned up using the Qiagen RNeasy columns following manufactures instructions. The cRNA (20 μg) was fragmented using the fragmentation buffer supplied as part of the Gene Chip Sample Cleanup Module (Affymetrix).; ; Image analysis and raw data description: The images were analyzed using MAS V.0 software provided by Affymetrix, Inc. The raw data output consists of several metrices: Signal, Detection, Detection p-value, Stat pairs, Stat pairs used. Signal is a measure of the abundance of the transcript. Detection is call that indicates whether the transcript is detected (P, present), undetected (A, absent), or at the limit of detection (M, marginal). Detection p-value is a measure of the significance of the detection call. Stat pairs, is the number of probe pairs for a particular probe set on an array. Stat pairs used, is the number of probe pairs per probe set used in the analysis.; ; Normalized and summarized data: All chips were scaled to a target intensigty of 500 to account for differences between the replicate chips and their hybridization efficiencies using Affymetrix GENECHIP MAS V.0 software. The entire dataset is available at gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) with the accession number GSE802. Three filters were serially used to obtain the list of annotated genes that demonstrated differential expression in intensity between sham and burn injured animals. In the first filter, only genes that were flagged as ‘present’ by the MAS V.0 analysis software in at least one of the time points in all replicate chips were considered for further analysis. This step eliminated all genes for which the expression data was not reproducible between the replicate chips. The genes that passed this criterion were subjected to a second filter where ANOVA was performed to test each gene independently for a statistical difference in expression between groups (0, 1, 4, 8 and 24 h). The output of the analysis is the probability (p value) thath a difference in expression can be observed by chance i.e., probability of getting a false positive. While the occurrence of false positives can be controlled by choosing a higher significance level (0.01 or 0.001) it also concomitantly increases the false negatives. Therefore, in this study we have chosen to work with ANOVA p-value cut-off 0.05. To reduce the occurrence of the false positives, we have used the false discovery rate (FDR) method (33) which adjusts the ANOVA p-value (cut-off 0.05) while taking the dependencies between the genes into consideration. The 695 genes that demonstrated a significant ANOVA p-value were then selected and their expression values averaged. The third filter selected 339 genes that were either up-regulated or down-regulated by at least 2-fold between any one time point (1, 4, 8 or 24h) and the 0h time point (Sham control). To determine the temporal profiles in the data, gene expression values were hierarchically clustered using the dChip software (www.dChip.org). The expression values for a gene across all samples were standardized by setting the mean to 0 and standard deviation to 1. The software then builds a hierarchical cluster tree based on centroid-linkage method using Pearson correlation coefficient as the distance metric. A set of genes were assigned to cluster groups empirically based on visual inspection of their temporal expression patterns.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordstime-courseMuralikrishna,,Vemula; Francois Berthiaume; Arul Jayaraman; Martin,L,YarmushName: Muralikrishna Vemula; Email: murali_vemula@hms.harvard.edu; Phone: 617-371-4927; Fax: 617-371-4951; Department: Center for Engineering in Medicine/Department of Surgery; Institute: Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children; Address: ; City: Boston; State: MA; Zip/postal_code: 02114; Country: USA L>Y7!!]1GGeneNote-Gene Normal tissue ExpressionGSE803Public on Nov 19 20032003-11-062005-05-29gNormal human tissue expression profilingotherOrit,,Shmueli; Hila Benjamin-Rodrig; Vered Chalifa-Caspi; Ron Ophir; Michael Shmoish; Itai Yanai; Marylin Safran; Doron Lancet; Shirley Horn-SabanName: Orit Shmueli; Email: orit.shmueli@weizmann.ac.il; Phone: 972-8-9343188; Fax: 972-8-9344113; Laboratory: Doron Lancet; Department: Molecular Genetics; Institute: Weizmann Institute of Science; Address: Rehovot; City: Rehovot; State: Israel; Zip/postal_code: 76100; Country: Israel !?7!!Y'_Transcriptional studies on the deubiquitinating enzyme Ubp10GSE804Public on Feb 01 20042003-11-062005-05-29$Transcriptional analises of ubp10 null mutant, wild type and related null mutants.; Keywords; Keywordsrepeat sampleIvan,,Orlandi; Maurizio Bettiga; Lilia Alberghina; Marina VaiName: Marina Vai; Email: marina.vai@unimib.it; Phone: +39.02.6448.3531; Fax: +39.02.6448.3565; Institute: Università degli Studi di Milano-Bicocca; Address: p.zza della Scienza 2; City: Milano; Zip/postal_code: 20126; Country: Italy G@7!!qa?Expression analysis of monocytes in response to interleukins-4 and -13GSE805Public on Jul 31 20042003-11-062005-05-29Human peripheral monocytes were icultured in vitro in the absence (control) and presence of interleukins-4 and -13otherP,,Chaitidis; R Kuban; U Ungethuem; H KuhnName: Hartmut Kuhn; Email: hartmut.kuehn@charite.de; Phone: +49-30-450528040; Fax: +49-30-450528905; Department: University Clinics Charite, Humboldt University; Institute: Institute of Biochemistry; Address: Monbijoustr. 2; City: Berlin; Zip/postal_code: D-10117; Country: Germany 6AG7!!M#U LT2_hydrogen_peroxide_2mM_RNAGSE806Public on May 10 20042003-11-062005-05-29^-Gene expression Salmonella enterica sv Typhimurium LT2 post treatment with 2mM hydrogen peroxidetime-courseFelisa,,Blackmer; Jonathan,G,Frye; Pui Cheng; Steffen Porwollik; Michael McClelland; Feilsa BlackmerName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA B?7!!5#1 SL1344_heat_shock_37C_RNAGSE807Public on May 10 20042003-11-062005-05-29Gene expression in Salmonella enterica sv Typhimurium SL1344 after heat shock to 37Ctime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA C?7!!5#O SL1344_heat_shock_42C_RNAGSE808Public on May 10 20042003-11-062005-05-29Gene expression in Salmonella enterica sv Typhimurium SL1344 after heat shock to 42Ctime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Emily Proctor; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA .DI7!!g#1 14028s:rpoH_heat_shock_37C_RNAGSE809Public on May 10 20042003-11-062005-05-29Gene expression in Salmonella enterica sv Typhimurium 14028s rpoH mutant strain IB314 after heat shock to 37Ctime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA E?7!!O'1 LT2_mitomycinC_2ug/ml_DNAGSE810Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium LT2 3h after treatment with 2ug/ml mitomycin Crepeat sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA +FM7!!U#1 14028s_hydrogen_peroxide_2mM_DNAGSE811Public on May 10 20042003-11-062005-05-29^-Gene content in Salmonella enterica sv Typhimurium 14028s after treatment with 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA GA7!!E'1 CT18_MitomycinC_2ug/ml_DNAGSE812Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhi CT18 3h after treatment with 2ug/ml Mitomycin Crepeat sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA %HK7!!S#1 DT104_hydrogen_peroxide_2mM_DNAGSE813Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium DT104 after treatment with 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA )IK7!!S+1 TA100_hydrogen_peroxide_2mM_RNAGSE814Public on May 10 20042003-11-062005-05-29Gene expression in Salmonella enterica sv Typhimurium TA100 after exposure to 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA 0JK7!!i#1 TA100_hydrogen_peroxide_2mM_DNAGSE815Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium TA100 (Ames strain) after exposure to 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA kKQ7!!Q+1 TAQ100F1_hydrogen_peroxide_2mM_DNAGSE816Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium TAQ100F1 (Ames strain, cured of Fels phages, and Fels1 reintroduced) 3h after exposure to 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA dLQ7!!K#1 TAQ100F2_hydrogen_peroxide_2mM_DNAGSE817Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages, and Fels2 reintroduced) after exposure to 2mM hydrogen peroxidetime-courseJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA fMI7!!O+1 TAQ100F2_mitomycinC_2ug/ml_DNAGSE818Public on May 10 20042003-11-062005-05-29Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages and Fels2 reintroduced) 3h after exposure to 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA cNK7!!G+1 S.enterica_log_vs_overnight_DNAGSE819Public on May 10 20042003-11-062005-05-29Gene content comparison of Salmonella enterica sv Typhimurium LT2, sv Typhi CT18 and sv Typhi TY2 cultures grown to log phase versus cultures grown overnightparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA #OE7!!M+1 CT18_Rifampicin_125ug/ml_DNAGSE820Public on May 10 20042003-11-072005-05-29Gene content of Salmonella enterica sv Typhi CT18 30min after treatment with 125ug/ml Rifampicinparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA 4PC7!!q+1 TY2_Rifampicin_125ug/ml_DNAGSE821Public on May 10 20042003-11-072005-05-29Gene content of Salmonella enterica sv Typhi TY2 after 30min treatment of log phase cells with 125ug/ml Rifampicinparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA 8QM7!!o+1 TY2_Chloramphenicol_300ug/ml_RNAGSE822Public on May 10 20042003-11-072005-05-29Gene expression of Salmonella enterica sv Typhi TY2 after 30min exposure of log cells to 300ug/ml Chloramphenicolparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA {{RQ7!!}+1 TAQ100F2_hydrogen_peroxide_2mM_RNAGSE823Public on May 10 20042003-11-072005-05-29Gene expression of Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain cured of Fels prohages and subsequent reintroduction of Fels2) 30min after exposure to 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA "SG7!!I+1 TY2_hydrogen_peroxide_2mM_DNAGSE824Public on May 10 20042003-11-072005-05-29Gene content of Salmonella enterica sv Typhi TY2 3h after treatment with 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA   "U{7!!-#Aging in heads from adult Drosophila males, w118 strainGSE826Public on Jan 18 20042003-11-082005-10-28=The w1118 strain is an inbred lab sto.TM7!![+1 SARB48_hydrogen_peroxide_2mM_DNAGSE825Public on May 10 20042003-11-072005-05-29Gene content of Salmonella enterica sv Paratyphi C SARB48 5h after treatment with 2mM hydrogen peroxideparallel sampleJonathan,G,Frye; Felisa Blackmer; Pui Cheng; Steffen Porwollik; Michael McClellandName: Michael McClelland; Email: mcclelland.michael@gmail.com; Phone: 858-450-5990; Fax: 858-550-3998; Department: ; Institute: Sidney Kimmel Cancer Center; Address: 10835 Road to the Cure; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USAck widely used in genetic and transgenic studies. w1118 males have a median life span of 35 days.; ; Adult males were collected within 24 hr after eclosion. Approximately 200 flies were maintained in constant darkness in each food bottle at 25°C and 70% humidity and were transferred to fresh bottles every 3-4 days. Transcripts were harvested at d3 and d47.; ; To separate the head from the rest of the body, flies were frozen and briefly vortexed in liquid nitrogen. Fly heads were collected using a sieve which retained fly bodies. Total RNA was extracted using Trizol (GIBCO/BRL). Poly(A) RNA was isolated using Oligotex resin (Qiagen). Samples were profiled with Affymetrix DrosGenome1 GeneChips, using standard Affymetrix protocol.time-courseSige,,ZouName: Sige Zou; Email: szou@worms.ucsf.edu; Phone: 415-502-6462; Laboratory: Jan Lab; Department: Physiology Department; Institute: University of California, San Francisco; Address: ; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USA oo VS7!!''Oxidative stess in Drosophila headsGSE827Public on Jan 18 20042003-11-082005-05-29=Profiled the effect of oxidative stress on gene expression in the heads of adult Drosophila. The flies were fed sucrose with 15mM paraquat (experimental condition) or regular sucrose (control condition) for 30 hours, before harvesting at adult d3.; Keywords; Keywordsdose responseSige,,ZouName: Sige Zou; Email: szou@worms.ucsf.edu; Phone: 415-502-6462; Laboratory: Jan Lab; Department: Physiology Department; Institute: University of California, San Francisco; Address: ; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USA II3Wo7!!?+wAgenes/pathways underlying lipoprotein homeostasisGSE828Public on Nov 10 20032003-11-102005-05-29.The aim of this study was to identify novel genes and pathways underlying lipoprotein homeostasis. The liver expression profile of mild hyperlipidemic E3L transgenic mice was compared to that of the wild-type B6 mice.parallel sampleArja,,Kreeft; Corina Moen; Marten Hofker; Rune Frants; Erno Vreugdenhil; Marion Gijbels; Louis Havekes; Nicole DatsonName: Nicole Datson; Email: datson_n@lacdr.leidenuniv.nl; Phone: (+31)71-5276222; Department: Medical Pharmacology; Institute: Leiden University; Address: ; City: Leiden; Zip/postal_code: 2333 CC; Country: Netherlands 33IXY7!! 1Laminin binding/non-binding germ cellsGSE829Public on Mar 16 20042003-11-102005-07-214Comparison of laminin binding and laminin non-binding germ cellsotherNikolaus,,Schultz; F,Kent,Hamra; Karen,M,Chapman; Dana,M,Grellhesl; Jennifer,T,Cronkhite; Robert,E,Hammer; David,L,GarbersName: Nikolaus Schultz; Email: schultz@cbio.mskcc.org; Phone: 646-888-2604; Laboratory: David Garbers; Department: Green Center for Reproductive Biology Sciences; Institute: The University of Texas Southwestern Medical Center; Address: 5323 Harry Hines Blvd.; City: Dallas; State: TX; Zip/postal_code: 75390-9051; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE829/GSE829_RAW.tar }Y)7!!)1Rat germ cellsGSE830Public on Mar 16 20042003-11-102005-06-284Rat germ cellsotherF,Kent,Hamra; Nikolaus Schultz; Karen,M,Chapman; Dana,M,Grellhesl; Jennifer,T,Cronkhite; Robert,E,Hammer; David,L,GarbersName: Nikolaus Schultz; Email: schultz@cbio.mskcc.org; Phone: 646-888-2604; Laboratory: David Garbers; Department: Green Center for Reproductive Biology Sciences; Institute: The University of Texas Southwestern Medical Center; Address: 5323 Harry Hines Blvd.; City: Dallas; State: TX; Zip/postal_code: 75390-9051; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE830/GSE830_RAW.tar magnetic bead selection (Milteny rat anti mouse IgG2a+2b beads) on an AutoMacs.; HS27a cells were plated in T75 flasks at approximately 80% confluence. The next day 1.5x10E6 freshly isloated human CD14+ cells were added to the culture. At 3 days the cultures were washed 3x with Hank’s buffer to remove nonadherent monocytes. Co-cultures and HS27a cultured alone were harvested by brief trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42ºC in the presence of 0.5mM dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP. After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA from HS27a and HS27a-monocyte cocultures was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.; Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data tables.repeat sampleNorihiro,,Awaya; Mineo Iwata; Lynn Graf; Beverly Torok-StorbName: Lynn Graf; Email: lgraf@fhcrc.org; Phone: 206-667-4545; Fax: 206-667-5978; Laboratory: Torok-Storb; Department: Clinical Research Division; Institute: Fred Hutchinson Cancer Research Center; Address: 1100 Fairview Ave. N. D1-100; City: Seattle; State: WA; Zip/postal_code: 98109; Country: USA; Web_link: none ;;4[?7!!c#+%Adult aging in C. elegansGSE832Public on Jan 18 20042003-11-112005-05-29=We wished to study normal adult aging in C. elegans. We competitively hybridized a suZ-7!!;'stroma+monocytesGSE831Public on Dec 22 20032003-11-102005-10-28Gene expression of adherent cells in a coculture of the human bone marrow stromal cell line HS-27a and peripheral blood monocytes (CD14+ cells) was compared to HS-27a cultured alone. Microarray experiments were conducted using CD14+ cells from 7 healthy donors over a period of >7 months. Monocytes were isolated by ficoll separation of whole blood, followed by labelling cells with CD14 monoclonal antibody Tuek4 anderies of experimental samples (experimental variable: adult age) against a common reference sample.; ; We use the CF512 fer-15(b26) II; fem-1 (hc17) IV mutant strain, which has defective spermatids which fail to activate into spermatozoa at 25C. Culturing this strain at 25C prevented self-fertilization and therefore eliminated contributions from embryonic transcripts. CF512 animals develop an otherwise-normal germ line; their lifespan and aging are similar to wild-type animals.; ; We axenized eggs and then synchronized animals via L1 arrest. Populations were very tightly synchronized. Animals were cultured at 25C. Samples were extracted and hybridized as described in protocols at http://microarrays.org.; Keywordstime-courseColeen,T,MurphyName: Coleen,T,Murphy; Email: cmurphy@worms.ucsf.edu; Phone: 415-341-8864; Laboratory: Kenyon lab; Department: Biochemistry Department; Institute: University of California, San Francisco; Address: ; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USA .\G7!!csUAmyotrophic lateral sclerosisGSE833Public on Nov 14 20032003-11-112005-06-28yIdentification of amyotrophic lateral sclerosis (ALS) associated genes. Post mortem spinal cord grey matter from sporadic and familial ALS patients compared with controls.otherFernando,,Dangond; Robert,H,Brown; Steven,R,GullansName: Fernando Dangond; Email: fdangond@rics.bwh.harvard.edu; Phone: 617-768-8597; Department: ; Institute: Brigham and Women's Hospital Laboratories; Address: ; City: Cambridge; State: MA; Zip/postal_code: 02139; Country: USA ^]7!!ik{Saccharomyces cerevisiae engineered for xylose metabolismGSE835Public on Nov 13 20042003-11-132005-05-29eResponse of Saccharomyces cerevisiae engineered for xylose metabolism to changes in carbon source and aerationorderedYong-Su,,Jin; Jose,M,Laplaza; Thomas,W,JeffriesName: Thomas,William,Jeffries; Email: twjeffries@fs.fed.us; Phone: 608 231 9453; Fax: 608 231 9262; Laboratory: USDA, FS, Forest Products Laboratory; Institute: Institute for Microbial and Biochemical Technology; Address: One Gifford Pinchot Drive; City: Madison; State: WI; Zip/postal_code: 53705; Country: USA !!c_%7!!angiogenesisGSE837Public on Nov 28 20032003-11-192005-05-29HUVECs (human umbilical cord vein endothelial cells) are treated with the angiogenic factors VEGF-A (vascular endothelial growth factor-A) and PlGF (placental growth factor) in low or high serum media.otherName: Cristin Print; Email: cgp22@cam.ac.uk; Phone: 44-1223-333-726; Department: ; Institute: Cambridge University; Address: ; City: Cambridge; Zip/postal_code: CB2 1QP; Country: United Kingdomt^!7!!M+5EChemokine and receptor expression by WT and LIGHT-expressing tumor tissuesGSE836Public on Dec 30 20032003-11-172005-05-29`A study to compare chemokine and receptor expression by LIGHT-positive vs. negative tumor tissueparallel sampleYangxin,,Fu; Ping YuName: Yang-Xin Fu; Email: yfu@midway.uchicago.edu; Phone: 773-702-0929; Laboratory: Yang-Xin Fu; Department: Pathology; Institute: U. of Chicago; Address: ; City: Chicago; State: IL; Zip/postal_code: 60615; Country: USAmpled multiple times over periods ranging from several weeks up to 6 months. We demonstrate stable patterns of gene expression that differ between individuals. Among the genes whose expression varies by individual is a group of genes responsive to interferon stimulation. Certain individuals ( approximately 10-20% of those tested) showed higher baseline levels and lower inducibility of these genes in response to in vitro interferon stimulation. These studies demonstrate the feasibility of using DNA microarrays to measure the variations in gene expression of PBL from different individuals in response to environmental and genetic factors.otherJerald,P,Radich; Mao Mao; Sergey Stepaniants; Matt Biery; Terry Ward; Greg Schimmack; Sumire Kobayashi; Michael Carleton; John Castle; Johanna Lampe; Peter,S,Linselyhttp://www.rii.comName: Mao Mao; Email: mao_mao@merck.com; Phone: 4258237349; Department: Biology; Institute: Rosetta Inpharmatics; Address: ; City: Kirkland; State: WA; Zip/postal_code: 98034; Country: USA o`+7!!CW1Individual-specific variation of gene expression in peripheral blood leukocytesGSE838Public on Dec 31 20032003-11-202005-05-29PDNA microarray technology is used to determine gene expression profiles of various cell types, especially abnormal cells, such as cancer. By contrast, relatively little attention has been given to expression profiling of normal tissues. Here we describe studies of gene expression in peripheral blood leukocytes (PBL) from normal individuals sa ffa_7!!-#Bacillus anthracis Stern 34F2 sporulationGSE840Public on Jan 08 20042003-11-212005-06-28Timecourse from log phase growth to sporulation in Bacillus anthracis Stern 34F2time-courseHongbin,,Liu; Nicholas,H,Bergman; Brendan Thomason; Shamira Shallom; Alyson Hazen; Joseph Crossno; David,A,Rasko; Jacques Ravel; Timothy,D,Read; Scott,N,Peterson; John Yates III; Philip,C,HannaName: David Rasko; Email: drasko@tigr.org; Phone: 301-838-0000; Fax: 301-838-0208; Department: Microbial Genomics; Institute: The Institute for Genomic Research; Address: 9712 Medical Center Drive; City: Rockville; State: MD; Zip/postal_code: 20850; Country: USA [[!b]7!!G!Mutation of GATA3 in Human Breast TumorsGSE841Public on May 24 20042003-11-242005-07-19g0293T epithelial kidney cell line was infected with retrovirus containing pBabe puro empty plasmid or with pBabe puro plasmid containing either GATA3 wild type or mutation R367-L. Stable colonies were selected, grown, and their mRNAs harvested. mRNA from three independent transfections of 293T cells with the empty plasmid was pooled and used as the reference RNA. Dye flips were performed resulting in four arrays.; ; This series also contains two additional arrays (GSM13007 & GSM13008) not in the publication.otherJerry,,Usary; Charles,M,PerouName: Charles Perou; Email: cperou@med.unc.edu; Phone: 919-843-5740; Fax: 919-843-5718; Department: CB#7295; Institute: University of North Carolina at Chapel Hill; Address: 102 Mason Farm Road; City: Chapel Hill; State: NC; Zip/postal_code: 27599-7295; Country: USA VV&c7!!]'m}Naive, EAE placebo-treated and EAE 1,25(OH)2D3-treated groupsGSE842Public on Dec 01 20032003-11-252005-05-29B10.PL mice with severe (stage 2.5-3) experimental autoimmune encephalomyelitis were treated with placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA was extracted for microarray analysis. Naive mice serve as controls. Individual samples were hybridized to individual microarrays.; Keywords; Keywords; Keywords; Keywordsrepeat sampleKaren,M,Spach; Laura,B,Pedersen; Faye,E,Nashold; Brian,S,Yandell; Tsuyoshi Kayo; Tomas,A,Prolla; Colleen,E,HayesName: Karen,Marie,Spach; Email: spach@nutrisci.wisc.edu; Phone: 608-263-5376; Fax: 608-262-3453; Laboratory: Colleen Hayes; Department: Nutritional Sciences / Biochemistry; Institute: University of Wisconsin-Madison; Address: 433 Babcock Drive; City: Madison; State: WI; Zip/postal_code: 53706-1544; Country: USA +d]7!!1#CLongitudinal analysis of developing neointimal vascular proliferation and pulmonary hypertension in ratsGSE843Public on Dec 02 20032003-11-262005-05-29%P6 timepoints: Day 0 (normal controls), progressively developing neointimal vascular proliferation and pulmonary hypertension in vehicle treated animals (Days 14, 21, 28 and 35) and triptolide-treated animals at Day 35.; ; Replicates:; 6 for Day 0 (normal); 2 for Daty 14; 3 each for Days 21, 28, 35 and Triptolide -treated at day 35 (T); time-courseName: Peter,N.,Kao; Email: peterkao@stanford.edu; Phone: 650-725-0570; Fax: 650-725-5489; Department: Pulmonary and Critical Care Medicine; Institute: Stanford University Medical Center; Address: 300 Pasteur Drive; City: Stanford; State: CA; Zip/postal_code: 94305-5236; Country: USA Gf'7!! ;YPTSD Raw DataGSE845Public on Nov 20 20042003-11-282005-05-29VPTSD - Posttraumatic stress disorder.; 33 samples taken from PMBCs o5e37!!'+Control LG vs Px LGGSE844Public on Nov 30 20032003-11-262005-05-29,Control rat lacrimal gland samples representing a normal unoperated, a sham, and paired contralateral controls. Experimental LG samples representing paired and unpaired contralateral controls. Paired contralateral control LGs represent LG from the same animal, one side was operated and the other side unoperated.repeat sampleDoan,H,Nguyen; Hiroshi Toshida; Jill Schurr; Roger,W,Beuerman; Beuerman,W,RogerName: Doan Nguyen; Email: dnguye@lsuhsc.edu; Phone: 504-412-1200; Department: ; Institute: LSU Eye Center/LSUHSC; Address: ; City: New Orleans; State: LA; Zip/postal_code: 70112; Country: USAf survivors of psychological trauma, in two time points: in ER, few hours after the truma, and four months later. Some of the patients devepled chronic PTSD (17 samples) and others recovered and set to be the Control group (16 samples). This is the raw data consists of 12,600 probes from U95A chip.; Samples are labeled with 3 tags: P/C for PTSD or Control, ER/M4 - for time point of sample, D/ND for Decrement or Non-decrement symptoms over time. (e.g. sample 23C-M4-D was taken 4 months after trauma from patient 23 which belongs to the control group and showed decrease in symptoms) . Samples include the expression value, the GeneBank accession number and Affymetrix indication of valid calls.otherRonnen,H,Segman; Noa Shefi; Tanya Goltser; Nir Friedman; Naftali Kaminski; Arieh ShalevName: Noa Shefi; Email: shefi@cs.huji.ac.il; Phone: 972-3-6964979; Laboratory: Computational Biology; Department: Computer Science; Institute: Hebrew University; Address: ; City: Jerusalem; Zip/postal_code: 91904; Country: Israel vh57!!1+IHS to HR progressionGSE847Public on Jan 01 20042003-12-022005-05-29X(Seven pairs of hormone sensitive and hormone refractory prostate cancer xenograftsparallel sampleCharlie,,Chen; Charles SawyersName: Charlie Chen; Email: chenc@ucla.edu; Phone: 310-206-5111; Institute: University of California at Los Angeles; Address: ; City: Los Angeles; State: CA; Zip/postal_code: 90095; Country: USAg!7!!{'gConversionGSE846Public on Jan 01 20042003-12-022005-05-29X(AR overexpression converts antagonists to weak agonistsdose responseCharlie,,Chen; Derek Welsbie; Charles SawyersName: Charlie Chen; Email: chenc@ucla.edu; Phone: 310-206-5111; Institute: University of California at Los Angeles; Address: ; City: Los Angeles; State: CA; Zip/postal_code: 90095; Country: USA miq7!!y])E2 and SERM Treatment of MCF-7 Breast Cancer CellsGSE848Public on May 01 20042003-12-022006-09-25xMCF-7 breast cancer cells were treated with E2, ICI 182,789 (ICI), Raloxifene (Ral), and/or trans-hydroxytamoxifen (TOT) for 8 or 48 h. Duplicate samples are labeled set A or set B.otherJonna,,Frasor; Benita,S,KatzenellenbogenName: Jonna Frasor; Email: jfrasor@life.uiuc.edu; Phone: (217)333-7838; Laboratory: Benita S. Katzenellenbogen; Department: Molecular and Integrative Physiology; Institute: University of Illinois; Address: ; City: Urbana; State: IL; Zip/postal_code: 61801; Country: USA 99CjY7!!-Genomic profile of the mouse intestineGSE849Public on Dec 04 20032003-12-032005-05-298 week-old male Hsd:ICR(CD-1) mice were fed ad libitum a standard chow (Harlan Teklad diet 2018S) and housed in groups of five. Animals were then divided into 3 pools (n=10) and sacrificed. The small intestine was extracted and divided into three sections, where the first 2-3 cm after the stomach comprised the duodenum, the middle third the jejunum, and the section before the ileo-ceco-colic junction comprised the ileum. Colon was not divided into proximal and distal sections and was treated as a single intestinal section.otherDavid,M,Mutch; Pascale Anderle; Muriel Fiaux; Robert Mansourian; Karine Vidal; Walter Wahli; Gary Williamson; Matthew-Alan RobertsName: Pascale Anderle; Email: Pascale.Anderle@isrec.unil.ch; Phone: +41 692 5859; Department: ; Institute: ISREC; Address: ; City: Epalinges; Zip/postal_code: 1066; Country: Switzerland E0E_l-7!!]'9sliver, 48h sugarGSE851Public on Feb 09 20042003-12-052005-10-28@Mice used in this study were 129/sv males, 8-15 weeks of age, which were housed individually and received water ad libitum. Normal fed animals were fed before and during the 48h experiment with standard food ad libitum. Sugar fed animals were fed before the experiment with standard food ad libitum and during the 48h experiment with 50% (w/v) sugar solution (40% glucose, 10% sucrose). Mice Lkk7!!o/%Effect 14-3-3 mutation on mRNA levels in yeast.GSE850Public on Dec 01 20042003-12-052005-05-29 Studies on the effect of a bmh2 mutation on the genome-wide steady-state mRNA levels in Saccharomyces cerevisiae.otherPaul,,van HeusdenName: Paul van Heusden; Email: Heusden@RULBIM.Leidenuniv.nl; Phone: 31 71 5274996; Institute: Institute of Biology; Address: Wassenaarseweg 64; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlandswere killed by CO2 asphyxiation. The livers were snap-frozen in liquid nitrogen and stored at -80 degrees C. Total RNA was prepared using the Nucleospin RNA L kit (Macherey-Nagel, Düren, Germany), with an additional step in which the final eluate was used for a subsequent elution step. PolyA RNA was extracted with the Ambion (Ambion Inc, Austin, USA) Purist kit according to the manufacturer's protocols. Equal amounts of polyA RNA were pooled to generate pools of all animals. Pool1, normal; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleMatthias,,Bauer; Anne,C,Hamm; Joerg,D,Katzenberger; Michael,J,Pankratz; Anne,C,Gählerhttp://www.fzk.de/microarray; www.fzk.de/microarrayName: Michael,J.,Pankratz; Email: michael.pankratz@itg.fzk.de; Phone: ++49 +7247 82 6087; Fax: ++49 +7247 82 3354; Laboratory: Pankratz; Department: Institute of Genetics; Institute: Forschungszentrum Karlsruhe; Address: P.O. Box 3640; City: Karlsruhe; Zip/postal_code: 76021; Country: Germany; Web_link: www.fzk.de/microarrayxperiment. Mice were killed by CO2 asphyxiation. The livers were snap-frozen in liquid nitrogen and stored at -80 degrees C. Total RNA was prepared using the Nucleospin RNA L kit (Macherey-Nagel, Düren, Germany), with an additional step in which the final eluate was used for a subsequent elution step. PolyA RNA was extracted with the Ambion (Ambion Inc, Austin, USA) Purist kit according to the manufacturer's protocols. Equal amounts of polyA RNA were pooled to generate pools of all animals. Pool1, normal; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleMatthias,,Bauer; Anne,C,Hamm; Joerg,D,Katzenberger; Michael,J,Pankratzhttp://www.fzk.de/microarray; www.fzk.de/microarrayName: Michael,J.,Pankratz; Email: michael.pankratz@itg.fzk.de; Phone: ++49 +7247 82 6087; Fax: ++49 +7247 82 3354; Laboratory: Pankratz; Department: Institute of Genetics; Institute: Forschungszentrum Karlsruhe; Address: P.O. Box 3640; City: Karlsruhe; Zip/postal_code: 76021; Country: Germany; Web_link: www.fzk.de/microarray Q#n17!!'sliver, 24h starvedGSE853Public on Feb 09 20042003-12-052005-10-28@Mice used in this study were 129/sv males, 8-15 weeks of age, which were housed individually and received water ad libitum. Normal fed animals were fed before and during the 48h experiment with standard food ad libitum. Starved animals were fed before the experiment with standard food ad libitum and were starved during the 24h e#m17!!'sliver, 48h starvedGSE852Public on Feb 09 20042003-12-052005-10-28@Mice used in this study were 129/sv males, 8-15 weeks of age, which were housed individually and received water ad libitum. Normal fed animals were fed before and during the 48h experiment with standard food ad libitum. Starved animals were fed before the experiment with standard food ad libitum and were starved during the 48h experiment. Mice were killed by CO2 asphyxiation. The livers were snap-frozen in liquid nitrogen and stored at -80 degrees C. Total RNA was prepared using the Nucleospin RNA L kit (Macherey-Nagel, Düren, Germany), with an additional step in which the final eluate was used for a subsequent elution step. PolyA RNA was extracted with the Ambion (Ambion Inc, Austin, USA) Purist kit according to the manufacturer's protocols. Equal amounts of polyA RNA were pooled to generate pools of all animals. Pool1, normal; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleMatthias,,Bauer; Anne,C,Hamm; Joerg,D,Katzenberger; Michael,J,Pankratzhttp://www.fzk.de/microarray; www.fzk.de/microarrayName: Michael,J.,Pankratz; Email: michael.pankratz@itg.fzk.de; Phone: ++49 +7247 82 6087; Fax: ++49 +7247 82 3354; Laboratory: Pankratz; Department: Institute of Genetics; Institute: Forschungszentrum Karlsruhe; Address: P.O. Box 3640; City: Karlsruhe; Zip/postal_code: 76021; Country: Germany; Web_link: www.fzk.de/microarrayng, n=10), 14 months (mid-aged, n=10), and 24 months (aged, n=10) were trained sequentially on two tasks: Morris Spatial Water Maze (SWM) and Object Memory Task (OMT). The training/testing sequence lasted 7 d, and hippocampal tissue was collected 24 hr later. Training and testing occured on each day except for days 2 and 3 of the 7 d sequence.; (01/10/05: Series was updated to correct mislabeling of all sample signal values within the Young Treatment Group); Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleEric,M,Blalock; Kuey-Chu Chen; Keith Sharrow; James,P,Herman; Nada,M,Porter; Thomas,C,Foster; Phillip,W,LandfieldName: Eric,M,Blalock; Email: emblal@uky.edu; Phone: 859-323-8033; Fax: 859-323-1981; Laboratory: Landfield; Department: Molecular and Biomedical Pharmacology; Institute: University of Kentucky; Address: 800 Rose St.; City: Lexington; State: KY; Zip/postal_code: 40475; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE854/GSE854_RAW.tar _Sp7!!{#Qg12hr, 1d, 3d, and 5d exposure of beta-amyloid to astrocytesGSE856Public on Dec 09 20032003-12-082005-05-29Cortical type-I astrocytes were cultured on the beta-amyloid peptide 25-35 fragment for 12hr, 1d, 3d, and 5d.; Keywordstime-courseWilliam,C,Spencer; David,R,CanningName: William,Clayton,Spencer; Email: david.canning@murraystate.edu; Phone: 270 762-5475; Fax: 270 762-2788; Laboratory: David Canning; Department: Department of Biological Sciences; Institute: Murray State University; Address: P.O. Box 9; City: Murray; State: KY; Zip/postal_code: 42071; Country: USAoW7!!'o?1Gene Microarrays in Hippocampal AgingGSE854Public on Jan 10 20052003-12-052005-06-28W_Male Fischer 344 rats aged 4 months (youHowever, motor deterioration continued unabated. Microarray analysis of global gene expression revealed that many genes significantly up- or down-regulated in untreated R6/2 mice had returned towards normal levels after treatment. Thus dysregulated gene expression was reversed by the combination treatment in the R6/2 mice and probably underlies the observed improvements in cognitive function. Our study shows that cognitive decline caused by a genetic mutation can be slowed by a combination drug treatment, and gives hope that cognitive symptoms in HD can be treated.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedA,J,Morton; Mark,J,Hunt; Angela,K,Hodges; Paul,D,Lewis; Stephen,B,Dunnett; Lesley JonesName: Lesley Jones, Angela Hodges; Email: jonesl1@cf.ac.uk, Angela.Hodges@iop.kcl.ac.uk; Phone: +44 2920 745175; Department: Psychological Medicine; Institute: Cardiff University School of Medicine; Address: Heath Park; City: Cardiff; Zip/postal_code: CF14 4XN; Country: United Kingdom II+qA7!!#;GTriple treatment R6/2 miceGSE857Public on Jun 01 20042003-12-082005-12-21Huntington’s disease is a genetic disease caused by a single mutation. It is characterised by progressive movement, emotional and cognitive deficits. R6/2 transgenic mice carrying the Huntington’s disease mutation have a progressive neurological phenotype, including deterioration in cognitive function. The mechanism underlying the cognitive deficits in R6/2 mice is unknown, but dysregulated gene expression, reduced neurotransmitter levels and abnormal synaptic function are present before the cognitive decline becomes pronounced. Our goal here was to ameliorate the cognitive phenotype in R6/2 mice using a combination drug therapy (tacrine, moclobemide and creatine) aimed boosting neurotransmitter levels in the brain. Treatment from 5 weeks of age prevented deterioration in two different cognitive tasks until at least 12 weeks. (Macherey-Nagel, Düren, Germany), with an additional step in which the final eluate was used for a subsequent elution step. PolyA RNA was extracted with the Ambion (Ambion Inc, Austin, USA) Purist kit according to the manufacturer's protocols. Equal amounts of polyA RNA were pooled to generate pools of all animals. Pool1, normal; Keywords; Keywords; Keywords; Keywords; Keywords; ; This SuperSeries is composed of the following subset Series:; GSE851: liver, 48h sugar; GSE852: liver, 48h starved; GSE853: liver, 24h starvedSuperSeriesMatthias,,Bauer; Anne,C,Hamm; Melanie Bonaus; Michael,J,Pankratz; Joerg,D,Katzenberger; Anne,C,Gählerhttp://www.fzk.de/microarrayRefer to individual SeriesName: Michael,J.,Pankratz; Email: michael.pankratz@itg.fzk.de; Phone: ++49 +7247 82 6087; Fax: ++49 +7247 82 3354; Laboratory: Pankratz; Department: Institute of Genetics; Institute: Forschungszentrum Karlsruhe; Address: P.O. Box 3640; City: Karlsruhe; Zip/postal_code: 76021; Country: Germany; Web_link: www.fzk.de/microarray mjmqs57!!-;YPTSD Normalized dataGSE860Public on Nov 20 20042003-12-092005-05-29VPTSD - Posttraumatic stress disorder.; 33 samples taken from PMBCs of survivors of psychological trauma, in two time points: in ER, few hours after th r=7!!#YEAMouse feeding experimentGSE858Public on Feb 09 20042003-12-082006-04-25@Mice used in this study were 129/sv males, 8-15 weeks of age, which were housed individually and received water ad libitum. Normal fed animals were fed before and during the 48h experiment with standard food ad libitum. Sugar fed animals were fed before the experiment with standard food ad libitum and during the 48h experiment with 50% (w/v) sugar solution (40% glucose, 10% sucrose). Mice were killed by CO2 asphyxiation. The livers were snap-frozen in liquid nitrogen and stored at -80 degrees C. Total RNA was prepared using the Nucleospin RNA L kit e truma, and four months later. Some of the patients devepled chronic PTSD (17 samples) and others recovered and set to be the Control group (16 samples). This is the normalized active genes: 4512 probes from U95A chip.; The raw data is available in series GSE845.; Samples are labeled with 3 tags: P/C for PTSD or Control, ER/M4 - for time point of sample, D/ND for Decrement or Non-decrement symptoms over time. (e.g. sample 23C-M4-D-Norm was taken 4 months after trauma from patient 23 which belongs to the control group and showed decrease in symptoms) . Samples include the expression value, the GeneBank accession number and Affymetrix indication of valid calls.; Keywords; Keywords; KeywordsotherRonnen,H,Segman; Noa Shefi; Tanya Goltser; Nir Friedman; Naftali Kaminski; Arieh ShalevName: Noa Shefi; Email: shefi@cs.huji.ac.il; Phone: 972-3-6964979; Laboratory: Computational Biology; Department: Computer Science; Institute: Hebrew University; Address: ; City: Jerusalem; Zip/postal_code: 91904; Country: Israel HH4t#7!!''IaDifferential expression of Aspergillus genes as a result of disrupting maf1GSE861Public on Dec 09 20042003-12-092005-05-29We identified a 14-3-3 homolog (maf1) in an EST library made under conditions conducive to aflatoxin biosynthesis. Disruption of this gene in A. flavus by site directed mutagenesis abolished aflatoxin production. The maf1 mutant was morphologically similar to wild type but had reduced conidiation and growth on some media. DNA expression analysis of the wild type and maf1 mutant revealed that the mutation affected the expression profile of a set of genes associated with aflatoxin production.; Keywords; Keywords; Keywordsrepeat sampleAhmad,M,Fakhoury; Gary,A,PayneName: Ahmad Fakhoury; Email: amfakhou@siu.edu; Phone: 919-515-6995; Laboratory: Payne; Department: Plant Pathology; Institute: North Carolina State University; Address: ; City: Raleigh; State: NC; Zip/postal_code: 27695; Country: USA FuU7!! 'q?BR effects on WT and yucca seedlingsGSE862Public on Aug 31 20042003-12-092005-10-28Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hoursrepeat sampleJennifer,L,Nemhauser; Todd,C,Mockler; Joanne ChoryName: Jennifer Nemhauser; Email: nemhauser@salk.edu; Phone: 8584534100 x1128; Laboratory: Chory; Department: PBIO; Institute: Salk Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA wg7!!+aCNrf2 Knockout vs. Wildtype mice, liver sampleGSE864Public on Dec 16 20032003-12-vA7!!_'%?Auxin effects on seedlingsGSE863Public on Jul 31 20042003-12-092005-10-28Five-day old light-grown Arabidopsis seedlings were immersed 10 µM indole-3-acetic acid (auxin) or waterrepeat sampleYunde,,Zhao; Xinhua Dai; Helen,E,Blackwell; Stuart,L,Schreiber; Joanne ChoryName: Jennifer Nemhauser; Email: nemhauser@salk.edu; Phone: 8584534100 x1128; Laboratory: Chory; Department: PBIO; Institute: Salk Institute; Address: ; City: La Jolla; State: CA; Zip/postal_code: 92037; Country: USA102005-05-29In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver of Nrf2 knockout and wildtype mice at 5 month age.; Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13431, 13435) for the female Nrf2 wildtype group, two replicates (GSM 13439, 13441) for the male Nrf2 wildtype group, two replicates (GSM 13436, 13437) for the female Nrf2 knockout group, and two replicates (GSM 13438, 13440) for the male Nrf2 knockout group.parallel sampleJiang,,Li; Thor,D,Stein; Jeffrey,A,JohnsonName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USA vvxi7!! +aCNrf2 Knockout vs. Wildtype mice, spleen sampleGSE865Public on Dec 16 20032003-12-102005-05-29In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the spleen of Nrf2 knockout and wildtype female mice at 5 month age.; Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13470, 13472) for the female Nrf2 wildtype group and two replicates (GSM 13467, 13469) for the female Nrf2 knockout group.; parallel sampleJiang,,Li; Thor,D,Stein; Jeffrey,A,JohnsonName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USA  y7!!-cCP 1hrGSE866Public on Feb 24 20042003-12-102005-10-28embryos exposed to 40 uM 4-hydroperoxycyclophosphamide (4CP) for 1 hour at 37°CotherName: Richard Beyer; Email: dbeyer@u.washington.edu; Phone: 206-616-7378; Laboratory: Center for Ecogenetics and Environmental Health; Department: ; Institute: University of Washington; Address: 4225 Roosevelt Way, NE, Suite 100; City: Seattle; State: WA; Zip/postal_code: 98105; Country: USA; Web_link: http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html SzK7!!9+aCNrf2 Knockout vs. Wildtype miceGSE867Public on Dec 16 20032003-12-102006-04-25燮In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver (GSE864) and spleen (GSE865) of Nrf2 knockout and wildtype mice at 5 months of age.; ; This SuperSeries is composed of the following subset Series:; GSE864: Nrf2 Knockout vs. Wildtype mice, liver sample; GSE865: Nrf2 Knockout vs. Wildtype mice, spleen sampleparallel sampleJiang,,Li; Thor,D,Stein; Jeffrey,A,JohnsonName: Jiang Li; Email: jli2@pharmacy.wisc.edu; Phone: 608-2624789; Fax: 608-2625345; Laboratory: Jeffrey A. Johnson; Department: School of Pharmacy; Institute: University of Wisconsin Madison; Address: 777 Highland Ave.; City: Madison; State: WI; Zip/postal_code: 53705; Country: USAked hypophosphatemic) mice at 5 weeks of age. The mice were C57BL/6J. Normal wild-type mice, hemizygous Hyp (Hyp/Y) male mice, or heterozygous (Hyp/+) female mice were used. The gene is dominant, so that the two genders are equally affected with low renal retention of phosphate and severity of their bone disease. RNA from 3 mice were pooled for each microarray. The arrays were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2001, Affymetrix, Inc., Santa Clara, CA), rev. 1, Part number 701021. The data for each array were scaled to an average signal value of 500 for all genes on the array.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleRalph,A,Meyer; Martha,H,MeyerName: Ralph,A.,Meyer; Email: ralpham@aol.com; Laboratory: Cannon Research Center, Rm. 304; Department: Orthopaedic Research Laboratory; Institute: Carolinas Medical Center; Address: P.O. Box 32861; City: Charlotte; State: NC; Zip/postal_code: 28232-2861; Country: USA |7!!cHS 1hrGSE869Public on Feb 24 20042003-12-102005-10-28embryos exposed to 43°C for 15 minutes (HS) followed by 1 hour at 37°CotherName: Richard Beyer; Email: dbeyer@u.washington.edu; Phone: 206-616-7378; Laboratory: Center for Ecogenetics and Environmental Health; Department: ; Institute: University of Washington; Address: 4225 Roosevelt Way, NE, Suite 100; City: Seattle; State: WA; Zip/postal_code: 98105; Country: USA; Web_link: http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html0{7!!i'G#Mouse Kidney - Effect of Low Phosphate Diet in Normal and Hyp MiceGSE868Public on May 10 20042003-12-102005-05-29>This is a study of the change in gene expression in mouse kidney after feeding control (1.0% P) or low phosphate diet (0.03% P) for 3 or 5 days to normal or Hyp (X-lin }7!!cHS 5hrGSE870Public on Feb 24 20042003-12-102005-10-28embryos exposed to 43°C for 15 minutes (HS) followed by 5 hours at 37°CotherName: Richard Beyer; Email: dbeyer@u.washington.edu; Phone: 206-616-7378; Laboratory: Center for Ecogenetics and Environmental Health; Department: ; Institute: University of Washington; Address: 4225 Roosevelt Way, NE, Suite 100; City: Seattle; State: WA; Zip/postal_code: 98105; Country: USA; Web_link: http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html  ~S7!!_}iu1Muscle, normal extraocular, profileGSE873Public on Dec 31 20032003-12-112005-07-20Molecular definition of human extraocular muscles (EOM). Human EOM were compared with limb (quadriceps femoris) muscle.; Keywords; Keywords; Keywords; Keywords; KeywordsotherManuel,D,Fischer; J,R,Gorospe; Marina Bakay; Daniel Kjellgren; Fatima Pedrosa-Domellof; Eric,P,Hoffman; Tejvir,S,Khuranahttp://www.uphs.upenn.edu/pmi/members/khurana/Name: Dominik Fischer; Email: fischerd@mail.med.upenn.edu; Phone: +1 215 573 2640; Laboratory: Khurana Lab; Department: ; Institute: Pennsylvania Muscle Institute; Address: ; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE873/GSE873_RAW.tar RR4]7!!1UGenome-wide regulation by TFIID and SAGAGSE885Public on Feb 27 20042003-12-112005-05-29VTFIID and SAGA share a common set of TAFs, regulate chromatin, and deliver TBP to promoters. Here we examine their relationship within the context of the Saccharomyces cerevisiae genome-wide regulatory network. We find that while TFIID and SAGA make overlapping contributions to the expression of all genes, TFIID function pj7!!#1KM109GSE884Public on Feb 12 20042003-12-112005-05-29Time-course experiment of healthy primary skeletal muscle cells; KM109time-courseEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlandsredominates at ~90% and SAGA at ~10% of the measurable genome. Strikingly, SAGA-dominated genes are largely stress-induced and TAF-independent, and are down-regulated by the coordinate action of a variety of chromatin, TBP, and RNA polymerase II regulators. In contrast, the TFIID-dominated class is less regulated, but is highly dependent upon TAFs including those shared between TFIID and SAGA. These two distinct modes of transcription regulation might reflect the need to balance inducible stress responses with the steady output of housekeeping genes.; Keywords; Keywords; KeywordsotherKathryn,L,Huisinga; B. Franklin Pughhttp://www.molecule.org/content/article/abstract?uid=PIIS1097276504000875Name: B. Franklin,L,Pugh; Email: bfp2@psu.edu; Laboratory: B. Franklin Pugh; Department: Biochemistry and Molecular Biology; Institute: Pennsylvania State University; Address: 452 N. Frear; City: University Park; State: PA; Zip/postal_code: 16803; Country: USA; Web_link: http://www.bmb.psu.edu/faculty/pugh/pugh.html TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G). Approximately 20% of yeast genes contain a TATA box. Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters. Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions.; A strain containing amino terminal HA-tagged TBP and its parental untagged counterpart BY4741 (Resgen) were grown at 23?C in CSM to OD600; Keywords; KeywordsotherAndrew,D,Basehoar; Sara,J,Zanton; B Franklin PughName: Frank Pugh; Email: bfp2@psu.edu; Laboratory: Pugh Laboratory; Department: Biochemistry and Molecular Biology; Institute: The Pennsylvania State University; Address: 452 North Frear Laboratory; City: University Park; State: PA; Zip/postal_code: 16802; Country: USA # 7!!/cCP 5hrGSE888Public on Feb 24 20042003-12-112005-10-28embryos exposed to 40 uM 4-hydroperoxycyclophosphamide (4CP) for 5 hours at 37°CotherName: Richard Beyer; Email: dbeyer@u.washington.edu; Phone: 206-616-7378; Laboratory: Center for Ecogenetics and Environmental Health; Department: ; Institute: University of Washington; Address: 4225 Roosevelt Way, NE, Suite 100; City: Seattle; State: WA; Zip/postal_code: 98105; Country: USA; Web_link: http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.htmlsI7!!w%Mus musculus cornea experimentGSE887Public on Jan 02 20042003-12-112005-05-292PURPOSE: To provideN7!!o'Identification and distinct regulation of yeast TATA-box containing genesGSE886Public on Mar 05 20042003-12-112005-05-29Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea.otherBarbara,L,Norman; Janine,A,Davis; Joram,P,PiatigorskyName: Barbara Norman; Email: norman@helix.nih.gov; Phone: 301-402-4342; Fax: 301-402-0781; Laboratory: Laboratory of Molecular & Developmental Biology; Department: National Eye Institute; Institute: National Institutes of Health; Address: MSC2730, 9000 Rockville Pike; City: Bethesda; State: MD; Zip/postal_code: 20892; Country: USA v 7!!='+Gene expression profile at 1hr after common bile duct ligationGSE889Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 1hr after common bile duct ligation. Hybridization was carried out four times including color swap to eliminate any dye bias.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan v 7!!='+Gene expression profile at 3hr after common bile duct ligationGSE890Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 3hr after common bile duct ligation. Hybridization was carried out four times including color swap to eliminate any dye bias.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan x 7!!?'+Gene expression profile at 12hr after common bile duct ligationGSE891Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 12hr after common bile duct ligation. Hybridization was carried out four times including color swap to eliminate any dye bias.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan zz7!!a'+Gene expression profile at 12hr after ANIT administrationGSE892Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 12hr after alpha-naphtylisothiocyanate administration. Hybridization was carried out four times including color swap to eliminate any dye bias.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan zz7!!a'+Gene expression profile at 18hr after ANIT administrationGSE893Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 18hr after alpha-naphtylisothiocyanate administration. Hybridization was carried out four times including color swap to eliminate any dye bias.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan h 7!!-'+ Gene expression profile at 24hr after ANIT administrationGSE894Public on Dec 13 20032003-12-122005-05-29Gene expression profile at 24hr after alpha-naphtylisothiocyanate administration. Hybridization was carried out four times including color swap.repeat sampleKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan t 7!!%#1 HPP4_cDNAGSE896Public on Feb 12 20042003-12-122005-05-29Time series experiment on healthy human primary skeletal muscle cells (HPP4)time-courseEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlandsu !7!!%#1 KM108_cDNAGSE895Public on Feb 12 20042003-12-122005-05-29Timecourse experiment of healthy human primary skeletal muscle cells (KM108)time-courseEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlands tt 7!!1'1 Molecular profiles of dystrophin-deficient and normal murine muscleGSE897Public on Apr 12 20042003-12-122005-05-29Expression profiles of six skeletal muscle types in mdx, mdx5cv and wildtype mice.otherJudith,N,Haslett; Alvin,T,Kho; Mei Han; Despina Sanoudou; Jay,M,Volinski; Alan,H,Beggs; Isaac,S,Kohane; Louis,M,Kunkel; Issac,S,KohaneName: Judith Haslett; Email: mhan@enders.tch.harvard.edu; Phone: +1-617-355-7576; Department: ; Institute: Harvard Medical School; Address: ; City: Boston; State: MA; Zip/postal_code: 02115; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE897/GSE897_RAW.tarexposure but without ligation of the common bile duct. After the CBDL or sham operation, animals were allowed access to food and water ad libitum.; Groups of three rats were sacrificed under ether anesthesia at 1, 3 and 12 hr after the CBDL or sham operation. At the time of sacrifice, the right lateral liver lobe was removed and flash-frozen in liquid nitrogen and stored at -80 °C.; Total RNA isolated from frozen livers using TRIzol reagent (Invitrogen Co., Carlsbad, CA) was mixed to minimize variation among animals. Poly(A) RNA was purified using Oligotex-dT30 (Takara Shuzo Co., Ltd., Kyoto, Japan) in accordance with manufacturer’s instructions. Fluorescence-labeled probes were prepared by reverse transcription using a superscript II reverse transcriptase (Invitrogen Co.) and cyanine-3- and cyanine-5-dUTP (Perkin-Elmer Inc., Wellesley, MA). Poly(A) RNAs derived from rats that has undergone CBDL and from those that has undergone a sham operation were labeled with cyanine-3 and cyanine-5, respectively, and vise varsa. Fluorescence-labeled probes were purified using a MinElute PCR Products Purification Kit (Quiagen GmbH, Hilden, Germany) in accordance with manufacturer’s instructions. Each purified probe was suspended in hybridization buffer containing 1.6 mg/mL poly(A) (Roche Diagnostics, Basel, Switzerland) and yeast tRNA (Roche Diagnostics), 0.67 mg/mL herring sperm, 16% 20 x SSC and 0.3% SDS and applied to a cDNA microarray containing 1,800 rat genes on a slide glass (Asahi Technoglass Co., Tokyo, Japan). Three house-keeping genes (GAPDH, HPRT and b-actin) and rat unrelated traits (Lambda DNA) were also spotted on the slide as internal positive and negative controls, respectively.; Hybridization was carried out twice to eliminate any dye bias. In one experiment, duplicate slides were hybridized with probes derived from CBDL and control rats that had been labeld with cyanine-3 and cyanine-5, respectively. In a replicate experiment, other duplicate slides were hybridized with probes derived from CBDL rats and control rats that had been labeled with cyanine-5 and cyanine-3, respectively (color swap). Then, the slides were cover-slipped and incubated in a sealed chamber (Asahi Technoglass Co.) for 16 hrs under a humidified (65 °C) condition. After being washed in low-stringency buffer (2 x SSC and 0.1% SDS), high-stringency buffer (0.2 x SSC and 0.1% SDS) and 0.2 x SSC and then rinsing with 99.5% ethanol, the slide was dried by centrifugation at low speed and used for scanning.; Fluorescence was scanned by using a ScanArray 4000 (Packard BioChip Technologies, Billerica, MA) and quantified by using QuantArray Software (Packard BioChip Technologies, Billerica, MA).; time-courseKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan H W7!!#+ Common bile duct ligation time-courseGSE898Public on Dec 13 20032003-12-122005-10-28Male Sprague-Dawley rats weighing 250-300 g were purchased from Japan SLC Co. (Shizuoka, Japan). The animals were housed under a daily controlled 12-h light and 12-h dark cycle at 23 °C with free access to rat chow (Japan SLC Co.) and water for 1 week prior to the experiments.; Rats were laparotomized under ether anesthesia in each experiment, and the common bile duct of each rat was ligated between the liver hilus and small intestine. Control animals underwent a sham operation with te) dissolved in olive oil (7.5 mg/mL). Control animals received an injection of the same volume of olive oil.; Groups of three rats were sacrificed under ether anesthesia at 12, 18, 24 hr after ANIT or olive oil administration. At the time of sacrifice, the right lateral liver lobe was removed and flash-frozen in liquid nitrogen and stored at -80 °C. Total RNA isolated from frozen livers using TRIzol reagent (Invitrogen Co., Carlsbad, CA) was mixed to minimize variation among animals. Poly(A) RNA was purified using Oligotex-dT30 (Takara Shuzo Co., Ltd., Kyoto, Japan) in accordance with manufacturer’s instructions. Fluorescence-labeled probes were prepared by reverse transcription using a superscript II reverse transcriptase (Invitrogen Co.) and cyanine-3- and cyanine-5-dUTP (Perkin-Elmer Inc., Wellesley, MA). Poly(A) RNAs derived from rats that has administrated ANIT and from those that has administrated olive oil were labeled with cyanine-5 and cyanine-3, respectively, and vise varsa. Fluorescence-labeled probes were purified using a MinElute PCR Products Purification Kit (Quiagen GmbH, Hilden, Germany) in accordance with manufacturer’s instructions. Each purified probe was suspended in hybridization buffer containing 1.6 mg/mL poly(A) (Roche Diagnostics, Basel, Switzerland) and yeast tRNA (Roche Diagnostics), 0.67 mg/mL herring sperm, 16% 20 x SSC and 0.3% SDS and applied to a cDNA microarray containing 1,800 rat genes on a slide glass (Asahi Technoglass Co., Tokyo, Japan). Three house-keeping genes (GAPDH, HPRT and b-actin) and rat unrelated traits (Lambda DNA) were also spotted on the slide as internal positive and negative controls, respectively.; Hybridization was carried out twice to eliminate any dye bias. In one experiment, duplicate slides were hybridized with probes derived from rats which were administrated ANIT and control rats that had been labeld with cyanine-3 and cyanine-5, respectively. In a replicate experiment, other duplicate slides were hybridized with probes derived from ANIT-treated and control rats that had been labeled with cyanine-5 and cyanine-3, respectively (color swap). Then, the slides were cover-slipped and incubated in a sealed chamber (Asahi Technoglass Co.) for 16 hrs under a humidified (65 °C) condition. After being washed in low-stringency buffer (2 x SSC and 0.1% SDS), high-stringency buffer (0.2 x SSC and 0.1% SDS) and 0.2 x SSC and then rinsing with 99.5% ethanol, the slide was dried by centrifugation at low speed and used for scanning.; Fluorescence was scanned by using a ScanArray 4000 (Packard BioChip Technologies, Billerica, MA) and quantified by using QuantArray Software (Packard BioChip Technologies, Billerica, MA).time-courseKensuke,,KojimaName: Kensuke Kojima; Email: kchiba@p.chiba-u.ac.jp; Phone: 81-43-290-2919; Fax: 81-43-290-2919; Laboratory: Laboratory of Pharmacology and Toxicology; Department: Graduate School of Pharmaceutical Sciences; Institute: Chiba University; Address: ; City: Chiba; State: Chiba; Zip/postal_code: 263-8522; Country: Japan iy7!!9#+Alpha-naphtylisothiocyanate administration time-courseGSE900Public on Dec 13 20032003-12-122005-10-28Male Sprague-Dawley rats weighing 250-300 g were purchased from Japan SLC Co. (Shizuoka, Japan). The animals were housed under a daily controlled 12-h light and 12-h dark cycle at 23 °C with free access to rat chow (Japan SLC Co.) and water for 1 week prior to the experiments.; Rats were intraperitoneally injected with 75 mg/kg body weight of ANIT (alpha-naphtylisothiocyananique to T cell activation. Best results were achieved by identification of genes that were most highly coregulated with the T-cell-specific transcript interleukin 2 (IL2) in a "compendium" of experiments involving both T cells and other cell types. Among the genes most highly coregulated with IL2 were many genes known to function during T cell activation, together with ESTs of unknown function. Four of these ESTs were extended to novel full-length clones encoding T-cell-regulated proteins with predicted functions in GTP metabolism, cell organization, and signal transduction.otherJerald,P,Radich; Mao Mao; Sergey Stepaniants; Matt Biery; Terry Ward; Greg Schimmack; Sumire Kobayashi; Michael Carleton; John Castle; Johanna Lampe; Julja Burchard; Janell,M,Schelter; Hongyue Dai; Yudong,D,He; Peter,S,Linselyhttp://www.rii.comName: Mao Mao; Email: mao_mao@merck.com; Phone: 4258237349; Department: Biology; Institute: Rosetta Inpharmatics; Address: ; City: Kirkland; State: WA; Zip/postal_code: 98034; Country: USA  =7!!qQ1T lymphocyte activation gene identification by coregulated expression on DNA microarraysGSE902Public on Feb 01 20042003-12-122005-06-28QHigh-capacity methods for assessing gene function have become increasingly important because of the increasing number of newly identified genes emerging from large-scale genome sequencing and cDNA cloning efforts. We investigated the use of DNA microarrays to identify uncharacterized genes specifically involved in human T cell activation. Activation of human peripheral blood T lymphocytes induced significant changes in hundreds of transcripts, but most of these were not unique to T cell activation. Variation of experimental parameters and analysis techniques allowed better enrichment for gene expression changes u MS7!!Q+E 1EOM and hindlimb muscle developmentGSE903Public on Apr 01 20042003-12-122005-05-29Conserved and muscle group-specific gene expression patterns shape postnatal development of the novel extraocular muscle phenotype. Comparison of postnatal development of extraocular and hindlimb muscle between birth and P45.parallel sampleGeorgiana,,Cheng; Anita,P,Merriam; Bendi Gong; Patrick Leahy; Sangeeta Khanna; John,D,PorterName: Henry,J.,Kaminski; Email: henry.kaminski@case.edu; Phone: 216-368-0250; Fax: 216-368-1710; Laboratory: Henry J. Kaminski(henry.kaminski@case.edu); Department: Neurology; Institute: Case Western Reserve University; Address: 11100 Euclid Avenue; City: Cleveland; State: OH; Zip/postal_code: 44106-5068; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE903/GSE903_RAW.tar R7!!sAge MapGSE904Public on Nov 24 20042003-12-122005-05-29Analysis of the effect of aging and caloric restriction on liver tissueotherhttp://kiosk.grc.nia.nih.gov/docs/agemap/agemap.htmName: Kevin,G,Becker; Email: beckerk@grc.nia.nih.gov; Phone: 410-558-8360; Fax: 410-558-8669; Laboratory: Gene Expression and Genomics Unit; Department: Research Resources Branch; Institute: National Institute on Aging, NIH; Address: Triad 207 333 Cassell Drive; City: Baltimore; State: MD; Zip/postal_code: 21224; Country: USA; Web_link: http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm &c7!!s#cEmbryo exposure to heat shock and teratogenGSE905Public on Feb 24 20042003-12-152006-04-25^Analysis of embryos exposed to either:; ; [1] 40 uM 4-hydroperoxycyclophosphamide for 1 or 5 hours at 37°C; [2] 43°C heat shock for 15 minutes followed by 1 or 5 hours at 37°C; This SuperSeries is composed of the following subset Series:; GSE866: CP 1hr; GSE869: HS 1hr; GSE870: HS 5hr; GSE888: CP 5hrSuperSeriesR,,BeyerName: Richard Beyer; Email: dbeyer@u.washington.edu; Phone: 206-616-7378; Laboratory: Center for Ecogenetics and Environmental Health; Department: ; Institute: University of Washington; Address: 4225 Roosevelt Way, NE, Suite 100; City: Seattle; State: WA; Zip/postal_code: 98105; Country: USA; Web_link: http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.htmlofDflrx~ &,28>DJPV\bhntz "(.4:@FLRX^djpv|WXY[\]_`abcdfhiWXY[\]_`abcdfhijlnpqstuwxyz|}~    ÆņƆdžȆʆ̆͆ΆφІцӆԆՆֆ؆ ن!چ"ۆ%߆'(*+,-/0123456789:;<=@FGHI J LNOPQRSTUWX Y!Z"[$]&^-_/`1a3cAdBeCf L?7!!?+i1Gene expression profiling of Rhesus monkey extraocular muscle and its layers ˅0[7!!Y#1Skeletal muscle cell fusion time courseGSE906Public on Feb 12 20042003-12-152006-04-25Time course experiment of healthy primary skeletal muscle cells KM109, KM108 and HPP4 after initiation of fusion; ; This SuperSeries is composed of the following subset Series:; GSE884: KM109; GSE895: KM108_cDNA; GSE896: HPP4_cDNASuperSeriesEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlands(Porter lab)GSE907Public on Apr 01 20042003-12-152005-05-29۩Rhesus monkey extraocular muscle. Data set includes: (a) whole medial and lateral rectus muscle and (b) global and orbital muscle layers separately microdissected using a Leica LSM. All samples were expression profiled here using the Affymetrix human U133 A&B arrays. Data form part of publication: Investigative Ophthalmology and Visual Science 45 (in press), 2004.; Keywords; Keywords; Keywords; KeywordsorderedSangeeta,,Khanna; Georgiana Cheng; Bendi Gong; Michael,J,Mustari; John,D,PorterName: Sangeeta Khanna; Email: sxk128@po.cwru.edu; Phone: 216-844-1429; Fax: 216-844-4792; Laboratory: John D. Porter (john.porter@case.edu); Department: Neurology; Institute: Case Western Reserve University; Address: 11100 Euclid Avenue; City: Cleveland; State: OH; Zip/postal_code: 44106; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE907/GSE907_RAW.tar ?7!!#1KM109_Human oligo batch IGSE908Public on Feb 12 20042003-12-162005-05-29Timecourse experiment of healthy human primary myoblast cells (KM109)time-courseEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlands $A7!![#1KM109_Human oligo batch IIGSE909Public on Feb 12 20042003-12-162005-05-29Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109).time-courseEllen,,SterrenburgName: Ellen Sterrenburg; Email: E.sterrenburg@lumc.nl; Phone: +31 71 527 6611; Laboratory: Center for Human and Clinical Genetics; Department: Center for Human and Clinical Genetics; Institute: Leiden University Medical Center; Address: Wassenaarseweg 72; City: Leiden; Zip/postal_code: 2333 AL; Country: Netherlands XX$S7!!'_COGRX5, PET117 and MLP1 yeast mutantsGSE910Public on Dec 29 20032003-12-162005-05-29>Transcriptome comparisons between grx5, pet117 and mlp1 mutants. All of them are referenced to the same parental wild type sample using three independent samples and three independent nylon macroarrays. Each replicate pair (wt/mutant), hybridized on the same membrane, was normalized by lowess method.; z-tests were performed to evaluate differential gene expression.; Keywords; Keywords; KeywordsotherJose,,Garcia-Martinez; Jose,E,Perez-Ortinhttp://scsie.uv.es/chipsdnaName: Jose,E.,Perez-Ortin; Email: jose.e.perez@uv.es; Phone: 34 963 544446; Fax: 34 963 544635; Laboratory: Yeast Functional Genomics; Department: Bioquimica y Biologia Molecular; Institute: Universitat de Valencia; Address: Dr. Moliner 50; City: Burjassot; State: Valencia; Zip/postal_code: E46100; Country: Spain; Web_link: http://scsie.uv.es/chipsdna 55G 7!! 531Identification of LEAFY targets during reproductive transitionGSE911Public on Dec 18 20032003-12-172005-06-28Global analysis of gene expression in 9 day old LEAFY-GR, 35S::LFY or Landsberg erecta seedlings treated with the steroid dexamethasone and/or the protein synthesis inhibitor cycloheximide.otherDilusha,A,William; Yanhui Su; Michael,R,Smith; Meina Lu; Don,A,Baldwin; Doris WagnerName: Doris Wagner; Email: wagnerdo@sas.upenn.edu; Phone: 215-898-0483; Department: Biology; Institute: University of Pennsylvania; Address: ; City: Philadelphia; State: PA; Zip/postal_code: 19104; Country: USAftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE911/GSE911_RAW.tar !Y7!!Wm9Systemic Leaf Wound Response in TomatoGSE917Public on Feb 17 20042003-12-182005-06-28xWild type systemic leaf wound response vs. response in mutants lacking NADPH oxidase (Rboh); KeywordsotherMoshe,,Sagi; Olga Davydov; Saltanat Orazova; Zhazira Yesbergenova; Ron Ophir; Johannes,W,Stratmann; Robert FluhrName: Robert Fluhr; Email: robert.fluhr@weizmann.ac.il; Phone: 972-8-9342175; Department: Plant Sciences; Institute: Weizmann Institute of Science; Address: ; City: Rehovot; Zip/postal_code: 76100; Country: Israel ??=}7!!} Rosetta (Merck) Expression Validated Gene HybridizationsGSE918Public on Dec 18 20032003-12-182006-07-27Rosetta (Merck) Expression Validated Gene HybridizationsotherEric,E,Schadt; Stephen,W,Edwards; Debraj GuhaThakurta; Dan Holder; Lisa Ying; Vladimir Svetnik; Amy Leonardson; Kyle,W,Hart; Archie Russell; Guoya Li; Guy Cavet; John Castle; Zhengyan Kan; Ronghua Chen; Andrew Kasarskis; Mihai Margarint; Mike Caceres; JasName: Stephen,W,Edwards; Email: stephen_edwards@merck.com; Phone: 425 636 6409; Department: Research Genetics; Institute: Rosetta Inpharmatics (Merck & Co.); Address: ; City: Seattle; State: WA; Zip/postal_code: 98034; Country: USA; Web_link: www.rii.comhesized using Superscript reverse transcriptase (Invitrogen) and a T7-(dT)24 primer, purified by phenol/chloroform extraction using Phase Lock Gel tubes (Eppendorf), and precipitated with ethanol. Labeled antisense RNA was generated with a BioArray kit (Enzo) and purified using an RNeasy kit (Qiagen). 25 mg of the fragmented cRNAs were used for hybridization to the arrays. Affymetrix instruments were used for hybridization, washing, staining and scanning of the arrays according to the provided instructions.; Data from four biological replications representing tissue grown and harvested at different times was collected. The average signals of all eight experiments were scaled to the target value of 500.; ; Keywords; Keywords; Keywords; Keywordsparallel sampleWolfgang,,Lukowitz; Adrienne Roeder; Dana Parmenter; Chris SomervilleName: Chris Somerville; Email: crs@stanford.edu; Phone: 650-325-1521 x203; Institute: Carnegie Institution; Address: ; City: Stanford; State: CA; Zip/postal_code: 94305; Country: USA XX?7!!g+{Comparison of WT and YODAGSE919Public on Dec 30 20032003-12-192005-05-29Wild type and yda-2 plants were germinated and grown on commercial potting mix in walk-in chambers with constant illumination (~150 micromoles per square meter per second) at 22oC. The aerial parts of the plants were harvested at the rosette stage, prior to bolting. Total RNA was prepared using Trizol reagent (Invitrogen) with the additional steps recommended for polysaccharide-rich tissues. Hybridization probes for the GeneChip AtGenome1 microarrays (Affymetrix) were prepared from 20 mg total RNA. All procedures followed Affymetrix protocols. Briefly, cDNA was synt ""Z7!!O'QCOSUS1GSE920Public on Jan 02 20042003-12-192005-05-29Transcriptome analysis of sus1 mutant in reference to its parental wild type reference. Iterative global median method was used for between sample normalization.; z-test was performed to evaluate differential gene expression.repeat sampleOreto,,Antunez; Jose,E,Perez-Ortinhttp://scsie.uv.es/chipsdnaName: Jose,E.,Perez-Ortin; Email: jose.e.perez@uv.es; Phone: 34 963 544446; Fax: 34 963 544635; Laboratory: Yeast Functional Genomics; Department: Bioquimica y Biologia Molecular; Institute: Universitat de Valencia; Address: Dr. Moliner 50; City: Burjassot; State: Valencia; Zip/postal_code: E46100; Country: Spain; Web_link: http://scsie.uv.es/chipsdna U57!!'1SCPB vs sham-controlsGSE921Public on Dec 20 20032003-12-192005-05-29heart from rats exposed to cardiopulmonary bypass (CPB) vs sham-operated controls; Keywords; Keywords; Keywords; Keywordsrepeat sampleMihai,V,PodgoreanuName: Mihai,Victor,Podgoreanu; Email: mihai.podgoreanu@duke.edu; Phone: (919) 681-4781; Fax: (919) 681-4776; Laboratory: Perioperative Genomics Laboratory; Department: Anesthesiology; Institute: Duke University Medical Center; Address: Genome Science Research Bldg.1, 595 LaSalle St, Ste#1027; City: Durham; State: NC; Zip/postal_code: 27710; Country: USA 55V7!!Q'#!Pseudomonas aeruginosa infection of Calu-3 human lung epithelial cellsGSE923Public on Oct 08 20042003-12-192005-10-28muThis series contains 5 groups of U133A arrays with targets from Calu-3 cell line post-infection with P aeruginosa strains. Calu-3 human lung epithelial cells were seeded onto 6-well plates and grown tׄeS7!!'1SCPB vs sham-operated controls (1.2)GSE922Public on Dec 20 20032003-12-192005-05-29hearts from rats exposed to cardiopulmonary bypass (CPB) vs sham-operated controls; Keywords; Keywords; Keywords; Keywordsrepeat sampleMihai,V,PodgoreanuName: Mihai,Victor,Podgoreanu; Email: mihai.podgoreanu@duke.edu; Phone: (919) 681-4781; Fax: (919) 681-4776; Laboratory: Perioperative Genomics Laboratory; Department: Anesthesiology; Institute: Duke University Medical Center; Address: Genome Science Research Bldg.1, 595 LaSalle St, Ste#1027; City: Durham; State: NC; Zip/postal_code: 27710; Country: USAo about 80% confluency. Epithelial monolayers were infected with 108 CFUs per ml of each bacterial strain for 60 min and then washed extensively with phosphate-buffered saline. The cultures were subsequently incubated in fresh RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 µg/ml gentamicin. After 6 h, total RNA from the cells was prepared with RNAzol and further purified with RNEasy for microarray hybridization. All arrays processed and globally scaled to 500 using MAS 5.; CONTROL (4 arrays) - no infection; FRD1 (4 arrays); FRD1234 (3 arrays); FRD440 (4 arrays); FRD875 (4 arrays); Keywords; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleLaura,M,Cobb; Josyf,C,Mychaleckyj; Daniel,J,Wozniak; Yolanda,S,López-BoadoName: Josyf Mychaleckyj; Email: jmychale@wfubmc.edu; Phone: 336-713-7540; Laboratory: MYCHALECKYJ; Department: Center for Human Genomics; Institute: Wake Forest Univ School of Medicine; Address: ; City: Winston-Salem; State: NC; Zip/postal_code: 27157; Country: USA K y7!!/1S Cardiopulmonary bypass (CPB) vs sham-operated controlsGSE924Public on Dec 20 20032003-12-192005-10-04RSheart from rats exposed to cardiopulmonary bypass (CPB) vs sham-operated controlsotherMihai,V,PodgoreanuName: Mihai,Victor,Podgoreanu; Email: mihai.podgoreanu@duke.edu; Phone: (919) 681-4781; Fax: (919) 681-4776; Laboratory: Perioperative Genomics Laboratory; Department: Anesthesiology; Institute: Duke University Medical Center; Address: Genome Science Research Bldg.1, 595 LaSalle St, Ste#1027; City: Durham; State: NC; Zip/postal_code: 27710; Country: USA }}!57!!'i_!A Comparison of Neonatal Rat Ventricular Myocytes Treated With Phenylephrine or PAMHGSE925Public on Mar 02 20042003-12-192006-11-01Neonatal rat ventricular myocytes cultured for 48 hours without stimulation, in the presence of twenty micromolar phenylephrine, or in the presence of one micromolar PAMH.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordsrepeat sampleErik,,Bush; Jens Fielitz; Lawrence Melvin; Michael Martinez-Arnold; Timothy McKinsey; Ryan Plichta; Eric OlsonName: Eric,N,Olson; Email: Eric.Olson@UTSouthwestern.edu; Phone: 214-648-1187; Fax: 214-648-1196; Laboratory: Olson Lab; Department: Molecular Biology; Institute: University of Texas Southwestern Medical Center at Dallas; Address: 6000 Harry Hines Blvd.; City: Dallas; State: TX; Zip/postal_code: 75390; Country: USA; Web_link: http://hamon.swmed.edu/~olsonlab/ l"[7!!U#1"Murine Testis Developmental Time CourseGSE926Public on Feb 01 20042003-12-222005-05-29QMurine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to MGU74v2 A, B, and C chips in duplicatetime-courseName: James Shima; Email: jezechiels@wsu.edu; Phone: 1-509-335-2240; Fax: 1-509-335-9688; Laboratory: Griswold Lab/Center for Reproductive Biology; Department: School of Molecular Biosciences; Institute: Washington State University; Address: 531 Fulmer Hall/POB 644660; City: Pullman; State: WA; Zip/postal_code: 99164-4660; Country: USA; Web_link: http://www.wsu.edu/~griswoldftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE926/GSE926_RAW.tar \\E%o7!!i5%Gene expression analysis of the developing cortexGSE929Public on Mar 27 20042003ޒ7$C7!!'_1$natural variation affy dataGSE928Public on Dec 31 20042003-12-242005-10-28Natural variation in gene expression among healthy human individuals has been largely unexplored. In order to understand the genetic basis of variation in gene expression between normal human individuals, we need to o܃j#K7!!7+-'#Effect of LAMR1-TP1. 092603MCM6GSE927Public on Dec 30 20032003-12-242005-05-29@Infected neonatal mouse cardiomyocyte; ; COMMENT: Submitter has not provided GEO with full dataset as described in Nat Genet. 2004 Feb;36(2):123-30.parallel sampleYoshihiro,,AsanoName: Yoshihiro Asano; Email: asano@medone.med.osaka-u.ac.jp; Phone: +81-6-6879-3472; Fax: +81-6-6879-3473; Institute: Osaka Univ.; Address: ; City: Suita, Osaka; Zip/postal_code: 565-0871; Country: Japanbtain genome-wide expression data from various populations. Studies in monozygotic twins could enable us to estimate the size of the contribution of genetic and environmental factors to the natural variation in gene expression. In this work, we report the gene expression analysis of 5 pairs of monozygotic twins and 3 unrelated individuals; Normal healthy twin pairs were recruited for the study. Three more normal individuals including two females and one male were recruited. First, labeled products were hybridized with the Affymetrix GeneChip Test3 arrays. If the results were judged satisfactory, hybridization was subsequently carried out with the HG U95A arrays as per manufacturer's instructions. Arrays were hybridized at 45°C for 16 hours. The array was then washed using an automated Gene Chip Fluidics Station 400. After washing, the array was stained with streptavidin-phycoerythrin and scanned with a HP Gene Array Scanner. The data was analyzed using Gene Chip Software for expression analysis (MAS 5). All Gene Chip experiments were performed at the Weizmann Institute of Science, Rehovot, Israel.; Following comparisons were carried out:; 1. Between female identical twin pair (GSM14480 and GSM14481; GSM29053 and GSM 29054; GSM 29055 and GSM 29056); 2. Between male identical twin pair (GSM14478 and GSM14479; GSM 29057 and GSM 29058); 3. Between unrelated female individuals (include GSM14483, GSM20645 also but exclude comparisons within same twin pairs); 4. Between unrelated male individuals (include GSM14477 but exclude comparisons between same twin pairs); repeat sampleAnu,,Sharma; Vineet,K,Sharma; Shirley,H,Saban; Doron Lancet; Srinivasan Ramachandran; Samir,K,BrahmachariName: Srinivasan Ramachandran; Email: ramu@igib.res.in, ramucbt@yahoo.com; Phone: 91-11-27666156 ext169; Fax: 91-11-27667471; Department: Functional Genomics Unit; Institute: Institute of Genomics and Integrative Biology; Address: Mall Road (Near Delhi University Campu); City: Delhi; State: Delhi; Zip/postal_code: 110007; Country: India-12-252005-05-29-The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; KeywordsorderedNobuo,,Funatsu; Takayoshi Inoue; Shun NakamuraName: Nobuo Funatsu; Email: funatsu@ncnp.go.jp; Phone: 81-042-346-1722; Fax: 81-042-346-1752; Department: Cellular Biology; Institute: National Institute of Neuroscience, NCNP; Address: 4-1-1 Ogawahigashi; City: Kodaira; State: Tokyo; Zip/postal_code: 187-8502; Country: Japan '_7!!_ 'Acyclic retinoid induction of HepG2 cellsGSE931Public on Apr 03 20042003-12-292005-05-29Acyclic retinoid induction of HepG2 cellsotherName: Motoyuki Otsuka; Email: otsuka-2im@h.u-tokyo.ac.jp; Phone: +81-3-3815-5411 ext 33070; Fax: +81-3-3814-0021; Department: Department of Gastroenterology; Institute: University of Tokyo; Address: ; City: Tokyo; Zip/postal_code: 113-8655; Country: JapanJ&W7!!Wk&Conditioned Taste Aversion experimentGSE930Public on Dec 22 20042003-12-292005-10-28Conditioned Taste Aversion experimentotherRicardo,,Chiesa; Humberto,G,Ortiz-Zuazaga; Sohaira Morales; Javier Pérez; Julio García; Sandra Peña de OrtizName: Humberto Ortiz-Zuazaga; Email: humberto@hpcf.upr.edu; Phone: (787)758-3054; Fax: (787)758-3058; Department: High Performance Computing facility; Institute: University of Puerto Rico; Address: PO BOX 23334; City: San Juan; State: PR; Zip/postal_code: 00931-3334; Country: USA; Web_link: http://www.hpcf.upr.edu/~humberto/ h(e7!!_(Syracuse High/Low Avoidance Learning in RatsGSE932Public on Dec 31 20032003-12-302005-06-28Comparisons of hippocampi of Syracuse High Avoidance (SHA) and Syracuse Low Avoidance (SLA) learning ratsotherShumin,,Zhang; Tara Amstein; F Robert Brush; Howard,G,GershenfeldName: Shumin Zhang; Email: smzhang2002@hotmail.com; Phone: 214 648 7382; Department: ; Institute: UT Southwestern; Address: ; City: Dallas; State: TX; Zip/postal_code: 75390-9070; Country: USA SSW*s7!!+mE*NIH/NIAID Chronic Granulomatous Disease NeutrophilsGSE935Public on Dec 31 20032003-12-302005-05-29 xPolymorphonuclear leukocytes (PMNs) were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, and XCGD6). TB)q7!!EK)Wild-type vs. Rb-/- Prostate Epithelial Cell LinesGSE934Public on Jan 05 20042003-12-302005-07-20Comparison of control wild-type and Rb-/- prostate epithelial cell lines under untreated and serum-free conditions; Keywords; KeywordsotherMichael,T,McCabe; Mark,L,DayName: Michael,Thomas,McCabe; Email: mccabem@umich.edu; Phone: (734)647-2528; Fax: (734)647-9271; Laboratory: Mark Day Lab; Department: Urology; Institute: University of Michigan; Address: 1500 E. Medical Center Drive; City: Ann Arbor; State: MI; Zip/postal_code: 48109-0944; Country: USAhe studies were performed in accordance with a protocol approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases, and the Institutional Review Board for Human Subjects at the University of Iowa. All studies were conducted according to Declaration of Helsinki principles.; PMNs (107) were combined with or without IgG and C3bi-coated latex beads (8 x 107) in wells of a 12-well tissue culture plate (pre-coated with 20% normal human serum) and centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis. For the purpose of these studies, activated or "Stimulated" PMNs are defined as those that have been stimulated by phagocytosis of IgG- and C3bi-coated latex beads. "Control" PMNs are defined as resting cells or those left unstimulated throughout the time-course. Following centrifugation, plates were incubated at 37 deg. C in a CO2 for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target (12 g) was performed as described in Methods. Labeling of samples, hybridization of cRNA with Hu95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols. Gene expression in healthy control and XCGD individuals was always compared at the same time points after phagocytosis; Keywordsparallel sampleScott,D,Kobayashi; Jovanka,M,Voyich; Kevin,R,Braughton; Adeline,R,Whitney; William,M,Nauseef; Harry,L,Malech; Frank,R,DeLeohttp://www.niaid.nih.gov/dir/labs/lhbp/deleo.htmName: Frank,R.,DeLeo; Email: fdeleo@niaid.nih.gov; Phone: 406-363-9448; Fax: 406-363-9394; Laboratory: Rocky Mountain Laboratories; Department: Laboratory of Human Bacterial Pathogenesis; Institute: National Institute of Allergy and Infectious Diseases; Address: 903 South 4th Street; City: Hamilton; State: MT; Zip/postal_code: 59840; Country: USAthe second wave, named mid-preimplantation gene activation (MGA), precedes the dynamic morphological and functional changes from the morula to blastocyst stage. Further expression profiling of embryos treated with inhibitors of transcription, translation, and DNA replication revealed that the translation of maternal RNAs is required for the initiation of ZGA. We propose a cascade of gene activation from maternal RNA/protein sets to ZGA gene sets and thence to MGA gene sets. The large number of genes identified as involved in each phase is a first step toward analysis of the complex gene regulatory networks.otherToshio,,Hamatani; Mark,G,Carter; Alexei,A,Sharov; Minoru,S,Kohttp://lgsun.grc.nia.nih.gov/microarray/22k/Hamatani/Hamatani-DevCell-analysis-data.xlsName: Minoru,S.H.,Ko; Email: kom@mail.nih.gov; Phone: 410-558-8359; Fax: 410-558-8331; Laboratory: Lab of Genetics; Department: NIA; Institute: NIH; Address: 333 Cassell Drive Suite 3000 ; City: Baltimore; State: MD; Zip/postal_code: 21224; Country: USA S+37!!G;+Dynamics of global gene expression changes during mouse preimplantation developmentGSE936Public on Jan 09 20042003-12-302007-03-22 Understanding preimplantation development is important both for basic reproductive biology and for practical applications including regenerative medicine and livestock breeding. Global expression profiles revealed and characterized the distinctive patterns of maternal RNA degradation and zygotic gene activation, including two major transient waves of de novo transcription. The first wave corresponds to zygotic genome activation (ZGA);  2,u7!! G;,prefrontal cortex (ctrl vs transgenic synaptic AChE)GSE937Public on May 01 20042004-01-022005-05-29total prefrontal cortex RNA in female FVB/N mice (control) versus transgenic female mice overexpressing the human synaptic AChEotherEran,,Meshorer; Hermona SoreqName: Eran Meshorer; Email: meshorer@vms.huji.ac.il; Phone: +972-2-6585454; Fax: +972-2-6586448; Laboratory: Molecular Biology; Department: Biological Chemistry; Institute: Life Sciences; Address: Givat Ram; City: Jerusalem; State: Israel; Zip/postal_code: 91904; Country: Israel @@<-97!!Uu -fumonisin biosynthesisGSE938Public on Jan 02 20042004-01-022005-10-28溾In the study, expression profiles in wild type and a fcc1 mutant were compared to identify genes with patterns of expression similar to the FUM genes. DNA microarrays were constructed with ESTs from cDNA libraries obtained from the fcc1 mutant and wild-type strain of F. verticillioides grown on maize kernels . By microarray methodology, gene expression was measured in the fcc1 mutant and the wild type during growth on maize and in a synthetic medium at pH 3 and 8. The results of the analysis provide potential candidate genes for future studies to determine their functional roles in fumonisin biosynthesis.otherAM,,Pirttilä; L,M,McIntyre; G,A,Payne; C,P,WoloshukName: Charles,P.,Woloshuk; Email: woloshuk@pudue.edu; Phone: 765 494 3459; Institute: Purdue University; Address: ; City: West Lafayette; State: IN; Zip/postal_code: 47907-2054; Country: USA ;/57!! }W /JHIII-MF & feeding-MGSE940Public on Dec 31 20042004-01-052005-10-03This series examines gene expression in the anterior midgut at several time points (2, 4, 8, & 16 h for males, 8 h for females) after topical application of juvenile hormone III (JHIII) or acetone (control) to adult beetles. In addition, gene expression in male anterior midguts were examined 24 h after phloem feeding or in unfed beetles.; Keywords: Norths.C7!!{+?u.Osteopontin vs empty vectorGSE939Public on Jan 07 20042004-01-052005-05-29Osteopontin tranfected vs empty vector breast cell lineparallel sampleAmy,,Cook; Ann,F,ChambersName: Gregory Bloom; Email: bloomgc@moffitt.usf.edu; Phone: 813 907 0609; Institute: Moffitt Cancer Center; Address: ; City: Tampa; State: FL; Zip/postal_code: 33612; Country: USA American pine engraver beetle; anterior midgut; juvenile hormone; pheromone biosynthesis; Coleoptera; Scolytidae; ; Publication reference:; ; Reference Type: Book Section; Authors: Tittiger, Claus; Keeling, Christopher I.; Blomquist, Gary J.; Year: 2005; Title: Some insights into the remarkable metabolism of the bark beetle midgut.; Editor: Romeo, J.T.; Book Title: Chemical ecology and phytochemistry of forest ecosystems; City: Toronto; Publisher: Elsevier; Volume: 39; Pages: 57-78; Series Title: Recent Advances in Phytochemistry; otherClaus,,Tittiger; Christopher,I,Keeling; Gary,J,Blomquisthttp://bioinformatics.unr.edu/beetle/Name: Christopher,Ian,Keeling; Email: ckeeling@mac.com; Phone: 775-784-1734; Fax: 775-784-1419; Laboratory: Dr. Claus Tittiger's Laboratory; Department: Department of Biochemistry/Mail Stop 330; Institute: University of Nevada, Reno; Address: 1664 North Virginia Street; City: Reno; State: NV; Zip/postal_code: 89557-0014; Country: USA; Web_link: http://bioinformatics.unr.edu/beetle/ (037!!{'0MastomysMouseMucosaGSE941Public on Jan 07 20042004-01-062005-05-29Analysis of gene expression in gastric mucosa from Mastomys treated for different time periods with Loxtidine; Keywordsrepeat sampleMark,,Kidd; Toshinori Hinoue; Kevin,D,Lye; Yi Wen; Irvin,M,ModlinName: Mark Kidd; Email: mkidd01@snet.net; Phone: 203 785-5429; Fax: 203 737-4067; Laboratory: Modlin Lab; Department: Surgery; Institute: Yale University School of Medicine; Address: 333 Cedar Street; City: New Haven; State: CT; Zip/postal_code: 06525; Country: USA z1#7!!?1MastomysRatGSE942Public on Jan 07 20042004-01-062005-05-29Analysis of gene expression in an enriched ECL cell population from the agstric mucosa of Mastomys treated with Loxtidine for 8-16 weeks, and from an animal that spontaneously developed an ECL cell carcinoid; KeywordsotherMark,,Kidd; Toshinori Hinoue; Kevin,D,Lye; Yi Wen; Irvin,M,ModlinName: Mark Kidd; Email: mkidd01@snet.net; Phone: 203 785-5429; Fax: 203 737-4067; Laboratory: Modlin Lab; Department: Surgery; Institute: Yale University School of Medicine; Address: 333 Cedar Street; City: New Haven; State: CT; Zip/postal_code: 06525; Country: USA v2Q7!!U#+%2C. elegans heat stress time courseGSE946Public on Jan 18 20042004-01-082005-05-29=We sought to study the effect of heat stress on gene expression in C. elegans. We cultured CF512 animals to adulthood at 25C (at which they are sterile). We then induced heat stress by switching the culture temperature to 30C.time-courseColeen,T,MurphyName: Coleen,T,Murphy; Email: cmurphy@worms.ucsf.edu; Phone: 415-341-8864; Laboratory: Kenyon lab; Department: Biochemistry Department; Institute: University of California, San Francisco; Address: ; City: San Francisco; State: CA; Zip/postal_code: 94143; Country: USA 73!7!![WG3heads onlyGSE947Public on Jan 31 20042004-01-082005-05-29Expression profile comparison of the heads of females of D. melanogaster, D. simulans and their hybrid.otherJose,M,Ranz; Kalsang Namgyal; Greg Gibson; Daniel,L,Hartlhttp://www.oeb.harvard.edu/hartl/lab/Name: Jose,M,Ranz; Email: jmr68@mole.bio.cam.ac.uk; Phone: 44 1223 766336; Laboratory: Michael Ashburner; Department: Genetics; Institute: University of Cambridge; Address: Downing; City: Cambridge; Zip/postal_code: cb2 3eh; Country: United Kingdom; Web_link: http://www.gen.cam.ac.uk/ F4!7!!qWG4whole bodyGSE948Public on Jan 31 20042004-01-082005-05-29Q-Expression profile comparison of females of D. melanogaster, D. simulans and their hybrid. RNA source: whole body.otherJose,M,Ranz; Kalsang Namgyal; Greg Gibson; Daniel,L,Hartlhttp://www.oeb.harvard.edu/hartl/lab/Name: Jose,M,Ranz; Email: jmr68@mole.bio.cam.ac.uk; Phone: 44 1223 766336; Laboratory: Michael Ashburner; Department: Genetics; Institute: University of Cambridge; Address: Downing; City: Cambridge; Zip/postal_code: cb2 3eh; Country: United Kingdom; Web_link: http://www.gen.cam.ac.uk/ r5W7!!)ag?5SARST analysis of arctic soil samplesGSE949Public on Jan 12 20042004-01-082005-06-28,Analysis of microbial community composition in arctic tundra and boreal forest soils using serial analysis of ribosomal sequence tags (SARST).otherJ,D,Neufeld; W Mohn; Z Yu; W Lam; W,W,Mohnhttp://www.microbiology.ubc.ca/Mohn/SARST.htmName: Josh,D,Neufeld; Email: jneufeld@interchange.ubc.ca; Phone: 604-822-5317; Department: Department of Microbiology & Immunology; Institute: University of British Columbia; Address: #300-6174 University Blvd.; City: Vancouver; State: BC; Zip/postal_code: V6T 1Z3; Country: Canada }6M7!!M7=6Testes gene expression and agingGSE950Public on Jan 08 20052004-01-082006-10-2514 bp RsaI SAGE analysis of testes from 3 month and 29 month BDF1 mice, and 14 month SAMP1 mice.otherJ,,Yao; T Chiba; J Sakai; K Hirose; M Yamamoto; A Hada; K Kuramoto; K Higuchi; M MoriName: Junjie Yao; Email: yjunjie@sch.md.shinshu-u.ac.jp; Phone: 0081-263-37-2692; Fax: 0081-263-36-3662; Laboratory: Aging Biology; Department: Aging and Adaptation; Institute: Shinshu university; Address: Asahi 3-1-1; City: Matsumoto; State: Nagano; Zip/postal_code: 390-8621; Country: Japan; Web_link: http://dept.md.shinshu-u.ac.jp/i-byotai/ 7 7!!!M3}7267B1, PC3M, LNCaP Methylation Profile vs. mRNA Expression LevelGSE951Public on Mar 21 20042004-01-092005-11-27NuTwo prostate immortalized cell lines, 267B1, RWPE-1, Ml-csv40, and five prostate cancer cell lines, PC3, PC3M, PC3M-Pro4, PC3M-LN4 and LNCaP are included in this experiment. Their methylation profile are detected using human promoter array (v11). mRNA expression level are profiled with Affymetrix U133A Arrays for 267B1 and PC3M.otherYipeng,,Wang; Michael McClellandhttp://www.ingentaconnect.com/content/neo/neo/2005/00000007/00000008/art00005#availName: Yipeng Wang; Email: ywang@skcc.org; Phone: 858-450-5990 x285; Institute: Sidney Kimmel Cancer Center; Address: ; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA hh8G7!!%o;18Transcriptome analysis in ratGSE952Public on Jan 27 20042004-01-132005-06-282Large scale transcriptome analysis of Wistar and Sprague Dawley rat tissues.otherJohn,R,Walker; Andrew,I,Su; David,W,Self; John,B,Hogenesch; Hilmar Lapp; Rainer Maier; Daniel Hoyer; Graeme BilbeName: John,Robert,Walker; Email: walker@gnf.org; Phone: 858-812-1636; Fax: 858-812-1746; Laboratory: RNA Dynamics; Department: Genomics; Institute: GNF; Address: 10675 John Jay Hopkins Drive; City: San Diego; State: CA; Zip/postal_code: 92121; Country: USA; Web_link: www.gnf.orgftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/series/GSE952/GSE952_RAW.tar W97!!k+QU9Effect of TERT and ATM on Gene Expression Profiles in Human FibroblastsGSE953Public on Jan 17 20042004-01-132005-05-29Gene expression profiling was performed by use of serial analysis of gene expression (SAGE) on BJ normal human skin fibroblasts, A-T cells, and BJ and A-T cells transduced with hTERT cDNA and expressing telomerase activity.; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywords; Keywordsparallel sampleAgnes,,Baross; Mike Schertzer; Scott,D,Zuyderduyn; Steven,J,Jones; Marco,A,Marra; Peter,M,LansdorpName: Agnes Baross; Email: abaross@bcgsc.ca; Phone: 604-877-6000/ ext. 3267; Fax: 604-877-6085; Laboratory: British Columbia Genome Sciences Centre; Institute: British Columbia Cancer Agency; Address: 600 West 10th Avenue; City: Vancouver; State: BC; Zip/postal_code: V5Z 4E6; Country: Canada ''U:57!!'=1:Day 1 anti-GBM mouseGSE954Public on Jan 15 20042004-01-132005-05-29Control total RNA, pooled from the kidney of five normal BALB/c mice, was used as a reference against total RNA extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 1 day.repeat sampleJu-Han,,Kim; Il Soo Ha; Chang-Il Hwang; Young-Ju Lee; Ji-Hoon Kim; Seung-Hee Yang; Yon Su Kim; Dong-Sup Lee; Yun Anna Cao; Sangdun Choi; Woong-Yang ParkName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA &&V;57!!'=1;Day 3 anti-GBM mouseGSE955Public on Jan 15 20042004-01-132005-05-29Control total RNA, pooled from the kidney of five normal BALB/c mice, was used as a reference against total RNA extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 3 days.repeat sampleJu-Han,,Kim; Il Soo Ha; Chang-Il Hwang; Young-Ju Lee; Ji-Hoon Kim; Seung-Hee Yang; Yon Su Kim; Dong-Sup Lee; Yun Anna Cao; Sangdun Choi; Woong-Yang ParkName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USA &&V<57!!'=177!!'=1>Day 16 anti-GBM mouseGSE958Public on Jan 15 20042004-01-132005-05-29Control total RNA, pooled from the kidney of five normal BALB/c mice, was used as a reference against total RNA extracted from the kidney of BALB/c mice injected with anti-GBM antibody for 16 days.repeat sampleJu-Han,,Kim; Il Soo Ha; Chang-Il Hwang; Young-Ju Lee; Ji-Hoon Kim; Seung-Hee Yang; Yon Su Kim; Dong-Sup Lee; Yun Anna Cao; Sangdun Choi; Woong-Yang ParkName: Sangdun Choi; Email: schoi@caltech.edu; Phone: 626-395-8732; Fax: 626-796-7066; Laboratory: Simon Lab; Department: Biology; Institute: California Institute of Technology; Address: 1200 E. California Blvd; City: Pasadena; State: CA; Zip/postal_code: 91125; Country: USAeb 16 20042004-01-142006-04-25OData processing included:; ; 1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization); ; 2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered.; ; 3. Filtering of low reproducibility intrachip replicated spots. Normal distribution was created with the value obtained from the formula: log2(Rax1/Rb) which means logarithm (two-based) of one ratio multiplied by the inverse of its replicate. This value for each gene shoud keep between the range of average ± 3SD. Those genes out of these range are flagged as -25; ; 4. Normalization of ratios was done by Lowess mathematical method. Correction factor was 0.33; This SuperSeries is composed of the following subset Series:; GSE960: wild type 0 hours exposure to congo red; GSE961: wild type 2 hours exposure to congo red; GSE962: wild type 4 hours exposure to congo red; GSE963: wild type 6 hours exposure to congo red; GSE964: slt2 mutant 4 hours exposure to congo red; GSE965: rlm1 mutant 4 hours exposure to congo red; GSE966: wild type two hours exposure to zymolyaseSuperSeriesRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier ArroyoRefer to individual SeriesName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar8-02-22OS. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. At this time cells were collected t=0h.; repeat sampleRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier Arroyo; Jose Manuel Rodríguez-PeñaName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar8-02-22OS. cerevisiae was grown on YEPD. For Congo Red experiments, yest cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 2hours of growth, frozen at -80 °C and processed for RNA extraction.; repeat sampleRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier Arroyo; Jose Manuel Rodríguez-PeñaName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar f"DfF_7!!O'sFwild type two hours exposure to zymolyaseGSE966Public on Feb 16 20042004-01-142TE_7!!'CsErlm1 mutant 4 hours exposure to congo redGSE965Public on Feb 16 20042004-01-142TD_7!!'CsDslt2 mutant 4 hours exposure to congo redGSE964Public on Feb 16 20042004-01-142BC[7!!w'CsCwild type 6 hours exposure to congo redGSE963Public on Feb 16 20042004-01-14200DB[7!!{'CsBwild type 4 hours exposure to congo redGSE962Public on Feb 16 20042004-01-14200BA[7!!w'CsAwild type 2 hours exposure to congo redGSE961Public on Feb 16 20042004-01-142008-02-22OS. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.; repeat sampleRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier Arroyo; Jose Manuel Rodríguez-PeñaName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar8-02-22OS. cerevisiae was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 6 hours of growth, frozen at -80 °C and processed for RNA extraction.repeat sampleRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier Arroyo; Jose Manuel Rodríguez-PeñaName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar008-02-22OS. cerevisiae slt2Δ strain was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 μg/ml. Cells were collected at 4 hours of growth, frozen at -80 °C and processed for RNA extraction.; repeat sampleRaúl,,García; Clara Bermejo; Cecilia Grau; Rosa Pérez; Jose Rodríguez-Peña; Jean Francois; César Nombela; Javier Arroyo; Jose Manuel Rodríguez-PeñaName: Javier Arroyo; Email: jarroyo@farm.ucm.es; Phone: 0034-913941746; Laboratory: U6-Javier Arroyo; Department: Microbiologia II; Institute: Facultad de Farmacia (UCM); Address: Plaza Ramon y Cajal S/N; City: Madrid; State: Madrid; Zip/postal_code: 28040; Country: Spain; Web_link: http://ucm.es/info/mfar