Gene Expression Omnibus (GEO) Overview

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DataSet	:	Series(GSE) x Platform(GPL). A set of related gene expression data.
Sample	:	Biological materials.
platform	:	Methods or instruments used for the gene expression profilings.

Human
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All
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	Platform ID	Title	Number of the probes	Institute	Submission date	Manufacturer	Species	Platform class	Reasoning of the classification Keywords used for the classification are shown with bold font.
1	GPL336	Porcine Brain Library array	3,888	Michigan State University	2003-06-12		Sus scrofa	cDNA Array	spotted DNA/cDNA, Porcine Brain Library array, cDNA microarray from porcine brain cDNA library
2	GPL331	STv3_MMCC	5,184	Vaccine Research Institute of San Diego	2003-05-29		Salmonella enterica	cDNA Array	spotted DNA/cDNA, STv3_MMCC, Custom made Salmonella array
3	GPL289	Segal_3	6,111	Stanford University	2003-04-15		Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, Segal_3, Used to examine wild type and ypl230w mutant under stationary phase.
4	GPL287	Segal_1	5,993	Stanford University	2003-04-15		Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, Segal_1, Used to examine wild type and kin82 mutant under heat shock.
5	GPL288	Segal_2	5,832	Stanford University	2003-04-15		Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, Segal_2, Used to examine wild type and ppt1 mutant under hypo-osmotic shock.
6	GPL347	rikDacFC6	882	The University of Tokyo	2003-06-24	Affymetrix	Saccharomyces cerevisiae	Tiling Array	in situ oligonucleotide, rikDacFC6, Highdensity Yeast Chromosome VI tiling oligo-nucleotide array which can analyze chromosome VI at 300bp resolution. Produced by Affymetrix. Can be purchased directly from Affymetrix. Product name rikDACF. P/N 510636. Keywords = chromosome VI tiling array
7	GPL337	RNA Processing	226	University of Toronto	2003-06-12		Saccharomyces cerevisiae	cDNA Array	spotted DNA/cDNA, RNA Processing, Home-made polylysine substrate (J. DeRisi protocol) Hedge et al., 2000 spotting, cross-linking and blocking protocol, Virtek spotter, Stealth pins (TeleChem), 8 replicates of each spot per array, Oligonucleotide spike-in controls
8	GPL341	[RAE230A] Affymetrix Rat Expression 230A Array	15,923	Affymetrix, Inc.	2003-06-19	Affymetrix	Rattus norvegicus	GeneChip	in situ oligonucleotide, [RAE230A] Affymetrix Rat Expression 230A Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html June 03, 2009: annotation table updated with netaffx build 28 June 21, 2012: annotation table updated with netaffx build 32
9	GPL342	[RAE230B] Affymetrix Rat Expression 230B Array	15,333	Affymetrix, Inc.	2003-06-19	Affymetrix	Rattus norvegicus	GeneChip	in situ oligonucleotide, [RAE230B] Affymetrix Rat Expression 230B Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Array B of GeneChip Rat Expression Set 230 Has 15333 entries and was indexed 09-Apr-2003 Sequences used in the design of the array were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 99 of UniGene (June 2002) and refined by analysis and comparison with a number of other publicly available databases including the Baylor College of Medicine Human Genome Sequencing Center's preliminary rat genome assembly (June 2002). In addition, sequences were analyzed for untrimmed low-quality sequence information, correct orientation, false clustering, alternative splicing and alternative polyadenylation.
10	GPL333	Qiagen Rat Oligonucleotide Array	4,273	University of Arizona	2003-06-04		Rattus norvegicus	Oligo Array	spotted oligonucleotide, Qiagen Rat Oligonucleotide Array, Rat genome oligo set comprises 4273 UniGene clones Keywords = Unigene Oligo Nucleotide Array
11	GPL339	[MOE430A] Affymetrix Mouse Expression 430A Array	22,690	Affymetrix, Inc.	2003-06-18	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [MOE430A] Affymetrix Mouse Expression 430A Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html The GeneChip Mouse Genome 430A 2.0 Array is accessioned in GEO as GPL8321. June 03, 2009: annotation table updated with netaffx build 28 June 07, 2012: annotation table updated with netaffx build 32
12	GPL340	[MOE430B] Affymetrix Mouse Expression 430B Array	22,575	Affymetrix, Inc.	2003-06-18	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [MOE430B] Affymetrix Mouse Expression 430B Array, Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html June 03, 2009: annotation table updated with netaffx build 28 June 21, 2012: annotation table updated with netaffx build 32
13	GPL321	M20K (Incyte mouse release 1.0 and Unigene1)	21,168	St. Jude Children's Research Hospital	2003-05-14		Mus musculus	cDNA Array	spotted DNA/cDNA, M20K (Incyte mouse release 1.0 and Unigene1), The M20K microarray includes 18,330 cDNA mouse clones from the Incyte mouse release 1.0 and Unigene 1 collections. The PCR amplified cDNA inserts were either obtained from Incyte or were amplified from replica plate cultures, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA). Printed slides were post-processed according to the procedures on the Stanford website with some modifications: http://cmgm.stanford.edu/pbrown/protocols/index.html.
14	GPL324	M3 (NIA Mouse 15K Clone Set)	17,329	St. Jude Children's Research Hospital	2003-05-14		Mus musculus	cDNA Array	spotted DNA/cDNA, M3 (NIA Mouse 15K Clone Set), The M3 microarray includes cDNAs from the NIA Mouse 15K cDNA clone collection. NIA Mouse 15K is derived from several early embryonic cDNA libraries, including blastocyst, preimplantation, embryonic stem cells, trophoblast stem cells, embryonic germ cells, and others. The cDNA inserts were amplified from replica plate cultures by PCR, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA). Printed slides were post-processed according to the procedures on the Stanford website with some modifications: http://cmgm.stanford.edu/pbrown/protocols/index.html.
15	GPL323	Ret13K (BMAP mouse Retinal library)	17,328	St. Jude Children's Research Hospital	2003-05-14		Mus musculus	cDNA Array	spotted DNA/cDNA, Ret13K (BMAP mouse Retinal library), The Ret13K microarray includes 12,243 mouse clones including BMAP mouse retinal clones and 220 clones from the Incyte mouse unigene 1 collection. The cDNA inserts were amplified from replica plate cultures by PCR, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA). Printed slides were post-processed according to the procedures on the Stanford website with some modifications: http://cmgm.stanford.edu/pbrown/protocols/index.html.
16	GPL285	MIT-Laboratory for Bioinformatics and Metabolic Engineering, 17K Mouse Arrays	17,280	Massachusetts Institute of Technology	2003-04-11		Mus musculus	Oligo Array	spotted oligonucleotide, MIT-Laboratory for Bioinformatics and Metabolic Engineering, 17K Mouse Arrays, Total RNA samples are generally isolated using either STAT60 or Qiagen's QIAquick Total RNA mini-kit. Total RNA control samples are labelled using Cy3 dCTP (Perkin-Elmer), and total RNA experimental samples were labelled using Cy5 dCTP (Perkin- Elmer) during reverse transcription. For reverse transcription 10 ug of total RNA was mixed with 2 uL of 10X Cy-labelled 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). The control RNA samples were additionally mixed with 2 uL of random hexamers. The reaction mixtures were incubated at 42 C for two hours. After the reverse transcription reactions, the RNA templates were degraded by addition of 2 uL of 1 N NaOH and incubation at 65 C for 10 minutes. The alkaline conditions were neutralized by addition of 2 uL of 1 N HCl. Experimental cDNA samples were then mixed with a control cDNA sample, and the mixtures were cleaned using a QIAquick Nucleotide Removal kit (Qiagen) as described by the manufacturer's instructions. The cleaned samples were concentrated in a speed vacufuge (Eppendorf) for 20 minutes at 65 C, and were dissolved in 32 uL of prewarmed hybridization buffer (Clontech Laboratories), quantified, and hybridized to prepared oligonucleotide microarrays. Hybridization occurred overnight at 55 C using Corning hybridization chambers. The following day the arrays were washed in Glass Hybridization Wash Solution (Clontech Laboratories), then in 1X SSC, and finally in 0.1X SSC. The arrays were dried by centrifugation and scanned using a GenePix 4000B scanner (Axon Instruments). The resulting data is downloaded and formatted in Excel (Microsoft), and analyzed using Matlab (The MathWorks, Inc.). These microarrays were prepared using GAPS glass slides (Corning), and a Virtek arrayer (Bio-Rad). Arrays contained 17,280 features, printed from a synthesized oligonucleotide mouse library (Operon). The library was suspended in 3X SSC, centrifuged, and loaded into the arrayer. Arrays were printed at approximately 50% humidity. Once printed, the probes were crosslinked 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 (Fluka AG), 239 mL 1-methyl-2-pyrrolidinone (EM Science), and 10.7 mL of 1 M boric acid (Fisher), pH 8.0. They were cleaned by rinsing twice in 250 mL of milli-Q water, followed by 250 mL of 95% ethanol (Pharmco Products). After blocking, they were dried using filtered air and stored in the dark at room temperature. ARRAY VALIDATION. Microarray printing and hybridization protocols were validated in our laboratory. For validation, we prepared arrays containing an approximately 13,000 gene sub-set of our oligonucleotide mouse library, printed in triplicate. Total RNA from fetal skeletal muscle and fetal brain were used for validation. Each sample contained an equal amount of RNA from the two sources. Validation experiments compared muscle RNA versus muscle RNA and brain RNA versus muscle RNA. Each sample was prepared as described above and conducted in duplicate. The arrays were processed, scanned, and the data obtained from the image files. Matlab was used to calculate basic statistics. The analysis required as input the gene identifiers from the Genepix (scanner) data output, the ratios of means of the Cy5/Cy3 pixel fluorescence corresponding to each gene identifier, the ratio of means normalization factor (used to correct for the difference in fluorescence and incorporation of the Cy5 and Cy3 fluorophores), and the adjusted flags corresponding to each gene identifier. The adjusted flags marked features that either did not possess basic fluorescence requirements sought by the imaging software or had less than 60% of their pixels' intensities greater than two standard deviations of the background intensity over the background intensity. Using these data as input, Matlab returned the gene identifier, the mean of replicate spots that were not flagged by our filters, the standard deviation of the unflagged replicates, the coefficient of variation among replicates, and the number of observations used in calculating the statistics for each gene. The coefficient of variation, CV, was calculated for each replicated gene expression. For the muscle versus muscle control arrays, the median CV across all probes was 10.2%. For the muscle versus brain arrays the median coefficient of variation across all probes was 9.8%. This indicates that for a gene transcription ratio of 1, we might expect the true value to lie between 0.9 and 1.1; similarly for a gene transcription ratio of 3, we might expect the true value to lie between 2.7 and 3.3. In duplicate arrays, 76% of the genes observed on one muscle versus muscle array were also observed on the duplicate; likewise 77% of the genes found on one muscle versus brain array were conserved on the duplicate. These data demonstrate the inter-array reproducibility by showing the majority of genes are reproducibly found in multiple replicate arrays. Keywords = mouse, dna microarrays, diabetes, hepatoma, hepatocytes, liver, muscle, adipose, hypothalamus
17	GPL313	Gladstone Mm_09042002 v2 mouse long oligo array	17,280	UCSF	2003-05-01		Mus musculus	Oligo Array	spotted oligonucleotide, Gladstone Mm_09042002 v2 mouse long oligo array, Spotted long oligonucleotide array produced using Operon Mouse Genome Oligo Set Version 2 probes. This set includes 16463 oligonucleotides designed based upon representative sequences in build 102 of the mouse UniGene database. 24 negative controls are included on these arrays as well as 13 controls from the Stratagene SpotReport Oligo Array Validation System. Keywords = spotted, long oligonucleotide
18	GPL344	M4(Incyte mouse Unigene1)	11,552	St. Jude Children's Research Hospital	2003-06-23		Mus musculus	cDNA Array	spotted DNA/cDNA, M4(Incyte mouse Unigene1), The M4 microarray includes 9,596 cDNA mouse clones from the Incyte mouse Unigene 1 collection. The PCR amplified cDNA inserts were either obtained from Incyte or were amplified from replica plate cultures, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA). Printed slides were post-processed according to the procedures on the Stanford website with some modifications: http://cmgm.stanford.edu/pbrown/protocols/index.html.
19	GPL346	M2(Incyte mouse release 1.0)	11,552	St. Jude Children's Research Hospital	2003-06-23		Mus musculus	cDNA Array	spotted DNA/cDNA, M2(Incyte mouse release 1.0), The M2 microarray includes 8,734 cDNA mouse clones from the Incyte mouse release 1.0 collection. The PCR amplified cDNA inserts were either obtained from Incyte or were amplified from replica plate cultures, purified and mechanically spotted onto polylysine-coated microscope slides using an OmniGrid robotic spotter (GeneMachines, San Carlo, CA). Printed slides were post-processed according to the procedures on the Stanford website with some modifications: http://cmgm.stanford.edu/pbrown/protocols/index.html.
20	GPL317	SHCO	43,008	Stanford University	2003-05-07		Homo sapiens	cDNA Array	spotted DNA/cDNA, SHCO, Tip Configuration: Standard 48 tip Columns per Sector: 30 Rows per Sector: 30 Column Spacing: 146 Row Spacing: 146

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