Gene Expression Omnibus (GEO) Overview

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.

Unclassified
(399)

All
(11,528)

SAGE NlaIII
(1)

SAGE RsaI
(0)

SAGE Sau3A
(0)

MPSS
(0)

Protein Array
(0)

Antibody
(0)

RT-PCR
(4)

HT-Seq
(91)

Other
(29)

All
(399)

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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	GPL9757	[stSmel_Mtra] SRL_SU Sinorhizobium meliloti/Medicago truncatula dual-genome SymbiosisChip, Affymetrix part number 510699	22,973	Stanford University	2009-12-07	Affymetrix	Sinorhizobium meliloti,Medicago truncatula	GeneChip	in situ oligonucleotide, [stSmel_Mtra] SRL_SU Sinorhizobium meliloti/Medicago truncatula dual-genome SymbiosisChip, Affymetrix part number 510699, The dual genome Affymetrix SymbiosisChip contains probe sets for S. meliloti ORFs annotated in 2001, intergenic regions over 150 bp, and ~10,000 probe sets corresponding to expressed sequence tags of the plant host, Medicago truncatula.
2	GPL11093	[scrGLYCO-v1F] Custom Affymetrix Glyco v1 GeneChip	1,814	The Scripps Research Institute	2010-10-22	Affymetrix	Homo sapiens,Mus musculus	GeneChip	in situ oligonucleotide, [scrGLYCO-v1F] Custom Affymetrix Glyco v1 GeneChip, The Glyco v1 array was designed in 2001 and consists of 3' probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from either species. Most of the human probe sets on the Glyco v1 array were taken directly from the commercial U133A,B human array although a substantial number of the probesets were custom designed by Affymetrix from accessions for genes not well represented by the U133A,B. At the time, the Mouse 430 array had not yet been released by Affymetrix so mouse probesets were all custom designed by Affymetrix for this array using the U133A,B design algorithms. In most cases, probesets consist of 11 probe pairs designed using the Perfect Match/Mismatch approach developed by Affymetrix.
3	GPL4652	[Medicago] Affymetrix Medicago Genome Array	61,278	Affymetrix, Inc.	2006-12-08	Affymetrix	Sinorhizobium meliloti,Medicago sativa,Medicago truncatula	GeneChip	in situ oligonucleotide, [Medicago] Affymetrix Medicago Genome 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 Medicago Genome Array is designed specifically to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. The Medicago Genome Array is particularly useful for agriculture researchers studying legume genomics and symbiotic relationships between nitrogen fixing bacteria and plants. Sequence information for this array was selected from data sources including the TIGR M. truncatula gene index (The Institute for Genomic Research, January 2005), gene predictions from the International Medicago Genome Annotation Group (IMGAG), gene predictions from the S. meliloti genome, and M. sativa EST information made available by TIGR. The array contains over 61,200 probe sets: 32,167 M. truncatula EST/mRNA-based and chloroplast gene-based probe sets; 18,733 M. truncatula IMGAG and phase 2/3 BAC prediction-based probe sets; 1,896 M. sativa EST/mRNA-based probe sets; and 8,305 S. meliloti gene prediction-based probe sets.
4	GPL11094	[GLYCOv2a520086F] Custom Affymetrix Glyco v2 GeneChip	4,682	The Scripps Research Institute	2010-10-22	Affymetrix	Homo sapiens,Mus musculus	GeneChip	in situ oligonucleotide, [GLYCOv2a520086F] Custom Affymetrix Glyco v2 GeneChip, The Glyco v2 array was designed in 2003 and consists of probesets targeting genes coding for glycosyl transferases, carbohydrate binding proteins, glycan degradation enzymes, nucleotide sugar transporters, mucins, adhesion molecules, chemokines, cytokines, growth factors and their receptors, interleukins and their receptors and proteoglycans. In addition, a set of "housekeeping" and control genes are included on the array. The array contains probe set for both mouse and human gene sequences and can be use to analyze RNA from both species. Most of the human and mouse probe sets on the Glyco v2 array were taken directly from the v1 array (based on commercial U133A,B human array) with some probesets designed by Affymetrix from accessions for genes not well represented by the U133A,B. Additional carbohydrate related genes were added to the v2 array relative to the v1 array. In most cases, probesets consist of 11 probe pairs designed using the Perfect Match/Mismatch approach developed by Affymetrix. Immediately prior to our deadline for submittal of the v2 array design, Affymetrix introduced format changes to their custom array product line that substantially increased the available space on the v2 array. To address we represented most probe sets in triplicate or duplicate on the array. For example, the probe set for thrombomodulin (THBD) appears as: 203887 _Copy1_at, 203887 _Copy2_at, 203887 _Copy3_at where each copy represents an identical and independent set of probe pairs targeting the thrombomodulin transcript.
5	GPL10714	[Agilent-021439] University of Chicago-Dual Species (Homo sapiens and Mus musculus) 87K array	87,107	University of Chicago	2010-07-21	Agilent	Homo sapiens,Mus musculus	Oligo Array	in situ oligonucleotide, [Agilent-021439] University of Chicago-Dual Species (Homo sapiens and Mus musculus) 87K array,
6	GPL16690	Yale Lu Human/Mouse microRNA v2.0	636	Yale University	2013-02-18	Lu Lab	Homo sapiens,Mus musculus,Human herpesvirus 4	Oligo Array	spotted oligonucleotide, Yale Lu Human/Mouse microRNA v2.0, miRBase release version 19
7	GPL7436	Wurdinger/Krichevsky miRNA array IV	435	MGH	2008-10-07	Thomas Wurdinger and Anna K. Krichevsky	Homo sapiens,Mus musculus,Rattus norvegicus	cDNA Array	spotted DNA/cDNA, Wurdinger/Krichevsky miRNA array IV,
8	GPL11306	WJC hsa mmu miRNA v7.1 01 (miRNA ID)	459	IMPPC	2010-12-10	Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen	Homo sapiens,Mus musculus	Oligo Array	spotted oligonucleotide, WJC hsa mmu miRNA v7.1 01 (miRNA ID),
9	GPL6485	WJC hsa mmu miRNA v7.1 01	2,304	University of Copenhagen	2008-02-13	Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen	Homo sapiens,Mus musculus	Oligo Array	spotted oligonucleotide, WJC hsa mmu miRNA v7.1 01,
10	GPL10232	Washington University School of Medicine Microarray Core Brugia malayi microarray V.2	36,248	University Hospital Bonn	2010-03-19	Washington University School of Medicine Microarray Core	Brugia malayi,Onchocerca volvulus,Wuchereria bancrofti,Wolbachia endosymbiont strain TRS of Brugia malayi	Oligo Array	spotted oligonucleotide, Washington University School of Medicine Microarray Core Brugia malayi microarray V.2,
11	GPL6429	Vanderbuilt University miRNA Bioarray	2,662	Vanderbilt University	2008-01-28	Ambion, Inc.	Homo sapiens,Mus musculus,Rattus norvegicus	Oligo Array	spotted oligonucleotide, Vanderbuilt University miRNA Bioarray, Manufactured using GE HealthcareÃ¢â‚¬â„¢s CodeLink (TM) 3-D Gel Matrix Technology Surface type: non-adsorptive Attachment: covalent The mirVana miRNA Bioarrays are an Ambion product that is manufactured by GE Healthcare and incorporates the CodeLinkÃ¢â€žÂ¢ 3-D Gel Matrix slide surface. This aqueous environment elevates the probes away from the surface of the slide, allowing for maximum interaction between the probes and targets.
12	GPL11674	UW/NimbleGen_humangorilla_custom_dupsdels	2,097,383	University of Washington	2011-01-31	Nimblegen	Gorilla gorilla,Homo sapiens	Oligo Array	in situ oligonucleotide, UW/NimbleGen_humangorilla_custom_dupsdels,
13	GPL9108	UW CombiMatrix Candidatus Accumulibacter phosphatis 12.5K	12,544	University of Wisconsin-Madison	2009-08-26	CombiMatrix	uncultured bacterium,Candidatus Accumulibacter phosphatis	Oligo Array	in situ oligonucleotide, UW CombiMatrix Candidatus Accumulibacter phosphatis 12.5K,
14	GPL14638	Utz Lab Whole Protein Autoantigen Array V2.0	144	Stanford University	2011-09-29	Utz Laboratory, Stanford University	Escherichia coli,Gallus gallus,Homo sapiens,Bos taurus,Oryctolagus cuniculus,Mus musculus	Other	spotted peptide or protein, Utz Lab Whole Protein Autoantigen Array V2.0,
15	GPL9059	Utz Lab Whole Protein Autoantigen Array V1.0	78	Stanford University	2009-08-19	Utz Laboratory, Stanford University	Escherichia coli,Gallus gallus,Homo sapiens,Bos taurus,Oryctolagus cuniculus,Mus musculus	Other	spotted peptide or protein, Utz Lab Whole Protein Autoantigen Array V1.0,
16	GPL14945	Utz lab histone protein and peptide array	87	Stanford University	2011-12-01	Laboratory of Paul J. Utz	Gallus gallus,Homo sapiens,Bos taurus	Other	spotted peptide or protein, Utz lab histone protein and peptide array,
17	GPL4220	UTTH_Mouse/P.bergheiANKA_44K_v1.0	42,034	University of Toronto	2006-08-25	Agilent Technologies	Plasmodium berghei,Mus musculus	Oligo Array	in situ oligonucleotide, UTTH_Mouse/P.bergheiANKA_44K_v1.0,
18	GPL8594	UTSW-Ambion mirVana Probe Set custom array	381	Baylor College of Medicine	2009-05-26	University of Texas Southwest Medical Center Microarray Core Facility	Homo sapiens,Mus musculus,Rattus norvegicus	Oligo Array	spotted oligonucleotide, UTSW-Ambion mirVana Probe Set custom array, The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.
19	GPL15674	Urocitellus parryii 9.6k	9,600	CAS-MPG partner institute for computational biology	2012-06-07	Wistar Institute	unidentified	cDNA Array	spotted DNA/cDNA, Urocitellus parryii 9.6k,
20	GPL9022	UON_Campylobacter oligo array v1	5,190	University of Nottingham	2009-08-12	University of Nottingham	unidentified,Campylobacter jejuni RM1221,Campylobacter coli RM2228	Oligo Array	spotted oligonucleotide, UON_Campylobacter oligo array v1,

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