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.

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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	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.
2	GPL11370	[olfactomw520640F] Custom Affymetrix olfactory genome tiling array	0	UCSF	2010-12-30	Affymetrix	Mus musculus	Tiling Array	in situ oligonucleotide, [olfactomw520640F] Custom Affymetrix olfactory genome tiling array, GeneChip CustomExpress format 49-7875 Olfactomw520640F
3	GPL11078	[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_13]	21,212	University of Copenhagen	2010-10-20	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENTREZG_13],
4	GPL11204	[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENST]	37,264	The Jackson Laboratory	2010-11-12	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [CDF: MoGene10stv1_Mm_ENST],
5	GPL11209	[HuGene10stv1_Hs_ENSG] Affymetrix GeneChip Human Gene 1.0 ST Array [Brainarray Version 12]	22,197	NCBI/NLM/NIH	2010-11-15	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [HuGene10stv1_Hs_ENSG] Affymetrix GeneChip Human Gene 1.0 ST Array [Brainarray Version 12],
6	GPL11028	[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf]	284,258	Oslo University Hospital, The Norwegian Radium Hospital	2010-10-08	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf], HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
7	GPL11180	[HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate	45,141	Affymetrix, Inc.	2010-11-08	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate, 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
8	GPL11320	[hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [transcript-level]	34,844	Stanford Genome Technology Center	2010-12-15	Affymetrix Inc	Homo sapiens	GeneChip	in situ oligonucleotide, [hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [transcript-level], Inflammation and the Host Response to Injury Program
9	GPL11319	[hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [exon-level]	557,413	Stanford Genome Technology Center	2010-12-15	Affymetrix Inc	Homo sapiens	GeneChip	in situ oligonucleotide, [hGlue2_0_v1] Glue Grant Human Transcriptome Array version 2.0 (GG-H) [exon-level], Inflammation and the Host Response to Injury Program
10	GPL11098	[Glyco_v4_Mm] Affymetrix Glyco v4 GeneChip	1,246	The Scripps Research Institute	2010-10-22	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [Glyco_v4_Mm] Affymetrix Glyco v4 GeneChip, The Glyco v4 array was designed in 2008 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. This array also includes "GC bin" probes (100 for each bin) for use in background correction. These probes are used as an alternative to the PM/MM-based background correction methods. Mismatch probes are not used on this array. There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file. The human CDF file is named: "GLYCOv4_Hs" and the mouse CDF file is named: "GLYCOv4_Mm". Probeset design: The v4 array uses 25 probes to target the first 600 bases from 3' end of each transcript. This region is called Probe Set Region 1 indicated by a psr1 in the probe set name. Up to 4 additional sets of 5 probes are used to target the transcript in 280 base increments upstream (towards the 5' end of the transcript) from the first 600 base region. These are indicated as psr2, psr3 and psr4 in the probeset name. If no psr appears in the probe set name, this indicates that probes are targeting Probe Set Region 1 and that no additional probe sets were designed upstream (towards the 5' end of the transcript) for this transcript accession. Generally only data from Probe Set Region 1 are shown. Data from psr2-4 is generally ignored. All probes are for antisense target and may include a suffix of "_s", "_x" consistent with Affymetrix probe design algorithms used for all commercial Affymetrix 3' arrays.
11	GPL11097	[Glyco_v4_Hs] Custom Affymetrix Glyco v4 GeneChip	1,259	The Scripps Research Institute	2010-10-22	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [Glyco_v4_Hs] Custom Affymetrix Glyco v4 GeneChip, The Glyco v4 array was designed in 2008 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. This array also includes "GC bin" probes (100 for each bin) for use in background correction. These probes are used as an alternative to the PM/MM-based background correction methods. Mismatch probes are not used on this array. There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file. The human CDF file is named: "GLYCOv4_Hs" and the mouse CDF file is named: "GLYCOv4_Mm". Probeset design: The v4 array uses 25 probes to target the first 600 bases from 3' end of each transcript. This region is called Probe Set Region 1 indicated by a psr1 in the probe set name. Up to 4 additional sets of 5 probes are used to target the transcript in 280 base increments upstream (towards the 5' end of the transcript) from the first 600 base region. These are indicated as psr2, psr3 and psr4 in the probeset name. If no psr appears in the probe set name, this indicates that probes are targeting Probe Set Region 1 and that no additional probe sets were designed upstream (towards the 5' end of the transcript) for this transcript accession. Generally only data from Probe Set Region 1 are shown. Data from psr2-4 is generally ignored. All probes are for antisense target and may include a suffix of "_s", "_x" consistent with Affymetrix probe design algorithms used for all commercial Affymetrix 3' arrays.
12	GPL11096	[GLYCOv3_Mm] Affymetrix Glyco v3 GeneChip	1,183	The Scripps Research Institute	2010-10-22	Affymetrix	Mus musculus	GeneChip	in situ oligonucleotide, [GLYCOv3_Mm] Affymetrix Glyco v3 GeneChip, The Glyco v3 array was designed in 2005 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. This custom chip is to tile pre-selected probes from the Affymetrix HGU133 set, the MOE430 sets, the v1 custom array, and the v2 custom array. We kept the original 11 probepairs from these pre-selected probes, while adding 10 more newly designed probepairs for a total of 21 probepairs per probeset within the 3' terminal 600 bases of each targeted transcript. Standard Affy controls (houskeeping and normalization genes) remain at 11 probepairs per probe set. This array also includes 8505 "GC bin" probes for use in background correction. GC content ranges from 3/25 to 25/25. These probes can be used as an alternative to the PM/MM-based background correction methods. There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file. The human CDF file is named: "GLYCOv3_Hs" and the mouse CDF file is named: "GLYCOv3_Mm".
13	GPL11095	[GLYCOv3_Hs] Custom Affymetrix Glyco v3 GeneChip	1,268	The Scripps Research Institute	2010-10-22	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [GLYCOv3_Hs] Custom Affymetrix Glyco v3 GeneChip, The Glyco v3 array was designed in 2005 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. This custom chip is to tile pre-selected probes from the Affymetrix HGU133 set, the MOE430 sets, the v1 custom array, and the v2 custom array. We kept the original 11 probepairs from these pre-selected probes, while adding 10 more newly designed probepairs for a total of 21 probepairs per probeset within the 3' terminal 600 bases of each targeted transcript. Standard Affy controls (houskeeping and normalization genes) remain at 11 probepairs per probe set. This array also includes 8505 "GC bin" probes for use in background correction. GC content ranges from 3/25 to 25/25. These probes can be used as an alternative to the PM/MM-based background correction methods. There are separate library files for human and mouse probesets. The human library file includes all probesets on the array except mouse probes and vis versa for the mouse library file. The human CDF file is named: "GLYCOv3_Hs" and the mouse CDF file is named: "GLYCOv3_Mm".
14	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.
15	GPL11157	[Cytogenetics_Array] Affymetrix Cytogenetics Whole-Genome 2.7M Array	2,795,708	Affymetrix, Inc.	2010-11-03	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [Cytogenetics_Array] Affymetrix Cytogenetics Whole-Genome 2.7M 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 #%chip_type=Cytogenetics_Array #%genome-version=hg19 #%genome-version-ucsc=hg19 #%genome-version-ncbi=GRCh37 #%genome-version-create_date=2009-02-00 #%dbsnp-date=2010-04-00 #%dbsnp-version=131 #%dgv-date=2010-03-00 #%dgv-version=9 #%hapmap-date=2008-01-08 #%hapmap-version=23 #%netaffx-annotation-date=2010-07-00 #%netaffx-annotation-netaffx-build=31
16	GPL11060	[CG_AGPa520460F] Affymetrix Adenoma Biomarker 46K Gene Chip v1.0	46,482	Clinical Genomics	2010-10-15	Affymetrix	Homo sapiens	GeneChip	in situ oligonucleotide, [CG_AGPa520460F] Affymetrix Adenoma Biomarker 46K Gene Chip v1.0,
17	GPL11250	ZB/SBS-NTU Plasmodium falciparum 3D7 IGR+ORF 16.8K v1.0	16,774	Nanyang Technological University, School of Biological Sciences	2010-11-29	ZB lab/SBS-NTU	Plasmodium falciparum	Oligo Array	spotted oligonucleotide, ZB/SBS-NTU Plasmodium falciparum 3D7 IGR+ORF 16.8K v1.0,
18	GPL11248	ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v1.1	11,372	Nanyang Technological University, School of Biological Sciences	2010-11-25	ZB lab/SBS-NTU	Plasmodium falciparum	Oligo Array	spotted oligonucleotide, ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v1.1,
19	GPL11298	Z. Jeffrey Chen Laboratory Spotted Arabidopsis 70mer Oligo Microarray version 1.0	27,649	The University of Texas at Austin	2010-12-08	The Jeffrey Chen Laboratory, The University of Texas at Austin	Arabidopsis thaliana	Oligo Array	spotted oligonucleotide, Z. Jeffrey Chen Laboratory Spotted Arabidopsis 70mer Oligo Microarray version 1.0, This oligonucleotide array is produced from the Operon Version 1.0. Spotted Arabidopsis 70-mer oligo-gene microarrays using 26,090 annotated genes were cooperatively developed with QIAGEN (Valencia, CA) and Operon (Alameda, CA) (LEE et al. 2004; TIAN et al. 2005; WANG et al. 2005). The 70-mer oligo was designed from the 3'-end of each annotated gene. Every feature was spotted once on each slide.
20	GPL11043	Yeast Splicing/Expression Chip v6.2-6.3	7,625	UCSC	2010-10-12	UCSC	Saccharomyces cerevisiae	Oligo Array	spotted oligonucleotide, Yeast Splicing/Expression Chip v6.2-6.3, This is an oligonucleotide microarray designed to measure splicing and expression in yeast. Each intron containing gene has 3 features (Splice Junction, Intron, Exon2). The SJ oligo symmetrically spans the splice junction with 20nt on each side. The SJ, Int, and Ex2 oligos are custom designed 40-mers. The array also contains the Operon Yeast Genome 70-mer Set. All of the SJ, Int, and Ex2 oligos are printed 4 times, the Operon 70-mers are printed twice each. Keywords = Splicing and Expression Supplementary files: GAL files representing 2 different print layouts.

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