Gene Expression Omnibus (GEO) Overview Version:2014-04-12Japanese page
An overview of the GEO entries broken down by the measurement platforms and the features of the measured samples.
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Data Unit : [ DataSet / Sample / Platform ] Show explanation>> <<Hide explanation
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.
The numbers shown in the tabs are the numbers of the data (series, samples or platforms) belonging to the groups.
  Human
(3,985)
  Primates
(80)
  Rodents
(1,907)
  Mammals
(359)
  Vertebrates
(450)
  Invertebrates
(1,139)
  Plants
(2,490)
  Bacteria
(1,901)
  Viruses
(90)
  Phages
(11)
  Unclassified
(542)
  All
(13,032)
 
  SAGE NlaIII
(83)
  SAGE RsaI
(1)
  SAGE Sau3A
(5)
  MPSS
(18)
  GeneChip
(809)
  Tiling Array
(1,310)
  cDNA Array
(2,770)
  Oligo Array
(5,679)
  Bead Array
(210)
  Protein Array
(1)
  Antibody
(28)
  RT-PCR
(209)
  HT-Seq
(1,710)
  Other
(187)
  All
(13,032)
 
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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 GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array 15,617 Affymetrix, Inc. 2004-07-01 Affymetrix Danio rerio
Danio rerio
GeneChip in situ oligonucleotide, [Zebrafish] Affymetrix Zebrafish 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 Affymetrix GeneChip Zebrafish Genome Array can be used to study gene expression of over 14,900 Danio rerio transcripts. Sequence information for this array was selected from the following public data sources: RefSeq (July 2003), GenBank (release 136.0, June 2003), dbEST (July 2003), and UniGene (Build 54, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript. This array was designed in collaboration with representative members of the Zebrafish community and the National Institutes of Health. Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences. Annotations derived from Affymetrix CSV file dated 6/23/2004
2 GPL18378 [ZebGene-1_1-st] Affymetrix Genechip Zebrafish ST Genome Array 1.1, brainarray version 15 [zebgene11st_Dr_ENTREZG] 23,877 Affymetrix, Inc. 2014-03-05 Affymetrix Danio rerio
Danio rerio
GeneChip in situ oligonucleotide, [ZebGene-1_1-st] Affymetrix Genechip Zebrafish ST Genome Array 1.1, brainarray version 15 [zebgene11st_Dr_ENTREZG], 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
3 GPL16933 [ZebGene-1_0-st] Zebrafish Gene 1.0 ST Array [transcript (gene) version] 75,212 Affymetrix, Inc. 2013-03-29 Affymetrix Danio rerio
Danio rerio
GeneChip in situ oligonucleotide, [ZebGene-1_0-st] Zebrafish Gene 1.0 ST Array [transcript (gene) version], 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 Jan 29, 2013: annotation table updated with netaffx build 33
4 GPL90 [YG_S98] Affymetrix Yeast Genome S98 Array 9,335 Affymetrix, Inc. 2002-02-19 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [YG_S98] Affymetrix Yeast Genome S98 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 08, 2012: annotation table updated with netaffx build 32
5 GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array 10,928 Affymetrix, Inc. 2005-06-09 Affymetrix Schizosaccharomyces pombe,Saccharomyces cerevisiae
Schizosaccharomyces pombe,Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [Yeast_2] Affymetrix Yeast Genome 2.0 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® Yeast Genome 2.0 Array contains probe sets to detect transcripts from both Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are the two most commonly studied species of yeast. Providing comprehensive coverage of both species, the GeneChip Yeast Genome 2.0 Array includes approximately 5,744 probe sets for 5,841 of the 5,845 genes present in S. cerevisiae and 5,021 probe sets for all 5,031 genes present in S. pombe
6 GPL166 [Ye6100SubD] Affymetrix Yeast Genome 6K SubD Array 1,644 Affymetrix, Inc. 2002-05-14 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [Ye6100SubD] Affymetrix Yeast Genome 6K SubD Array, Affymetrix GeneChip Yeast Genome 6K SubD Array Ye6100subD. Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time. Annotations derived from Affymetrix 'Ye6100subD Probe Set Description' file (31 KB, 3/28/03)
7 GPL165 [Ye6100SubC] Affymetrix Yeast Genome 6K SubC Array 1,642 Affymetrix, Inc. 2002-05-14 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [Ye6100SubC] Affymetrix Yeast Genome 6K SubC Array, Affymetrix GeneChip Yeast Genome 6K SubC Array Ye6100subC. Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time. Annotations derived from Affymetrix 'Ye6100subC Probe Set Description' file (30 KB, 3/28/03)
8 GPL164 [Ye6100SubB] Affymetrix Yeast Genome 6K SubB Array 1,656 Affymetrix, Inc. 2002-05-14 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [Ye6100SubB] Affymetrix Yeast Genome 6K SubB Array, Affymetrix GeneChip Yeast Genome 6K SubB Array Ye6100subB. Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time. Annotations derived from Affymetrix 'Ye6100subB Probe Set Description' file (31 KB, 3/28/03)
9 GPL163 [Ye6100SubA] Affymetrix Yeast Genome 6K SubA Array 1,651 Affymetrix, Inc. 2002-05-14 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae
GeneChip in situ oligonucleotide, [Ye6100SubA] Affymetrix Yeast Genome 6K SubA 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 Affymetrix GeneChip Yeast Genome 6K SubA Array Ye6100subA. Based upon the September 1996 release of the Saccharomyces Genome Database (SGD) and contains probes for the approximately 6100 ORFs identified at that time. Annotations derived from Affymetrix 'Ye6100subA Probe Set Description' file (31 KB, 3/28/03) Keywords = Yeast
10 GPL10263 [X_tropicalis] Affymetrix Xenopus tropicalis Genome Array 59,021 Affymetrix, Inc. 2010-03-29 Affymetrix Xenopus (Silurana) tropicalis
Xenopus tropicalis
GeneChip in situ oligonucleotide, [X_tropicalis] Affymetrix Xenopus tropicalis 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 This array was designed in close collaboration with the Xenopus research community as part of the Affymetrix® GeneChip Consortia Program. Sequences used in the design of the array were selected from the Xenopus tropicalis UniGene database (Build 30, July 2006), GenBank® mRNAs for Xenopus tropicalis (up to September 12, 2006), and predicted gene sets from both the DOE Joint Genome Institute (Xentr4 transcripts, file creation date August 17, 2005, download date May 25, 2006) and Ensembl (release 40, download date May 2006).
11 GPL10756 [X_laevis_2] Affymetrix Xenopus laevis Genome 2.0 Array 32,635 Affymetrix, Inc. 2010-08-03 Affymetrix Xenopus laevis
Xenopus laevis
GeneChip in situ oligonucleotide, [X_laevis_2] Affymetrix Xenopus laevis Genome 2.0 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
12 GPL1318 [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array 15,611 Affymetrix, Inc. 2004-06-30 Affymetrix Xenopus laevis
Xenopus laevis
GeneChip in situ oligonucleotide, [Xenopus_laevis] Affymetrix Xenopus laevis 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 Affymetrix GeneChip Xenopus laevis Genome Array can be used to study gene expression of over 14,400 Xenopus laevis transcripts. Sequence information for this array was selected from the following public data sources: GenBank (release 135.0, April 2003), dbEST (June 2003), and UniGene (Build 36, June 2003). Probe sets on the array were designed with 16 oligonucleotide pairs to detect each transcript. This array was designed in collaboration with representative members of the Xenopus community and the National Institutes of Health. More information on the design of this array can be found at www.xenbase.org Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on the Affymetrix array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences.
13 GPL3802 [wheat] Affymetrix Wheat Genome Array 61,290 Affymetrix, Inc. 2006-05-24 Affymetrix Triticum aestivum
Triticum aestivum
GeneChip in situ oligonucleotide, [wheat] Affymetrix Wheat 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 This array contains 61,127 probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat genome. Sequence information for the GeneChip Wheat Genome Array includes public content from Triticum aestivum UniGene Build #38 (build date April 24, 2004). Also included are ESTs from the wheat species T. monococcum, T. turgidum, and Aegilops tauschii, and GenBank full-length mRNAs from all species through May 18, 2004.
14 GPL1320 [Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) Genome Array 16,602 Affymetrix, Inc. 2004-07-01 Affymetrix Vitis vinifera
Vitis vinifera
GeneChip in situ oligonucleotide, [Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) 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® Vitis vinifera Genome Array is the first array to provide comprehensive coverage of the V. vinifera genome. 14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species can be interrogated. Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Sixteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip® Vitis vinifera (Grape) Genome Array. Sequences used in the design of the V. vinifera Genome Array were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 7, Oct 2003). Annotations derived from Affymetrix CSV file dated 6/23/2004
15 GPL10230 [Vharveyis520694F] US Naval Research Laboratory V campbellii BAA-1116 whole genome microarray 12,717 US Naval Research Laboratory 2010-03-19 Affymetrix Vibrio harveyi ATCC BAA-1116
Vibrio harveyi ATCC BAA-1116
GeneChip in situ oligonucleotide, [Vharveyis520694F] US Naval Research Laboratory V campbellii BAA-1116 whole genome microarray, Affymetrix DNA microarray (Vharveyi520694F) that targets 4831 total CDS from the fully assembled and annotated V. harveyi BAA-1116 genome (Naval Research Laboratory sequencing effort GenBank CP001223-5)
16 GPL162 [uwyRhodo1a] Rhodobacter sphaeroides 2.4.1 GeneChip 5,355 University of Wyoming 2002-05-10 Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1
GeneChip in situ oligonucleotide, [uwyRhodo1a] Rhodobacter sphaeroides 2.4.1 GeneChip, 4242 candidate protein-encoding gene models Keywords = genechip Keywords = microarray Keywords = expression profile Keywords = transcription
17 GPL10818 [UCDavis]-[Delta smelt]-[18240]-[V:1.2] 18,240 University of California at Davis 2010-08-18 UCDavis School of Veterinary Medicine:APC Hypomesus transpacificus
Hypomesus transpacificus
cDNA Array spotted DNA/cDNA, [UCDavis]-[Delta smelt]-[18240]-[V:1.2], ONLY CLONES OF INTEREST HAVE BEEN SEQUENCED AND IDENTIFIED.
18 GPL1352 [U133_X3P] Affymetrix Human X3P Array 61,359 Affymetrix, Inc. 2004-07-19 Affymetrix Homo sapiens
Homo sapiens
GeneChip in situ oligonucleotide, [U133_X3P] Affymetrix Human X3P 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 X3P Array was designed specifically for whole-genome expression profiling of formalin-fixed, paraffin-embedded (FFPE) samples, and is now available via the GeneChip Made-to-Order program. Resulting from a collaboration between Affymetrix and Arcturus, this array is optimized as part of a system solution together with the Paradise Reagent System from Arcturus for expression analysis of FFPE samples. FFPE samples introduce unique challenges for microarray analysis, including potential fragmentation and chemical modification of RNA molecules. In order to overcome these challenges, the Paradise Reagent System was developed to provide RNA isolation and amplification reagents optimized for FFPE samples. In addition, the X3P Array is designed to focus on interrogating sequences located closer to the 3' end of the transcripts compared with standard GeneChip arrays. Together, the reagents and array accommodate the characteristics of the FFPE RNA samples, enabling genome-wide profiling. The target sequences on the X3P Arrays are identical to those used for designing the Human Genome U133 Plus 2.0 Array, for a total of 47,000 transcripts with 61,000 probe sets, although the probes on the two types of arrays are significantly different. As a result of the modification to the probe selection criteria, the majority of the probe sets on the X3P arrays are selected from the 300 bases at the most 3' end of the transcripts. This is different from the standard Affymetrix design strategy which selects probe sets within the region of 600 bases proximal to the 3' ends. To select probes for the 47,000 transcripts, it was not possible to identify high-performance probe sets within the shorter 300 base probe selection region for approximately 4,000 transcripts. For these transcripts, two sets of probes are represented on the arrays: 1) the original probe sets from the standard HG-U133 Plus design are replicated on the X3P arrays, and 2) the new, more 3' probe sets are also included although they fell below the minimum probe score selection threshold. In addition, fewer than 200 transcripts from the HG-U133 Plus design are only represented by the HG-U133 Plus probe sets, where no probe sets within the smaller (300 bps) probe selection region could be found. Annotations derived from Affymetrix CSV file dated 6/23/2004
19 GPL4685 [U133AAofAv2] Affymetrix GeneChip HT-HG_U133A Early Access Array 22,944 Affymetrix Japan 2006-12-20 Affymetrix Homo sapiens
Homo sapiens
GeneChip in situ oligonucleotide, [U133AAofAv2] Affymetrix GeneChip HT-HG_U133A Early Access Array, HT-HG_U133A (early access version) high-throughput array (Affy part number 520276)
20 GPL9209 [TTHB8401a520105F] Riken Thermus thermophilus HB8 4K mRNA custom array, library Rev.2 3,492 RIKEN Harima Institute 2009-09-17 Affymetrix Thermus thermophilus HB8
Thermus thermophilus HB8
GeneChip in situ oligonucleotide, [TTHB8401a520105F] Riken Thermus thermophilus HB8 4K mRNA custom array, library Rev.2,
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