Gene Expression Omnibus (GEO) Overview Version：2013-04-06Japanese 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
(3,705)		   Primates
(37)		   Rodents
(1,748)		   Mammals
(295)		   Vertebrates
(402)		   Invertebrates
(1,004)		   Plants
(2,170)		   Bacteria
(1,636)		   Viruses
(78)		   Phages
(8)		   Unclassified
(399)		   All
(11,528)		  
  SAGE NlaIII
(37)		   SAGE RsaI
(0)		   SAGE Sau3A
(1)		   MPSS
(9)		   GeneChip
(78)		   Tiling Array
(226)		   cDNA Array
(558)		   Oligo Array
(799)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(0)		   HT-Seq
(432)		   Other
(26)		   All
(2,170)		  
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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 GPL6891 S. cerevisiae Tiling1.0R Array SNPScanner compatible 12,070,743 Cancer Research UK London Research Institute 2008-05-22 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae		 GeneChip in situ oligonucleotide, S. cerevisiae Tiling1.0R Array SNPScanner compatible, GEO platform for S.cerevisiae Tiling1.0R Sc03b_MR_v04 containing per base pair features compatible with SNPScanner output. Gresham, D. et al. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311, 1932-1936 (2006).
2 GPL6957 SAGE:17:NlaIII:Solanum phureja 7,625,793 2008-06-13 Solanum phureja
Solanum phureja		 SAGE NlaIII SAGE NlaIII, SAGE:17:NlaIII:Solanum phureja, This is a virtual platform for SAGE libraries generated for Solanum phureja using NlaIII as an anchor enzyme.
3 GPL6705 Illumina Arabidopsis thaliana SBS inflorescence (polyA RNA) 7,109,274 Delaware Biotechnology Institute 2008-04-08 Arabidopsis thaliana
Arabidopsis thaliana		 Other other, Illumina Arabidopsis thaliana SBS inflorescence (polyA RNA),
4 GPL1979 AtTile1F to Arabidopsis Tiling 1.0F 6,184,720 The Salk Institute 2005-04-20 Affymetrix Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, AtTile1F to Arabidopsis Tiling 1.0F, Affymetrix Whole Genome Tiling Array Chip designed by the Salk Institute and Affymetrix.
5 GPL1980 AtTile1R to Arabidopsis Tiling 1.0R 6,184,720 The Salk Institute 2005-04-20 Affymetrix Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, AtTile1R to Arabidopsis Tiling 1.0R, Affymetrix Whole Genome Tiling Array Chip designed by the Salk Institute and Affymetrix.
6 GPL7071 Small RNA SBS signatures indentified from maize using Illumina's SBS technnology 5,386,553 University of Delaware 2008-07-19 Zea mays
Zea mays		 Other other, Small RNA SBS signatures indentified from maize using Illumina's SBS technnology,
7 GPL6708 Illumina Arabidopsis thaliana SBS inflorescence (small RNA) 3,589,785 Delaware Biotechnology Institute 2008-04-08 Arabidopsis thaliana
Arabidopsis thaliana		 Other other, Illumina Arabidopsis thaliana SBS inflorescence (small RNA),
8 GPL7639 Arabidopsis thaliana genome tiling 1.0R array 2,876,199 UCLA 2008-11-14 Affymetrix Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis thaliana genome tiling 1.0R array, The Arabidopsis tiling array has 2.8 million probes, spaced 35 bases apart, with one 25 base probe within each window. Tiles most of the Arabidopsis genome.
9 GPL8620 Penn State Physcomitrella SOLiD sequencing 2,784,945 Pennsylvania State University 2009-06-01 Physcomitrella patens
Physcomitrella patens		 HT Sequencing MPSS, Penn State Physcomitrella SOLiD sequencing, Processed degradome signatures representing the 5' ends of uncapped, polyA+ mRNAs. AB SOLiD System 2.0
10 GPL9286 Yeast 2.7M whole genome tiling array (Sc03b_MR_V04) 2,697,594 UCLA 2009-09-24 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae		 Tiling Array in situ oligonucleotide, Yeast 2.7M whole genome tiling array (Sc03b_MR_V04),
11 GPL6670 CSIRO-PI Oryza Sativa small RNA sequences 2007 (Solexa sequenced) 2,683,656 CSIRO Plant Industry 2008-04-01 Oryza sativa
Oryza sativa		 HT Sequencing other, CSIRO-PI Oryza Sativa small RNA sequences 2007 (Solexa sequenced), Small RNAs from Oryza Sativa were sequenced from 1-5 days-after-fertilisation grains and 6-10 days-after-fertilisation grains, using the Solexa sequencing technology. This is the unique list of trimmed sequences obtained from these experiments
12 GPL4065 Affymetrix S. cerevisiae tiling 1.0R (Sc03b_MR_v03.bpmap) 2,660,310 University of Washington 2006-08-07 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae		 Tiling Array in situ oligonucleotide, Affymetrix S. cerevisiae tiling 1.0R (Sc03b_MR_v03.bpmap), Strain S288C Design based on October 2003 cerevisiae genome
13 GPL6476 Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (Sc03b_MR_v04) 2,635,714 FHCRC 2008-02-08 Affymetrix Saccharomyces cerevisiae
Saccharomyces cerevisiae		 Tiling Array in situ oligonucleotide, Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (Sc03b_MR_v04),
14 GPL8655 Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 1 2,434,281 University of Chicago 2009-06-04 Affymetrix Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 1, This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse A. thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along A. thaliana genome with ~35 bp resolution on both strands. The reference genome of the array design is Col-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR7.
15 GPL10855 Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 2 2,417,869 University of Chicago 2010-08-25 Affymetrix Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis thaliana SNP-tiling array AtSNPtile ver. 2, This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse A. thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along the A. thaliana genome with ~35 bp resolution. The reference genome for the array design is Columbia-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR9.
16 GPL9821 NimbleGen T. reesei 2.1M HD2 arrayCGH 2,163,898 VTT Technical Research Centre 2009-12-22 NimbleGen Hypocrea jecorina
Hypocrea jecorina		 Oligo Array in situ oligonucleotide, NimbleGen T. reesei 2.1M HD2 arrayCGH, Build: Trichoderma reesei v2.0 (http://genome.jgi-psf.org/Trire2/Trire2.home.html)
17 GPL15056 NimbleGen Zilberman Arabidopsis HD2 array [080709_AT8_DZ_ChIP_HX1] 2,160,801 University of California at Berkeley 2011-12-23 NimbleGen Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, NimbleGen Zilberman Arabidopsis HD2 array [080709_AT8_DZ_ChIP_HX1], TAIR 8 designname: 080709_AT8_DZ_ChIP_HX1 designid: 7848
18 GPL8790 NimbleGen Zea Mays 2.1M array 2,124,029 Iowa State University 2009-07-02 NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen Zea Mays 2.1M array, Probe sequences were aligned to Maize pseudomolecules from the Arizona Genome Institure (AGI) released on March, 20th, 2009 to determine their positions in the genome (positions are reflected in the Platform data table). Due to the fact that our array was designed using B73 genomic sequence and the high rate of polymorphism between B73 and Mo17, the CGH data violated the assumption for the regularly used Q-spline normalization to make two channels of hybridization intensities comparable. We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels. After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis. NimbleGen .ndf array description file linked below as supplementary file.
19 GPL13499 NimbleGen 2.1M Maize Methylation Array 2,120,701 University of Minnesota 2011-05-05 NimbleGen Zea mays
Zea mays		 Oligo Array in situ oligonucleotide, NimbleGen 2.1M Maize Methylation Array, Order ID#: OID29684 Native array description file: 100629_Zea_Mays_NS_CGH_HX1.ndf Native array description file: 100629_Zea_Mays_NS_CGH_HX1.pos The sequences of the oligonucleotides are available in the supplementary .ndf file.
20 GPL10686 NimbleGen 2.1M HD2 Arabidopsis HD2 Custom Array 2,053,677 Nara Institute of Science and Technology 2010-07-15 NimbleGen Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, NimbleGen 2.1M HD2 Arabidopsis HD2 Custom Array, The 2.1M HD2 array is custom-made by NimbleGen. The array covers entire genome of A. thaliana. BUILD: TAIR genome release TAIR8 Accession numbers of genome sequences used to make HD2 array: chromosome 1:NC_003070.6 chromosome 2:NC_003071.4 chromosome 3:NC_003074.5 chromosome 4:NC_003075.4 chromosome 5:NC_003076.5 NimbleGen description files linked below: 2008-08-06_RDKK096_Atha_CGH_HX1a.ndf 2008-08-06_RDKK096_Atha_CGH_HX1a.pos
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