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 GPL12620 Nimblegen Maize Whole-Genome Microarray 385K (VersionV1_4a.53) 92,492 Iowa State University 2011-02-01 NimbleGen Systems Inc. Zea mays
Zea mays
Tiling Array in situ oligonucleotide, Nimblegen Maize Whole-Genome Microarray 385K (VersionV1_4a.53), This platform version is based on gene-models (probe-sets) from Maize RefGen V1(4a.53) using the expression probes only. The original design is a custom NimbleGen design which used 385k probes. The array design has 330803 expression probes and 58339 tiling probes. Zea maize design from customer-provided regions with expression and tiling probes were placed into two different containers: 330803 expression probes (5 probes per gene, no additional replicates) and 58339 tiling probes (probe spacing of 45bp).
2 GPL11233 Agilent-027313 Yersinia pestis CO92 tiling array [YP_tiling_244k] 243,504 J. Craig Venter Institute 2010-11-19 Agilent Technologies Yersinia pestis CO92
Yersinia pestis CO92
Tiling Array in situ oligonucleotide, Agilent-027313 Yersinia pestis CO92 tiling array [YP_tiling_244k], Yersinia pestis tiling array. Arrays of this design have barcodes that begin with 16027313 or 2527313.. Orientation:. Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.. The ID column represents the Agilent Feature Extraction feature number.. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).. To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions..
3 GPL9778 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 1 2,160,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 1, JGI 4.1 (UCSC xenTro2)
4 GPL9779 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 2 2,160,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 2, JGI 4.1 (UCSC xenTro2)
5 GPL9780 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 3 2,160,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 3, JGI 4.1 (UCSC xenTro2)
6 GPL9781 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 4 2,160,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 4, JGI 4.1 (UCSC xenTro2)
7 GPL9782 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5a 720,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5a, JGI 4.1 (UCSC xenTro2)
8 GPL9783 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5b 720,000 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5b, JGI 4.1 (UCSC xenTro2)
9 GPL9784 NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5c 191,446 Radboud University 2009-12-10 NimbleGen Xenopus (Silurana) tropicalis
Xenopus tropicalis
Tiling Array in situ oligonucleotide, NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5c, JGI 4.1 (UCSC xenTro2)
10 GPL5159 NimbleGen pathogenic virus whole-genome tiling array_Patharray2 54,117 Genome Institute of Singapore 2007-05-11 NimbleGen Systems Inc. Viruses
Viruses
Tiling Array in situ oligonucleotide, NimbleGen pathogenic virus whole-genome tiling array_Patharray2, Pathogen detection chip Patharray2 is a tiling array covering the full genomes of 35 viruses (sequence downloaded from NCBI taxonomy webpage). Pathogen recognition signatures, comprising all probes which will hybridize to a given pathogen (including all similar probes from other pathogens which are predicted to cross-hybridize) were created. There are 7 replicates of each 40-mer probe, together with hybridization controls. The Platform data table reflects a condensed representation of the array. The complete array layout file (including the 7 replicates of each 40-mer probe) is linked as a supplementary file.
11 GPL15824 NimbleGen Custom Desulfovibrio alaskensis G20 Tiling [NimbleGen_G20_2082K_1] 2,005,818 Lawrence Berkeley Lab 2012-07-18 NimbleGen unidentified
unidentified
Tiling Array in situ oligonucleotide, NimbleGen Custom Desulfovibrio alaskensis G20 Tiling [NimbleGen_G20_2082K_1], NC_007519 100318_DdesG20_JK_EXP_HX1.ndf
12 GPL17859 091006_AD_ZM4_2_1M_exp_HX1 1,870,443 Lawrence Berkeley Lab 2013-10-29 NimbleGen unidentified
unidentified
Tiling Array in situ oligonucleotide, 091006_AD_ZM4_2_1M_exp_HX1, Genome sequence from refseq (main chromosome and 5 plasmids) Analysis was not based on gene annotation except that only coding probes were used to build the model of how genomic control intensity affects tiling intensity native array description file = 091006_AD_ZM4_2_1M_exp_HX1.ndf
13 GPL9285 Trypanosoma brucei Strain 927 Oligonucleotide Tiling Array 8,126 Seattle Biomedical Research Institute 2009-09-24 NimbleGen Trypanosoma brucei TREU927
Trypanosoma brucei TREU927
Tiling Array in situ oligonucleotide, Trypanosoma brucei Strain 927 Oligonucleotide Tiling Array, 60mer probes were designed to known coding regions of Trypanosoma brucei strain 927, Approximately 8 probes per gene were designed to each of the 8562 protein coding genes, and 3 probes were designed to each RNA gene. Each probe was placed on the chip in triplicate. Remaining space on the array was fillied with 50mer probes spaced evenly through unnannotated regions of the genome, though these probes were not considered in the final analysis. Only one copy of each unnannotated region probe was placed on each chip. The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features (and probe sequences) is linked as a supplementary file at the foot of this record. Native NimbleGen files (ndf, ngd) are also linked as supplementary files.
14 GPL10752 ENS SGDB Trichoderma atroviride Ta10_Tiling93_1 387,105 École Normale Supérieure 2010-08-02 Agilent Technologies Trichoderma atroviride
Trichoderma atroviride
Tiling Array in situ oligonucleotide, ENS SGDB Trichoderma atroviride Ta10_Tiling93_1, Trichoderma atroviride Tiling array. One probe has been design every 93 base every other strand. The probe design has been done according to T. atroviride v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Triat1/Triat1.home.html The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand. The first number merge to Ta suffix indicates the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV
15 GPL15612 NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (1 of 3) 2,123,031 University of Notre Dame 2012-05-25 NimbleGen Tribolium castaneum
Tribolium castaneum
Tiling Array in situ oligonucleotide, NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (1 of 3), This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (1 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
16 GPL15613 NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (2 of 3) 2,123,031 University of Notre Dame 2012-05-25 NimbleGen Tribolium castaneum
Tribolium castaneum
Tiling Array in situ oligonucleotide, NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (2 of 3), This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (2 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
17 GPL15614 NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (3 of 3) 2,123,030 University of Notre Dame 2012-05-25 NimbleGen Tribolium castaneum
Tribolium castaneum
Tiling Array in situ oligonucleotide, NimbleGen Tribolium castaneum Whole-genome Tiling Array Set (3 of 3), This is a Red flour beetle (Tribolium castaneum) whole-genome tiling array set (3 of 3) in HD2 1-plex format with 2.1M probes, manufactured by Roche NimbleGen.
18 GPL8305 Toxoplasma gondii ChIP-chip genome-wide tiling array 751,209 CNRS 2009-03-16 Nimblegen Toxoplasma gondii ME49
Toxoplasma gondii ME49
Tiling Array in situ oligonucleotide, Toxoplasma gondii ChIP-chip genome-wide tiling array, Tiling microarray encompassing 65 Mb of Toxoplasma gondii (strain ME49) genome (chromosomes Ia, Ib, II, III, IV, V, VIIa, VIIb, VIII, IX, X, XI and XII). RefSeq genome accession: NZ_ABPA00000000.1. 50mer probes selected at 82 bp interval spacing From : TOXODB release 4.0 Genomic sequence available at: http://toxodb.org/common/downloads/release-4.0/ Native NimbleGen files (ndf, pos) are linked below as supplementary files.
19 GPL15563 Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 1 of 2 367,002 Albert Einstein College of Medicine 2012-05-14 Nimblegen Toxoplasma gondii ME49
Toxoplasma gondii ME49
Tiling Array in situ oligonucleotide, Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 1 of 2, Tiling microarray encompassing 63 Mb of Toxoplasma gondii genome (reference genome strain ME49; chromosomes Ia, Ib, II, III, IV, V, VI, VIIa, VIIb, VIII, IX, X, XI and XII, and unmapped contigs). The genome wide chip was designed using the Nimblegen isothermal protocol design based upon Release 4.1 of the T. gondii ME49 genome (www.toxodb.org). The "target Tm" for all probes is 76 C. There are 392,074 probes total on each array for a total of 784,148 probes, including controls. Of these, 366,336 are T. gondii specific probes on each of two slides, Tiling1 and Tiling2 for a total of 732,672 toxo specific probes. The design name for each chip is 2007-05-02_Toxo_WG_tiling1 and 2007-05-02_Toxo_WG_tiling2. Genomic sequence available at: http://toxodb.org/common/downloads/release-4.1/ Native NimbleGen files (ndf, pos) are linked below as supplementary files.
20 GPL15564 Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 2 of 2 367,002 Albert Einstein College of Medicine 2012-05-14 Nimblegen Toxoplasma gondii ME49
Toxoplasma gondii ME49
Tiling Array in situ oligonucleotide, Toxoplasma gondii ME49 ChIP-chip genome-wide tiling array 2 of 2, Tiling microarray encompassing 63 Mb of Toxoplasma gondii genome (reference genome strain ME49; chromosomes Ia, Ib, II, III, IV, V, VI, VIIa, VIIb, VIII, IX, X, XI and XII, and unmapped contigs). The genome wide chip was designed using the Nimblegen isothermal protocol design based upon Release 4.1 of the T. gondii ME49 genome (www.toxodb.org). The "target Tm" for all probes is 76 C. There are 392,074 probes total on each array for a total of 784,148 probes, including controls. Of these, 366,336 are T. gondii specific probes on each of two slides, Tiling1 and Tiling2 for a total of 732,672 toxo specific probes. The design name for each chip is 2007-05-02_Toxo_WG_tiling1 and 2007-05-02_Toxo_WG_tiling2. Genomic sequence available at: http://toxodb.org/common/downloads/release-4.1/ Native NimbleGen files (ndf, pos) are linked below as supplementary files.
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