Gene Expression Omnibus (GEO) Overview Version´╝Ü2014-04-12Japanese 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
(9)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(1)
  GeneChip
(14)
  Tiling Array
(10)
  cDNA Array
(79)
  Oligo Array
(252)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(2)
  HT-Seq
(81)
  Other
(1)
  All
(450)
 
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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 GPL6541 CSIRO-Chicken-Solexa sequencing-embryo miRNA 608,750 University of Queensland 2008-03-02 Illumina/Solexa, USA Gallus gallus
Gallus gallus
HT Sequencing other, CSIRO-Chicken-Solexa sequencing-embryo miRNA,
2 GPL7207 Hubrecht Institute Zebrafish Zili- and Ziwi-interacting small RNAs (454 GS FLX system) 249,524 Hubrecht Institute 2008-08-26 Hubrecht Institute Danio rerio
Danio rerio
HT Sequencing MPSS, Hubrecht Institute Zebrafish Zili- and Ziwi-interacting small RNAs (454 GS FLX system),
3 GPL15124 University of Padova Anguilla anguilla 8x15K v1.0 15,449 University of Padova 2012-01-12 Agilent Technologies Anguilla anguilla
Anguilla anguilla
HT Sequencing in situ oligonucleotide, University of Padova Anguilla anguilla 8x15K v1.0, Target sequences to be included in the European eel microarray were obtained from the assembly of a total of 640,040 sequence reads obtained by 454 sequencing. The array included all annotated sequences with a blast hit to vertebrates and invertebrates but excluding bacteria, virus, plants, fungi and protozoa. For 12,296 contigs, the putative orientation was unambiguous and a single probe was designed. For 1,390 contigs, the putative orientation was ambiguous and two probes were designed. In order to minimize assembler redundancy, 163 contigs differing by less than 3 nucleotide changes were discarded. The final number of probes was 14,913. Probe design was carried out using Agilent eArray Interface which applies proprietary prediction algorithms to design 60-mer oligoprobes. Microarrays were synthesized in situ using the Agilent ink-jet technology with an 8x15K format (8 arrays in a single slide). Each array contained default positive and negative controls.
4 GPL16714 Agilent-036974 S. solea array (Feature Number version) 15,237 University of Padova 2013-02-22 Agilent Technologies Solea solea
Solea solea
HT Sequencing in situ oligonucleotide, Agilent-036974 S. solea array (Feature Number version), GE 8x15k oligo microarray that covers 14,531 annotated transcripts (Isotigs and Singletons) of the common sole (Solea solea). Roche 454 sequence reads were produced from a normalized cDNA library constructed using a mixture of RNAs from whole larvae (1-4-6-11-13-18-20-33 days posth hatching) and adult tissues (liver and intestine). All 454 sequences were then assembled into Isotigs, representing putative transcripts, by using Newbler 2.6 software with default settings. All assembled Isotigs are stored in the public database Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa) under accession number GAAQ00000000, while Singletons can be directly retrieved from the NCBI Sequence Read Archive (SRA) under accession number SRA058691. Microarray design has been carried out on the basis of 25,252 contigs (Isotigs) and 66,026 singletons (with a minimal length of 200 nt) obtained from the Roche 454 sequencing of a normalized cDNA library of sole larval stages (from 1 to 33 days post hatching) and adult tissues. Only annotated sequences were used for microarray design. One probe for annotated sequences with known orientation (14,357) was designed while, whenever possible, two probes with both orientations were designed for sequences with unknown/ambiguous orientation (174 indicated by Isotig/Singleton ID plus prefix S_ or AS_ ). A total of 14,701 oligonucleotide probes (60 nt) were in situ synthesized onto the array, using Agilent non-contact ink-jet technology (8 x 15K format, including default positive and negative controls). Probe ID on the array corresponds to transcript name (either Isotig or Singleton).
5 GPL16124 Agilent-036353 S.solea_v2 array (Feature Number version) 15,210 University of Padova 2012-10-01 Agilent Technologies Solea solea
Solea solea
HT Sequencing in situ oligonucleotide, Agilent-036353 S.solea_v2 array (Feature Number version), GE 8x15k oligo microarray that covers 12,836 annotated transcripts (Isotigs) of the common sole (Solea solea). Roche 454 sequence reads were produced from a normalized cDNA library constructed using a mixture of RNAs from whole larvae (1-4-6-11-13-18-20-33 days posth hatching) and adult tissues (liver and intestine). All 454 sequences were then assembled into Isotigs, representing putative transcripts, by using Newbler 2.6 software with default settings. All Isotigs are stored in the public database Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa) under accession number GAAQ00000000 (To be made publicly available after paper publication), transcripts sequences can be retrieved by using IsotigName as search criteria. One probe for annotated sequences with known orientation (10,987) was designed while, whenever possible, two probes with both orientations were designed for Isotigs with unknown/ambiguous orientation (1,849 indicated by Isotig ID plus prefix S_ or AS_ ). A total of 14,674 oligonucleotide probes (60 nt) were in situ synthesized onto the array, using Agilent non-contact ink-jet technology (8 x 15K format, including default positive and negative controls). Probe ID on the array corresponds to IsotigName. In situ long-oligonucleotide microarray.
6 GPL10164 Illumina Genome Analyzer (Danio rerio) 0 2010-03-10 Danio rerio
Danio rerio
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Danio rerio),
7 GPL10223 Illumina Genome Analyzer (Gallus gallus) 0 2010-03-18 Gallus gallus
Gallus gallus
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Gallus gallus),
8 GPL10241 Illumina Genome Analyzer IIx (Danio rerio) 0 2010-03-23 Danio rerio
Danio rerio
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer IIx (Danio rerio),
9 GPL10398 Illumina Genome Analyzer II (Lateolabrax japonicus) 0 2010-05-06 Lateolabrax japonicus
Lateolabrax japonicus
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer II (Lateolabrax japonicus),
10 GPL10484 AB SOLiD System 2.0 (Xenopus laevis) 0 2010-06-04 Xenopus laevis
Xenopus laevis
HT Sequencing high-throughput sequencing, AB SOLiD System 2.0 (Xenopus laevis),
11 GPL10515 Illumina Genome Analyzer (Hypophthalmichthys nobilis) 0 2010-06-08 Hypophthalmichthys nobilis
Hypophthalmichthys nobilis
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Hypophthalmichthys nobilis),
12 GPL10516 Illumina Genome Analyzer (Hypophthalmichthys molitrix) 0 2010-06-08 Hypophthalmichthys molitrix
Hypophthalmichthys molitrix
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Hypophthalmichthys molitrix),
13 GPL10658 AB SOLiD System 3.0 (Danio rerio) 0 2010-07-08 Danio rerio
Danio rerio
HT Sequencing high-throughput sequencing, AB SOLiD System 3.0 (Danio rerio),
14 GPL10692 Illumina Genome Analyzer (Anas platyrhynchos) 0 2010-07-15 Anas platyrhynchos
Anas platyrhynchos
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Anas platyrhynchos),
15 GPL11029 454 GS 20 (Petromyzon marinus) 0 2010-10-08 Petromyzon marinus
Petromyzon marinus
HT Sequencing high-throughput sequencing, 454 GS 20 (Petromyzon marinus),
16 GPL11102 454 GS (Danio rerio) 0 2010-10-22 Danio rerio
Danio rerio
HT Sequencing high-throughput sequencing, 454 GS (Danio rerio),
17 GPL11303 Illumina Genome Analyzer (Paralichthys olivaceus) 0 2010-12-10 Paralichthys olivaceus
Paralichthys olivaceus
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer (Paralichthys olivaceus),
18 GPL11347 Illumina Genome Analyzer II (Leucoraja erinacea) 0 2010-12-21 Leucoraja erinacea
Leucoraja erinacea
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer II (Leucoraja erinacea),
19 GPL11348 Illumina Genome Analyzer II (Scyliorhinus canicula) 0 2010-12-21 Scyliorhinus canicula
Scyliorhinus canicula
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer II (Scyliorhinus canicula),
20 GPL11349 Illumina Genome Analyzer II (Callorhinchus milii) 0 2010-12-21 Callorhinchus milii
Callorhinchus milii
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer II (Callorhinchus milii),
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