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.
RSS
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)
 
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 GPL1443 Massively Parallel Signature Sequencing - MPSS (classic method) 391,669 Lynx Therapeutics, Inc. 2004-09-10 Homo sapiens
Homo sapiens
MPSS MPSS, Massively Parallel Signature Sequencing - MPSS (classic method), Sequencing from the 3' most DpnII site from mRNA using Lynx's MPSS technology. MPSS allows a comprehensive survey of all expressed transcripts in a cell or tissue, without apriori knowledge. This dataset was annotated using a combination of LocusLink, Unigene (build 171) and the latest human build as provided from UCSC (hg16). Annotation Classe Table: Virtual Signature Class mRNA Orientation Poly-Adenylation Features Position 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 5' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown- Derived from Genomic Sequence Not applicable Not applicable Keywords = MPSS, mRNA sequencing, tags
2 GPL3776 Rice small RNA MPSS signatures 299,454 University of Delaware 2006-05-17 Oryza sativa
Oryza sativa
MPSS MPSS, Rice small RNA MPSS signatures, small RNA MPSS signatures represent the 5' end of endogenous small RNA (e.g. miRNA and siRNA that average 21-24 nt). These molecules are typically associated with gene silencing, not mRNA expression. All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630). The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567).
3 GPL5800 Arabidopsis mRNA MPSS signatures 297,313 University of Manchester 2007-09-04 MPSS Arabidopsis thaliana
Arabidopsis thaliana
MPSS MPSS, Arabidopsis mRNA MPSS signatures, mRNA MPSS signatures capture the 17 bases from near the 3' end of poly(A)+ transcripts. All MPSS was performed as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
4 GPL3777 Rice mRNA MPSS signatures 249,990 University of Delaware 2006-05-17 Oryza sativa
Oryza sativa
MPSS MPSS, Rice mRNA MPSS signatures, mRNA MPSS signatures capture the 17 bases from near the 3' end of poly(A)+ transcripts All MPSS was performed as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
5 GPL2675 Small RNA identification in Arabidopsis thaliana using modified MPSS 181,582 University of Delaware 2005-07-26 Arabidopsis thaliana
Arabidopsis thaliana
MPSS MPSS, Small RNA identification in Arabidopsis thaliana using modified MPSS, All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630). The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper associated with this dataset (Lu et al., 2005). The signatures with "flag = 1" match to tRNAs, rRNAs, snoRNAs and snRNAs.
6 GPL4337 Chicken mRNA MPSS signatures 142,022 Seoul National University 2006-09-17 LYNX Gallus gallus
Gallus gallus
MPSS MPSS, Chicken mRNA MPSS signatures, The generation of MPSS datasets in the gonad and PGCs samples was performed by Takara Biotechnology Cooperation (Shiga, Japan). Annotation Classe Table: Virtual Signature Class mRNA Orientation Poly-Adenylation Features Position Class PASa PATb Strand Position 1 yes yes Forward The first one 5’ to the PAS and PAT 2 yes no Forward The first one 5’to the PAS 3 no yes Forward The first one 5’ to the PAT 4 no no Forward The most 3’ signature of the sequence 5 yes/no yes/no Forward Not the most 3’ signature of the sequence 11 yes yes Reverse complement The first one 5’ to the PAS and PAT 12 yes no Reverse complement The first one 5’to the PAS 13 no yes Reverse complement The first one 5’ to the PAT 14 no no Reverse complement The most 3’ signature of the reverse complement strand of the cDNA sequence 15 yes/no yes/no Reverse complement Not the most 3’ signature of the reverse complement strand of the cDNA sequence 22 yes no unknown The first one 5’ to the polyA signal 23 no yes unknown The first one 5’ to the polyA tail 24 no no unknown The most 3’ signature of the sequence 25 yes/no yes/no unknown Not the most 3’ signature of the sequence 1000 NA NA Forward or reverse complement The signature has only chromosome matches 0 NA NA Forward or reverse complement The signature matches more than 100 chromosome loci
7 GPL7013 IPPE Rice MPSS 111,161 Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences 2008-07-01 Oryza sativa
Oryza sativa
MPSS MPSS, IPPE Rice MPSS, All MPSS was performed as described by Mineno et al.(Nucleic Acids Res. 2006 1765:1771).
8 GPL1010 MPSS [DpnII: Mus musculus] signature list 71,752 Solexa 2004-02-25 Mus musculus
Mus musculus
MPSS MPSS, MPSS [DpnII: Mus musculus] signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm. Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
9 GPL3835 MPSS inner ear signature list 61,662 National Institute on Deafness and Other Communication Disorders (NIDCD) 2006-06-01 Mus musculus
Mus musculus
MPSS MPSS, MPSS inner ear signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm. Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
10 GPL3062 oyster MPSS 52,828 Solexa, Inc. 2005-11-09 Crassostrea gigas
Crassostrea gigas
MPSS MPSS, oyster MPSS , Sequencing from the 3' most DpnII site from mRNA using Solexa's MPSS technology. MPSS allows a comprehensive survey of all expressed transcripts in a cell or tissue, without apriori knowledge.
11 GPL4571 MPSS 20bp [DpnII: Mus musculus] signature list 50,727 Harvard Medical School 2006-11-18 Mus musculus
Mus musculus
MPSS MPSS, MPSS 20bp [DpnII: Mus musculus] signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm. Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
12 GPL4572 MPSS 17bp [DpnII: Mus musculus] signature list 47,450 Harvard Medical School 2006-11-18 Mus musculus
Mus musculus
MPSS MPSS, MPSS 17bp [DpnII: Mus musculus] signature list, MPSS signatures detected in Lynx mouse transcriptome analysis experiment. To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm. Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position ------------------------------------------------------------------------------------------ 0 Either - Repeat Warning Not applicable Not applicable 1 Forward Strand Poly-A Signal, Poly-A Tail 3' most 2 Forward Strand Poly-A Signal 3' most 3 Forward Strand Poly-A Tail 3' most 4 Forward Strand None 3' most 5 Forward Strand None Not 3' most 6 Forward Strand Internal Poly-A Not 3' most 11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most 12 Reverse Strand Poly-A Signal 5' most 13 Reverse Strand Poly-A Tail 5' most 14 Reverse Strand None 5' most 15 Reverse Strand None Not 5' most 16 Reverse Strand Internal Poly-A Not 3' most 22 Unknown Poly-A Signal Last before signal 23 Unknown Poly-A Tail Last before tail 24 Unknown None Last in sequence 25 Unknown None Not last 26 Unknown Internal Poly-A Not 3' most 1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
13 GPL6177 Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F (Feature Number version) 45,220 Agilent Technologies 2007-11-21 Agilent Technologies Arabidopsis thaliana
Arabidopsis thaliana
MPSS in situ oligonucleotide, Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F (Feature Number version), The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. Arrays of this design have barcodes that begin with 16015059 or 2515059. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7299.
14 GPL2871 Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version) 44,290 Agilent Technologies 2005-09-23 Agilent Technologies Arabidopsis thaliana
Arabidopsis thaliana
MPSS in situ oligonucleotide, Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version), The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. Arrays of this design have barcodes that begin with 16012600 or 2512600. 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. *** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7270.
15 GPL7299 Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F (Probe Name version) 37,553 Agilent Technologies 2008-09-12 Agilent Technologies Arabidopsis thaliana
Arabidopsis thaliana
MPSS in situ oligonucleotide, Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F (Probe Name version), The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL6177.
16 GPL7270 Agilent-012600 Arabidopsis 3 Oligo Microarray G4142A (Probe Name version) 37,494 Agilent Technologies 2008-09-09 Agilent Technologies Arabidopsis thaliana
Arabidopsis thaliana
MPSS in situ oligonucleotide, Agilent-012600 Arabidopsis 3 Oligo Microarray G4142A (Probe Name version), The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL2871.
17 GPL5678 MPSS tags from techical comparison of SAGE and MPSS 30,099 University of Oxford 2007-07-27 Homo sapiens
Homo sapiens
MPSS MPSS, MPSS tags from techical comparison of SAGE and MPSS, A list of all tags obtained in a set of MPSS libraries used to analyse the transcriptome of a CD4+ T cell clone.
18 GPL17594 Arabidopsis thaliana MPSS 0 CINVESTAV 2013-08-20 Arabidopsis thaliana
Arabidopsis thaliana
MPSS MPSS, Arabidopsis thaliana MPSS,