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
(0)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(0)
  Tiling Array
(2)
  cDNA Array
(8)
  Oligo Array
(46)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(0)
  HT-Seq
(32)
  Other
(2)
  All
(90)
 
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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 GPL3719 Yang et. al. Oligoarray of CfMNPV select ORFs 192 University of Guelph 2006-05-02 Biotechnology Research Institute, Montreal, Canada Choristoneura fumiferana MNPV
Choristoneura fumiferana MNPV
Oligo Array spotted oligonucleotide, Yang et. al. Oligoarray of CfMNPV select ORFs, The array included 46 oligonucleotides (1.0 µg/µl) representing 23 CfMNPV ORFs, one for the coding strand and the other for the non-coding strand. Purified viral genomic DNA (50, 25, 5 ng/µl) was used as a positive control. A mixture of 18 viral oligonucleotides (50 ng/µl each) was served as a second positive control. The array included 2 oligos (At1 and At2) of Arabidopsis chlorophyll synthase gene to be hybridized with the spike RNA, and 2 oligos (HAT4, YaaJ) as negative controls. The array also included 5 insect internal control oligos. Each probe was printed in triplicate.
2 GPL6599 WUSTL Human Herpesvirus 1 389 Washington Univeristy School of Medicine 2008-03-18 Washington University School of Medicine Human herpesvirus 1
Human herpesvirus 1
Oligo Array spotted oligonucleotide, WUSTL Human Herpesvirus 1, To construct a gene-specific microarray of the Human Herpesvirus 1 (Herpes simplex virus type 1) genome, we designed 70-mer oligonucleotide array elements. Predicted and known HHV-1 genes were obtained from the strain 17 sequence on the NCBI website (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_001806). In addition, genes derived from mouse, common marker and selection genes, and mutant virus sequences were included. Arabidopsis elements were included for normalization. Oligonucleotides were designed from these sequences using ArrayOligoSelector.
3 GPL10356 WashU-Virgin gHV68 44k v1.0 42,525 Washington University-School of Medicine 2010-04-23 Agilent Murid herpesvirus 4
Murid herpesvirus 4
Oligo Array in situ oligonucleotide, WashU-Virgin gHV68 44k v1.0,
4 GPL10320 Virus 45K Microarray - Agilent 2517771 45,220 Columbia University 2010-04-12 Agilent Viruses
Viruses
Oligo Array in situ oligonucleotide, Virus 45K Microarray - Agilent 2517771,
5 GPL10319 Virus 45K Microarray - Agilent 25161471 45,220 Columbia University 2010-04-12 Agilent Viruses
Viruses
Oligo Array in situ oligonucleotide, Virus 45K Microarray - Agilent 25161471,
6 GPL11662 Viro5AGL-60k [Probe name version] 59,532 University of California, San Francisco 2011-01-27 Agilent Technologies Viruses
Viruses
cDNA Array spotted DNA/cDNA, Viro5AGL-60k [Probe name version], This platform includes more than 60000 oligonucleotides for the detection and discovery of both known and novel viruses. The sequences of ~36,000 of the viral probes on this platform have been previously published in the GEO database as MegaViro (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862). For comparison purposes, both 70mer and 60mer representations of these viral oligos are present. Some viral probes corresponding to phages and other less critical targets have been removed. More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens, (2) enhanced detection of specific viral families, and (3) subtyping of HIV/SIV strains. Control oligonucleotides are also included in the design.
7 GPL10898 Viro5AGL-60k 12,361 University of California, San Francisco 2010-09-08 Agilent Technologies Viruses
Viruses
cDNA Array spotted DNA/cDNA, Viro5AGL-60k, This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses. The sequences of ~36,000 of the viral
8 GPL15905 Viro5AG-60k (Probe Name version) 60,512 University of California, San Francisco 2012-08-08 Agilent Technologies Viruses
Viruses
cDNA Array spotted DNA/cDNA, Viro5AG-60k (Probe Name version), This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses. The sequences of 36,432 viral probes from this platform have been previously published in the GEO database as MegaViro (GPL1834), Viro3 (GPL3429), and Viro4 (GPL6862), collectively now designated as V3/V4 viral probe sets. For comparison purposes, both 70mer and 60mer representations of these viral oligos are present. Some viral probes corresponding to phages and other less critical targets have been removed. More than 20,000 additional probes have been added for (1) better subtyping of respiratory and diarrheal viral as well as nonviral pathogens, (2) enhanced detection of specific viral families, and (3) subtyping of HIV/SIV strains. Control oligonucleotides are also included in the design.
9 GPL10896 Viro5AG-60k 12,361 University of California, San Francisco 2010-09-08 Agilent Technologies Viruses
Viruses
cDNA Array spotted DNA/cDNA, Viro5AG-60k, This platform includes more than 60,000 oligonucleotides for the detection and discovery of both known and novel viruses. The sequences of ~36,000 of the viral
10 GPL13323 Viro5 17,496 University of California San Francisco 2011-03-23 DeRisi Lab, UCSF Viruses
Viruses
Oligo Array spotted oligonucleotide, Viro5, This platform includes ~17,500 oligonucleotides derived from ~2000 viral species. These oligonucleotides include all of those from the Viro4 platform (GPL6862) as well as ~1700 additional oligonucleoties derived from virus sequences added to databases since the creation of Viro4. This platform includes control oligonucleotides for human endogenous retroviruses, human genes, yeast intergenic sequences, and human papilloma virus sequences present in HeLa cells. Keywords = viruses, virus detection, virus discovery
11 GPL10897 Viro4AG-15k 12,361 University of California, San Francisco 2010-09-08 Agilent Technologies Viruses
Viruses
cDNA Array spotted DNA/cDNA, Viro4AG-15k, This platform includes ~15,000 oligonucleotides derived from ~1,200 viral species. The sequences of the 70mer microarray probes on this platform are identical to the Viro4 probes as previously reported
12 GPL6862 Viro4 15,776 University of California, San Francisco 2008-05-14 DeRisi Lab, UCSF Viruses
Viruses
Oligo Array spotted oligonucleotide, Viro4, This platform includes ~15,000 oligonucleotides derived from ~1200 viral species. The best-performing viral oligonucleotides from the Viro3 platform (GPL3429) were carried over to the Viro4 platform. The platform also includes additional viral oligonucleotides generated using a computer algorithm to obtain desired coverage of viral taxonomic groups (ViroTax, Fischer K, manuscript in preparation). This platform also includes the following control oligonucleotides: human endogenous retroviruses, highly expressed human genes, and yeast intergenic sequences.
13 GPL3429 Viro3 21,888 University of California, San Francisco 2006-02-07 DeRisi Lab, University of CA, San Francisco Viruses
Viruses
Oligo Array spotted oligonucleotide, Viro3, This platform includes ~22,000 oligonucleotides derived from ~1200 viral species and is an extension of the MegaViro platform (GPL1834), which contained ~11,000 oligonucleotides that were designed to represent regions of highest conservation among viral genomes (Wang D, Coscoy L, et al 2002). About 11,000 additional viral oligonucleotides were designed using all the viral sequences in GenBank as of April 2004. The new oligos were chosen using the ViroTax system (manuscript in preparation) such that all viral taxa represented in GenBank are distinguishable using the microarray to the extent possible given differential binding energies. This platform also includes 488 oligonucleotides from 35 bacterial species, 20 oligonucleotides from 2 human endogenous retroviruses, and 308 control oligonucleotides including 108 OPERON oligonucleotides of highly expressed human genes.
14 GPL16497 Utz lab influenza peptide array 72 Stanford University 2013-01-11 Laboratory of Paul J. Utz Influenza B virus,H1N1 subtype,H3N2 subtype
Influenza B virus,H1N1 subtype,H3N2 subtype
Other spotted peptide or protein, Utz lab influenza peptide array, Influenza - Orthomyxovidiae, H1N1 (A/Brisbane/59/2007), H3N2 (A/Brisbane/10/2007), and B (B/Brisbane/60/2008)
15 GPL8448 USDA/APHIS/FADDL Pan-viral 15K v4.2 15,744 USDA-APHIS 2009-04-15 Agilent Viruses
Viruses
Oligo Array spotted oligonucleotide, USDA/APHIS/FADDL Pan-viral 15K v4.2,
16 GPL8039 University of Guelph, 1152 CfMNPV genes array version 1 310 University of Guelph 2009-01-08 Biotechnology Research Institute, Montreal, Canada Choristoneura fumiferana MNPV
Choristoneura fumiferana MNPV
Oligo Array spotted oligonucleotide, University of Guelph, 1152 CfMNPV genes array version 1, The array included 292 oligonucleotide probes representing 146 CfMNPV ORFs, one for the coding strand and the other for the non-coding strand (for detection of antisense transcription). Purified CfMNPV viral genomic DNA in 10-fold serial dilutions was used as a positive control. A mixture of 20 viral oligonucleotides was served as a second positive control. The array included 2 oligos (At1 and At2) of Arabidopsis chlorophyll synthase for normalization between arrays, and 2 oligos (HAT4, YaaJ) as negative controls. The array also included 5 host insect internal control oligos. Each probe was printed in triplicate. This array represents a condensed array. The full array layout linked as a supplementary file.
17 GPL8338 Univ of Miss. Frog virus 3 (family Iridoviridae) array 124 Naval Medical Research Center 2009-03-24 Microarrays Inc. Frog virus 3
Frog virus 3
Oligo Array spotted oligonucleotide, Univ of Miss. Frog virus 3 (family Iridoviridae) array,
18 GPL6852 UMDNJ/Lukac Human herpesvirus 8/107+GAPDH 107 UMDNJ/NJ Medical School 2008-05-09 Lukac laboratory and Center for Applied Genomics/UMDNJ/NJ Medical School Human herpesvirus 8
Human herpesvirus 8
Oligo Array spotted oligonucleotide, UMDNJ/Lukac Human herpesvirus 8/107+GAPDH,
19 GPL1917 Single HHV-4 ViruChip 336 Tokyo Medical University 2005-03-17 Human herpesvirus 4
Human herpesvirus 4
Oligo Array spotted oligonucleotide, Single HHV-4 ViruChip, The ViruChip HHV-4(Celonex, Inc., Edmonton, Canada), the Epstein-Barr virus (EBV) DNA chip is made up of triplicate spots of 60-mer oligonucleotide specific probes for each EBV transcription unit. Human genes (Tubilin, G3PDH, Action, and ribo-S9) were included in order to standardize the amount of applied cDNA and to normalize the signals between samples and references. HIV genes were also printed to exclude non-specific hybridization. Keywords = EBV
20 GPL4893 Singapore Grouper Iridovirus 0.5K genomic DNA microarray 576 Sun yet-san university 2007-02-27 National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, People’s Republic of China. Iridovirus
Iridovirus
cDNA Array spotted DNA/cDNA, Singapore Grouper Iridovirus 0.5K genomic DNA microarray,
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