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
(0)		   SAGE RsaI
(0)		   SAGE Sau3A
(0)		   MPSS
(0)		   GeneChip
(0)		   Tiling Array
(1)		   cDNA Array
(8)		   Oligo Array
(40)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(0)		   HT-Seq
(27)		   Other
(2)		   All
(78)		  
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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 GPL366 MegaViroP1 12,032 University of California, San Francisco 2003-07-21 Viruses
Viruses		 Oligo Array spotted oligonucleotide, MegaViroP1, Spotted long oligonucleotide array on glass This platform includes 10814 oligonucleotides derived from 976 viral species. Most viral oligonucleotides were designed to represent regions of highest genomic conservation. The 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. Keywords = spotted Keywords = long oligonucleotide Keywords = viruses Keywords = viral discovery
2 GPL1834 MegaViroP1-P7 12,504 University of California, San Francisco 2005-02-02 Viruses
Viruses		 Oligo Array spotted oligonucleotide, MegaViroP1-P7, Spotted 70-mer nucleotide array on glass. This platform includes ~11,000 oligonucleotides derived from ~1000 viral species. Most viral oligonucleotides were designed to represent regions of highest conservation among viral genomes. The 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. This platform is essentially the same as GPL366, except 316 new viral oligos from 32 viruses sharing little sequence homology with other viruses have been added; these oligos were selected from protein coding regions using ArrayOligoSelector software (Bozdech Z, Zhu J, et. al 2003). Keywords = viruses, virus detection, virus discovery
3 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
4 GPL2730 Pathogen Chip 719 Stanley Medical Research Institute 2005-08-08 custom Viruses
Viruses		 Oligo Array spotted oligonucleotide, Pathogen Chip, Synthetic long oligonucleotide probes spotted in duplicate on glass. The platform includes 567 oligonucleotides derived from specific viruses. Viral oligonucleotides were designed based on open reading frames from highly conserved and heterogenic regions within viral families. Viral genes reflecting different stages of infection were also included, to potentially define the stage of viral infection. The platform also includes 17 oligonucleotides from parasites, 11 oligonucleotides from bacterial species and 120 oligonucleotides from housekeeping human genes.
5 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.
6 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.
7 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,
8 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.
9 GPL5725 IAH/VLA Virus Detection Array VA1 5,824 The Roslin Institute 2007-08-08 IAH/VLA Viruses
Viruses		 Oligo Array spotted oligonucleotide, IAH/VLA Virus Detection Array VA1,
10 GPL6501 MSU_Rose_Env_Vir_v3 10,848 Rose_Lab@MSU 2008-02-19 Gulari Research Group Univ of Michigan Viruses
Viruses		 Oligo Array in situ oligonucleotide, MSU_Rose_Env_Vir_v3,
11 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.
12 GPL6701 Hannon Lab Solexa Flock house virus 20,338 Cold Spring Harbor Labs 2008-04-07 Flock house virus
Flock house virus		 HT Sequencing other, Hannon Lab Solexa Flock house virus,
13 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,
14 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.
15 GPL7090 CombiMatrix_Influenza A_12,000_design 5200 12,020 CombiMatrix Corp 2008-07-23 CombiMatrix Corporation Influenza A virus
Influenza A virus		 Oligo Array in situ oligonucleotide, CombiMatrix_Influenza A_12,000_design 5200, Semiconductor based array with in situ synthesized oligonucleotides that can be used with electrochemical detection.
16 GPL7229 OHSU_macaque_RRV_252_v1 252 Oregon Health & Science University 2008-08-28 Oregon Health & Science University/Spotted Microarray Core Macaca mulatta rhadinovirus 17577
Macaca mulatta rhadinovirus 17577		 Oligo Array spotted oligonucleotide, OHSU_macaque_RRV_252_v1,
17 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.
18 GPL8066 AH/VLA Virus Detection Array LP1 1.6K 1,600 Veterinary Laboratories Agency 2009-01-13 IAH/VLA Viruses
Viruses		 Oligo Array spotted oligonucleotide, AH/VLA Virus Detection Array LP1 1.6K,
19 GPL8185 IAH/VLA/CEFAS Virus Detection Array 6K VA3 6,048 The Roslin Institute 2009-02-12 IAH/VLA Viruses
Viruses		 Oligo Array spotted oligonucleotide, IAH/VLA/CEFAS Virus Detection Array 6K VA3, Microarray for the detection of viruses, produced by the IAH, the VLA and CEFAS.
20 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,
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