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
(0)
  cDNA Array
(0)
  Oligo Array
(1,179)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(3)
  HT-Seq
(0)
  Other
(22)
  All
(1,901)
 
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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.
21 GPL8970 JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain Pestoides_F 8,141 J. Craig Venter Institute 2009-07-31 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 19K v4 array designed primarily based on strain Pestoides_F, This set includes 7359 oligonucleotides, has 19200 spots distributed in 48 blocks.
22 GPL11443 Yersinia pestis cDNA microarray 8,010 Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China 2011-01-12 Beijing Institute of Microbiology and Epidemiology, Beijing, China Yersinia pestis
Yersinia pestis
cDNA Array spotted DNA/cDNA, Yersinia pestis cDNA microarray,
23 GPL3885 JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain CO92 5,329 J. Craig Venter Institute 2006-06-19 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain CO92, This set includes 4826 oligonucleotides, has 30000 spots distributed in 48 blocks.
24 GPL4199 JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM 5,329 J. Craig Venter Institute 2006-08-22 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM, This set includes 4826 oligonucleotides, has 30000 spots distributed in 48 blocks.
25 GPL4201 JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain CO92 5,329 J. Craig Venter Institute 2006-08-22 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain CO92, This set includes 4645 oligonucleotides, has 11520 spots distributed in 48 blocks.
26 GPL4202 JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain KIM 5,329 J. Craig Venter Institute 2006-08-22 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 11K v1 array designed primarily based on strain KIM, This set includes 4645 oligonucleotides, has 11520 spots distributed in 48 blocks.
27 GPL5907 JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain CO92 5,329 J. Craig Venter Institute 2007-09-18 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain CO92, This set includes 4826 oligonucleotides, has 25392 spots distributed in 48 blocks.
28 GPL5908 JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain KIM 5,329 J. Craig Venter Institute 2007-09-18 JCVI PFGRC Yersinia pestis
Yersinia pestis
Oligo Array spotted oligonucleotide, JCVI PFGRC Yersinia pestis 25K v3 array designed primarily based on strain KIM, This set includes 4826 oligonucleotides, has 25392 spots distributed in 48 blocks.
29 GPL5937 AMMS_PBS_Y. pestis 201 4,005 Institute of Microbiology and Epidemiology 2007-09-27 State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences Yersinia pestis
Yersinia pestis
cDNA Array spotted DNA/cDNA, AMMS_PBS_Y. pestis 201,
30 GPL17599 Yersinia intermedia ATCC 29909 384k array 389,123 UW-Madison 2013-08-20 NimbleGen Yersinia intermedia ATCC 29909
Yersinia intermedia ATCC 29909
Oligo Array in situ oligonucleotide, Yersinia intermedia ATCC 29909 384k array, NimbleGen design name Yersinia intermedia ATCC 29909, NimbleGen design ID OID 30956. A whole-genome-tiled array design with ~320,000 probes representing 3953 genes that included 3887 protein coding genes (and 18 likely pseudogenes), 12 non-coding RNAs and 36 tRNAs. The design includes random GC and other control probes. Yin29909_overlap_DF
31 GPL15652 UF_Wang_Xfa_2x105K_version 1.0 2,058 University of Florida 2012-06-04 Agilent Xylella fastidiosa 9a5c,Xylella fastidiosa Temecula1
Xylella fastidiosa 9a5c,Xylella fastidiosa Temecula1
Oligo Array in situ oligonucleotide, UF_Wang_Xfa_2x105K_version 1.0,
32 GPL10380 NimbleGen_Xylella fastidiosa 9a5c_4x72K array 2,832 Instituto Agronomico de Campinas 2010-05-04 NimbleGen Xylella fastidiosa 9a5c
Xylella fastidiosa 9a5c
Oligo Array in situ oligonucleotide, NimbleGen_Xylella fastidiosa 9a5c_4x72K array, Design Name: TI160492 probe size: 60mer Catalog design for Xylella fastidiosa 9a5c (Taxonomy Id: 160492) covering NC_002488 (Xylella fastidiosa 9a5c, complete genome), NC_002489 (Xylella fastidiosa 9a5c plasmid pXF1.3, complete sequence), NC_002490 (Xylella fastidiosa 9a5c plasmid pXF51, complete sequence). Probes selected for 2832/2832 sequences. Median number of probes/sequence is 13 with an average of 13.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content. The design (.ndf) file and description (.ngd) file are linked below as Supplementary files.
33 GPL793 CAGE-Xylella USP - v.1 9,216 Institute for Systems Biology 2003-12-22 Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, CAGE-Xylella USP - v.1, DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use. Keywords = xylella fastidiosa Keywords = genomotyping Keywords = DNA microarray Keywords = comparative genomics
34 GPL794 CAGE-Xylella USP - v.2 9,216 Institute for Systems Biology 2003-12-22 Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, CAGE-Xylella USP - v.2, DNA Microarray Construction. PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). Primers (18-23mers) with equivalent predicted melting temperature were designed with the use of a perl program that ran PRIMER3 (http://www-genome.wi.mit.edu/genome_software/other/primer3.html) for the complete CDS list, automatically testing many parameter settings and also guaranteeing that primers hybridized only to a single genome location. Oligonucleotides were synthesized by MWG and Operon Technologies. Genomic or cosmid DNA, obtained in the X. fastidiosa genome sequencing project (Simpson et al. 2000), were used as template in the first round of PCR amplification, and 200-fold-diluted PCR products were used as templates for PCR reamplification to increase product concentration when necessary. The reactions were done in 96-well plates. The mixture in each well contained 100 ng of DNA, 0.5 U of Biolase Taq polymerase (Bioline), 0.2 mM of each dNTP (Invitrogen), 1.5 mM MgCl2 and the primers at 0.5 uM, in a total volume of 100 ul. A 5min denaturing step at 95oC was applied, followed by 40 cycles of 95oC for 45s, 50oC for 30s, 72oC for 1min and a final step at 72oC for 10min. 4 ul of each PCR reaction were checked for product size and concentration by electrophoresis in 1.2% agarose gels. The amplicons were then purified with 96-well MultiScreen purification plates (Millipore) and an equal volume of dimethyl sulfoxide was added to the purified products (~100 ng/ul final concentration). Generation III DNA spotter (Amersham Biosciences) was used to array the samples onto coated type-7 glass slides (Amersham Biosciences). After deposition, the probes were crosslinked to the slides by applying 50 mJ of UV light and the slides were stored desiccated at ~10% relative humidity at room temperature until use. Keywords = xylella fastidiosa Keywords = genomotyping Keywords = DNA microarray Keywords = comparative genomics
35 GPL2708 Xylella USP microarray v2 (Koide et al. 2004 J.Bact.) 4,608 Universidade de São Paulo 2005-07-31 Instituto de Química da Universidade de São Paulo (IQ-USP) Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, Xylella USP microarray v2 (Koide et al. 2004 J.Bact.),
36 GPL3409 Xylella USP microarray v1 (Koide et al. 2004 J.Bact.) 4,608 Universidade de São Paulo 2006-02-01 Instituto de Química da Universidade de São Paulo (IQ-USP) Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, Xylella USP microarray v1 (Koide et al. 2004 J.Bact.),
37 GPL9024 IQ-USP Xylella fastidiosa 9.2K v2.0. 4,608 Universidade de São Paulo 2009-08-12 IQ-USP microarray facility Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, IQ-USP Xylella fastidiosa 9.2K v2.0.,
38 GPL4683 Xylella fastidiosa 9a5c Biochip v.2.0 2,688 UFABC - Universidade Federal do ABC 2006-12-19 Laboratório de Genômica Estrutural e Funcional - Núcleo Integrado de Biotecnologia - Universidade de Mogi das Cruzes Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, Xylella fastidiosa 9a5c Biochip v.2.0, Xylella fastidiosa, isolate 9a5c
39 GPL9337 NimbleGen Xylella fastidiosa 2K 2,036 UC-Berkeley 2009-10-01 NimbleGen Xylella fastidiosa
Xylella fastidiosa
Oligo Array in situ oligonucleotide, NimbleGen Xylella fastidiosa 2K,
40 GPL7554 UNESP Xylella fastidiosa array version 1 493 Max-Delbruck Center for Molecular Medicine 2008-11-04 Sao Paulo State University (UNESP) Jaboticabal Campus. Laboratory of Biochemistry of microorganisms and plants (LBMP). Xylella fastidiosa
Xylella fastidiosa
cDNA Array spotted DNA/cDNA, UNESP Xylella fastidiosa array version 1,
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