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
(87)		   Tiling Array
(49)		   cDNA Array
(284)		   Oligo Array
(1,073)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(3)		   HT-Seq
(129)		   Other
(11)		   All
(1,636)		  
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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 GPL16797 Custom NimbleGen Shewanella oneidensis MR-1 Tiling v2 [NimbleGen_MR1_2005K_1] 2,023,636 University of California 2013-03-15 NimbleGen Shewanella oneidensis MR-1
Shewanella oneidensis MR-1		 Tiling Array in situ oligonucleotide, Custom NimbleGen Shewanella oneidensis MR-1 Tiling v2 [NimbleGen_MR1_2005K_1], NC_004347 and NC_004349 100318_Shew_one_MR1_JK_EXP_HX1.ndf
2 GPL15823 Custom NimbleGen Shewanella oneidensis MR-1 Tiling [NimbleGen_MR1_2005K_1] 1,937,190 Lawrence Berkeley Lab 2012-07-18 NimbleGen Shewanella oneidensis MR-1
Shewanella oneidensis MR-1		 Tiling Array in situ oligonucleotide, Custom NimbleGen Shewanella oneidensis MR-1 Tiling [NimbleGen_MR1_2005K_1], NC_004347 and NC_004349 100318_Shew_one_MR1_JK_EXP_HX1.ndf
3 GPL11291 Porphyromonas gingivalis W83 genomic tiling array mapped format 409,807 The Forsyth Institute 2010-12-07 Roche NimbleGen Inc. Porphyromonas gingivalis W83
Porphyromonas gingivalis W83		 Tiling Array in situ oligonucleotide, Porphyromonas gingivalis W83 genomic tiling array mapped format, The probe set printed on the array consists of 380,000 unique oligonucleotide sequences. On this particular platform, all the 380k unique probes were mapped to all the matched loci of the reference genome, thus each unique probe sequence may appear multiple times due to the repeated probe sequence found in the genome.
4 GPL11276 Genome Institute of Singapore Burkholderia pseudomallei 390K tiling array [2007-02-26_BpK96243_Yiting_FT] 392,778 Genome Institute of Singapore 2010-12-03 NimbleGen Burkholderia pseudomallei K96243
Burkholderia pseudomallei K96243		 Tiling Array in situ oligonucleotide, Genome Institute of Singapore Burkholderia pseudomallei 390K tiling array [2007-02-26_BpK96243_Yiting_FT], aCGH experiments were performed using oligonucleotide microarrays comprising > 390,000 50-mer probes providing tiling coverage of the Bp K96243 reference genome (15 bp overlap) (NimbleGen, Reykjavik, Iceland)
5 GPL7369 Institute for Systems Biology NimbleGen Halobacterium 391k tiling array 391,015 Institute for Systems Biology 2008-09-24 Nimblegen Halobacterium sp. NRC-1
Halobacterium sp. NRC-1		 Tiling Array in situ oligonucleotide, Institute for Systems Biology NimbleGen Halobacterium 391k tiling array,
6 GPL7231 Lactococcus lactis pangenome 385K short oligo array 389,479 CMBI 2008-08-29 NimbleGen Systems Inc. (Madison, WI, USA) Lactococcus lactis
Lactococcus lactis		 Tiling Array in situ oligonucleotide, Lactococcus lactis pangenome 385K short oligo array, All genomic, plasmid and single gene or operon DNA sequences (1988 sequences in July 2005, constituting 10.7 Mb) of L. lactis were collected from the NCBI CoreNucleotide database and were deposited in a local database. This included complete genome sequences of L. lactis strain IL1403 (2.35 Mb, accession number AE005176) and fragments of the genome of strain SK11 (2.43 Mb, Genbank record GI:62464763). Additionally, draft genome sequences consisting of 547 contigs (2.3 Mb) of L. lactis ssp. lactis strain KF147 (NIZOB2230) and 961 contigs (2.6 Mb) of L. lactis ssp. lactis KF282 (NIZOB2244W) were added to this database. Redundant stretches of DNA were removed from the database, where a stretch of DNA was defined as redundant if it differed from another piece of DNA by at most 2 nucleotides over a window of 100 nucleotides. For the remaining non-redundant 7 Mb of DNA, a 32-mer tiling design was defined by starting an oligomer approximately every 19 nucleotides, resulting in a total of 386,298 probes. We also designed 3181 random probes with their sequence absent in the non-redundant 7 Mb of DNA and they were randomly located on the array. Probes target mainly L. lactis ssp. lactis IL1403 public genome and then incomplete genome of L. lactis ssp. cremoris SK11 (now it is completed). Recently, closely related genome of strain L. lactis ssp. cremoris MG1363 has been published. All these 3 genomes are publicly available at NCBI databases. Since there is no reference strain the probes target DNA from different strains, hence, there is no positions file (*.pos). The .ndf file is linked below as a supplementary file.
7 GPL10416 NimbleGen E. coli K12 Mg1655 385K array 389,307 National Yang-Ming University 2010-05-15 NimbleGen Escherichia coli str. K-12 substr. MG1655
Escherichia coli str. K-12 substr. MG1655		 Tiling Array in situ oligonucleotide, NimbleGen E. coli K12 Mg1655 385K array, This is a commercial 385K high density tiling array from NimbleGen for E. coli K12 MG1655 (Cat. No. 05542901001). The design contains 50-mer probe with 24 bp median probe spacing and the control probes are also included. native array description file: 2006-07-18_Ecoli_K12_ChIP.ndf native array description file: 2006-07-18_Ecoli_K12_ChIP.pos
8 GPL9409 Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling 385,673 KULeuven 2009-10-08 Nimblegen Rhizobium etli CFN 42
Rhizobium etli CFN 42		 Tiling Array in situ oligonucleotide, Rhizobium etli CFN 42 385K 071203_ReCFN42JM_Tiling, Whole genome expression tiling array for Rhizobium etli CFN42, representing the forward strand of the chromosome and all 6 plasmids (NC_007761, NC007762, NC_007763, NC_007764, NC_004041, NC_007765, NC_007766), included repeat regions, 60mers, Ctrl (RNA) probes replicated 50 times, ERCC probes replicated 6 times, probe interval 13bp
9 GPL8468 NimbleGen Halobacterium 385K tiling array 385,440 Institute for Systems Biology 2009-04-22 Nimblegen Halobacterium sp. NRC-1
Halobacterium sp. NRC-1		 Tiling Array in situ oligonucleotide, NimbleGen Halobacterium 385K tiling array, 50mer oligo probe every 13nt. Native NimbleGen files (ndf, pos) are linked below as supplementary files.
10 GPL8942 CBCB Listeria monocytogenes 385K v1.0 385,000 University of Maryland 2009-07-28 Nimblegen Listeria monocytogenes,Listeria monocytogenes EGD-e,Listeria monocytogenes serotype 4b str. F2365,Listeria monocytogenes serotype 1/2a str. F6854,Listeria monocytogenes serotype 4b str. H7858,Listeria monocytogenes FSL F2-515,Listeria monocytogenes FSL J1
Listeria monocytogenes,Listeria monocytogenes EGD-e,Listeria monocytogenes serotype 4b str. F2365,Listeria monocytogenes serotype 1/2a str. F6854,Listeria monocytogenes serotype 4b str. H7858,Listeria monocytogenes FSL F2-515,Listeria monocytogenes FSL J1		 Tiling Array in situ oligonucleotide, CBCB Listeria monocytogenes 385K v1.0, This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. The tiled strains by GenBank TaxID are: 265669, 267409, 267410, 393116, 393117, 393118, 393119, 393120, 393122, 393123, 393124, 393125, 393128, 393130, 393131, 393132, 393133, 401650, 393121, 169963. IMPORTANT: The genomic positions in the data table only represent the position on a single genome. The supplementary files contain the mapping of probes to pan-genomic positions. The columns in the supplementary "probe_mapping" file are: ID_REF: Probe ID. Each probe can appear in multiple rows depending on how many genomes it targets. GI_RANGE: Sequence GenBank GI and probe mapping location. RANGE_STRAND: Strand on the GI sequence the probe maps to. MISMATCH: Number of mismatches between probe and genomic sequence, 0 or 1.
11 GPL3786 SKCC Salmonella 380K tiling array 382,864 Vaccine Research Institute of San Diego 2006-05-19 NimbleGen Salmonella
Salmonella		 Tiling Array in situ oligonucleotide, SKCC Salmonella 380K tiling array, This set includes 382864 46~50mer oligonucleotides, mostly 50-mers. The probes were designed based on Salmonella typhimurium LT2 (NC_003197.1) genome, with a moving window of about 12 bases.
12 GPL4458 Escherichia coli MG1655 382K 50-mer tiling array 382,177 Harvard University 2006-10-17 NimbleGen Escherichia coli
Escherichia coli		 Tiling Array in situ oligonucleotide, Escherichia coli MG1655 382K 50-mer tiling array,
13 GPL9112 UCSD Nimblegen Geobacter sulfurreducens 381K Tiling Array 2007 (Probe) 381,174 UCSD 2009-08-27 NimbleGen Geobacter sulfurreducens PCA
Geobacter sulfurreducens PCA		 Tiling Array in situ oligonucleotide, UCSD Nimblegen Geobacter sulfurreducens 381K Tiling Array 2007 (Probe), NimbleGen design name 2007-10-02_Gsulf_Palsson_Tiling, NimbleGen design ID 6481. A tiling array design for Geobacter Sulfurreducens PCA with 50-mer probe spaced 20bp apart across the genome. This design also contains control probes.
14 GPL7177 Streptococcus pneumoniae whole genome tiling array 379,366 MSU 2008-08-18 NimbleGen Systems Inc. Streptococcus pneumoniae
Streptococcus pneumoniae		 Tiling Array in situ oligonucleotide, Streptococcus pneumoniae whole genome tiling array, Maskless Array Synthesizer (MAS) technology
15 GPL8708 UW-Madison Escherichia coli K-12 MG1655 tiling array (YD Design) 378,238 UW-Madison 2009-06-11 Nimblegen Escherichia coli str. K-12 substr. MG1655
Escherichia coli str. K-12 substr. MG1655		 Tiling Array in situ oligonucleotide, UW-Madison Escherichia coli K-12 MG1655 tiling array (YD Design),
16 GPL8147 Nimblegen 385k tiling array 081031_RDI_UK_Bsubtilis_FT 376,000 Newcastle University 2009-02-03 Nimblegen Bacillus subtilis
Bacillus subtilis		 Tiling Array in situ oligonucleotide, Nimblegen 385k tiling array 081031_RDI_UK_Bsubtilis_FT,
17 GPL7790 Escherichia coli K-12 MG1655 tiling array (Nimblegen Design) 374,408 University of Wisconsin-Madison 2008-12-12 Nimblegen Escherichia coli
Escherichia coli		 Tiling Array in situ oligonucleotide, Escherichia coli K-12 MG1655 tiling array (Nimblegen Design),
18 GPL8387 UCSD, NimbleGen_E_coli_MG1655_371K Tiling_Array_2005 371,034 UCSD 2009-04-03 NimbleGen Escherichia coli str. K-12 substr. MG1655
Escherichia coli str. K-12 substr. MG1655		 Tiling Array in situ oligonucleotide, UCSD, NimbleGen_E_coli_MG1655_371K Tiling_Array_2005, NimbleGen design name 2005-04-20_Palsson_Ecoli_ChIP, NimbleGen design ID 1881. A tiling array design for Escherichia coli K12 MG1655 with 50-mer probe spaced 25bp apart across the genome. This design also contains control probes.
19 GPL11167 NimbleGen Desulfovibrio vulgaris 385k array 367,070 Lawrence Berkeley Lab 2010-11-05 NimbleGen Desulfovibrio vulgaris str. Hildenborough
Desulfovibrio vulgaris str. Hildenborough		 Tiling Array in situ oligonucleotide, NimbleGen Desulfovibrio vulgaris 385k array, Includes genome sequence (Genbank AE017285.1) and plasmid pDV sequence (Genbank AE017286.1) 385k custom tiling array designed to examine the intergenic regions. The probes (50-mer) have 46 bp overlap in the intergenic regions and a 20 bp overlap in the coding regions Design ID: 081029
20 GPL10463 UW_Rhodobacter_sphaeroides_2.4.1_385K_v2 353,081 University of Wisconsin - Madison 2010-05-27 NimbleGen Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1		 Tiling Array in situ oligonucleotide, UW_Rhodobacter_sphaeroides_2.4.1_385K_v2, Oligo probes are 45bp in average, tiling the genome sequences with about 35-bp overlap between consecutive probes. Every other probe hybridizes to the reverse strand. Native array description file: 2007-06-20_R_sphaeroides_long85_v2.ndf Native array description file: 2007-06-20_R_sphaeroides_long85_v2.pos
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