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
(83)		   SAGE RsaI
(1)		   SAGE Sau3A
(5)		   MPSS
(17)		   GeneChip
(677)		   Tiling Array
(1,257)		   cDNA Array
(2,714)		   Oligo Array
(5,069)		   Bead Array
(183)		   Protein Array
(1)		   Antibody
(22)		   RT-PCR
(144)		   HT-Seq
(1,218)		   Other
(129)		   All
(11,528)		  
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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 GPL10772 URGV Arabidopsis thaliana CHROMO4_2 array 21,800 INRA - CNRS - UEVE 2010-08-10 URGV Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array spotted DNA/cDNA, URGV Arabidopsis thaliana CHROMO4_2 array, The entire TIGR4 Arabidopsis thaliana ec. Col chromosome 4 assembly was used to design a genomic tiling microarray. This ~18.6 Mb sequence represented on the microarray starts downstream of the nucleolar organizing region (NOR) comprising the 5’ terminus of the chromosome. Notably, it contains several megabases of pericentromeric heterochromatin. In the microarray design, annotation was intentionally ignored, thus ensuring that repeated and unique sequences were equally represented. PCR primer pairs were selected using the Primer3 software. Probe selection was first accomplished by BLASTN analysis of sequential 100-bp windows of sequence along chromosome 4 against the whole genome to discriminate between unique and repeated DNA. Whenever a window gave at least one hit with 85% identity elsewhere in the genome, that window was marked as repeated, or unique otherwise. This information was then used to define repeated and unique segments of at least 300bp along the chromosome, as follows. Repeat segments were composed of successive repeat windows, possibly interrupted by series of contiguous unique windows spanning less than 300bp in each case. Conversely, unique segments were composed of successive unique windows, never interrupted by more than 300bp of contiguous repeat windows. Series of alternate unique and repeated windows were treated as repeat segments. Within each repeated or unique segment, PCR primer pairs were then selected using the Primer3 software and a routine that ensured maximum coverage of the segment and limited overlap between successive probes. Briefly, primer pairs were designed from both ends of the segment, considering sequential 1.2 kb windows, amplicon sizes ranging from 850 bp to 1.2 kb (optimum 1 kb) and primers (19-23 nt each, optimum 21 nt, 40-60% GC) with similar melting temperatures in the 57°C­63°C range (optimum 60°C). Each new 1.2 kb window was positioned 50 bp within the end of the preceding amplicon. Successive amplicons could therefore overlap by up to 50 bp or be separated by up to 250 bp. When no primer pair was found in a given window, window size was increased to 1.4 kb, and if still unsuccessful, amplicons were finally designed using the forward and reverse primers of the upstream and downstream amplicons, respectively. When the last (central) window of a segment was less than 1.2kb but more than 300bp, primer pair selection was carried out by considering the actual size of that window plus 50bp on either side. Using this approach, 21,405 amplicons were designed with an average size of ~950bp. An additional 356 amplicons were designed that cover 36 genes of interest and neighboring sequences located on the other 4 chromosomes. Most amplicons were produced using BAC clones as templates, and all amplicons were verified by gel electropheresis.
2 GPL6176 Thalassiosira pseudonana NimbleGen 36mer oligo tiling array 1,253,590 University of Washington 2007-11-21 University Wisconsin, Madison; Biotechnology Center Thalassiosira pseudonana CCMP1335
Thalassiosira pseudonana CCMP1335		 Tiling Array in situ oligonucleotide, Thalassiosira pseudonana NimbleGen 36mer oligo tiling array, The layout files for the individual chips that make up the 8-array set are linked below as supplementary files.
3 GPL10011 HGU-MRC-Bickmore Mouse Hoxb/d 22K tiling v1.0 5,002 Medical Research Council 2010-02-04 University of Liverpool Microarray Facility Mus musculus
Mus musculus		 Tiling Array spotted oligonucleotide, HGU-MRC-Bickmore Mouse Hoxb/d 22K tiling v1.0, Tiling path array of oligos on HoxB and HoxD clusters :1 oligo / 250 bp in the core region containing the Hox genes,1 oligo / 500 bp in the flanking regions,1 oligo / 50kb outside flanking regions.These tiling oligos are designed alternatively on each strand. The position number (NCBI built m35) in the files is the 5’ base for the forward oligos and the 3’ for the reverse oligos (so one given oligo and the corresponding reverse oligo have the same position number). Other regions on the array are:Oct4 exons, promoter, flanking regions with low resolution,Sox2 exons, promoter, flanking regions with low resolution, Nanog exons, promoter. Control genes for array are; Ncl : exons, promoter, flanking regions with low resolution, RPL19 exons, Rrm2 exons, HPRT exons, promoter, c-myc, exons and other regions contains MAR and CTCF binding sites, Hbb-b1 exons and regulatory elements, Cdkn1a exons, promoter and regulatory elements, Oprk1 exons and regulatory elements and Mouse major and minor satellite DNA. Mismatch control oligos are the same as the oligos in exons but containing 1, 3, 5,7 ,10 mismatches. (NB : the Ncl mismatch oligos have been designed on the wrong strand). Other control probes are NM_000015.1 and Drosophila sequences.
4 GPL7247 SWEGENE_BAC_33K_Full 36,288 SCIBLU - Swegene Centre for Integrative Biology at Lund University 2008-09-04 Swegene DNA Microarray Resource Centre Homo sapiens
Homo sapiens		 Tiling Array spotted DNA/cDNA, SWEGENE_BAC_33K_Full, The 33k tiling BAC Array set contains 33,370 large-insert clones with complete genome coverage. The clone set consists of the 32k BAC clone library (GEO accession GPL4723) with additional clones located in the telomeric regions (Knight SJ et al., Am J Hum Genet 2000) and clones covering microdeletion syndromes (Vissers LE et al., Am J Hum Genet 2003).
5 GPL4723 SWEGENE_BAC_32K_Full 34,992 SCIBLU - Swegene Centre for Integrative Biology at Lund University 2007-01-05 Swegene DNA Microarray Resource Centre Homo sapiens
Homo sapiens		 Tiling Array spotted DNA/cDNA, SWEGENE_BAC_32K_Full, The 32k BAC Re-Array set Ver. 1.0 (32,433 BAC clones) was obtained from the BACPAC Resource Center at Children's Hospital Oakland Research Institute, Oakland (CA, US). The average resolution of the whole genome tiling clone set is 46kb. Clones were mapped to human genome build 17 (UCSC Human Genome Browser)
6 GPL5840 klingenkhh_BAC_32K_Full 31,958 Dept of Clinical Genetics 2007-09-12 Swegene DNA Microarray Resource Centre Homo sapiens
Homo sapiens		 Tiling Array spotted DNA/cDNA, klingenkhh_BAC_32K_Full, The 32k BAC Re-Array set Ver. 1.0 (32,433 BAC clones) was obtained from the BACPAC Resource Center at Children's Hospital Oakland Research Institute, Oakland (CA, US). The average resolution of the whole genome tiling clone set is 46kb. Clones were mapped to human genome build 17 (UCSC Human Genome Browser)
7 GPL14901 UCSF/Sil lab-Histoplasma capsulatum-G217Borfs2 14,976 University of California 2011-11-17 Sil Lab, UCSF Ajellomyces capsulatus
Ajellomyces capsulatus		 Tiling Array spotted oligonucleotide, UCSF/Sil lab-Histoplasma capsulatum-G217Borfs2, This is a revision of UCSF/Sil lab-Histoplasma capsulatum-G217Bprint2 (GEO accession GPL6125) adding 15 oligos relative to the original design. The new oligo IDs are prefixed with G217Borfs2. G217Borfs2.38n17 targets MS8 (GenBank AF292398) which is incorrectly merged with HISTO_ZT.Contig181-snap.97 in the predicted gene set, and the remaining 14 target novel transcripts identified during preliminary analysis of whole genome tiling array data (published with a revised and expanded set of novel transcripts in BMC Microbiol. 11:216).
8 GPL9931 Ectocarpus siliculosus tiling array ChIP1 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP1, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
9 GPL9932 Ectocarpus siliculosus tiling array ChIP2 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP2, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
10 GPL9933 Ectocarpus siliculosus tiling array ChIP3 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP3, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
11 GPL9934 Ectocarpus siliculosus tiling array ChIP4 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP4, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
12 GPL9935 Ectocarpus siliculosus tiling array ChIP5 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP5, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
13 GPL9936 Ectocarpus siliculosus tiling array ChIP6 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP6, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
14 GPL9937 Ectocarpus siliculosus tiling array ChIP7 386,131 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP7, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
15 GPL9938 Ectocarpus siliculosus tiling array ChIP8 386,130 Systemix Institute 2010-01-15 Roche-Nimblegen Ectocarpus siliculosus
Ectocarpus siliculosus		 Tiling Array in situ oligonucleotide, Ectocarpus siliculosus tiling array ChIP8, 50-mer probes tiling the entire Ectocarpus siliculosus genome Control probes were placed on all arrays for monitoring hybridization quality and data normalization.
16 GPL11368 NimbleGen Mouse CGH Whole-Genome Tiling Array [080411_MM9_CGH_HX1] 2,090,470 NimbleGen Systems, Inc. 2010-12-29 Roche NimbleGen Inc. Mus musculus
Mus musculus		 Tiling Array in situ oligonucleotide, NimbleGen Mouse CGH Whole-Genome Tiling Array [080411_MM9_CGH_HX1], NimbleGen description files linked below: 080411_MM9_CGH_HX1.ndf 080411_MM9_CGH_HX1.pos
17 GPL10989 NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9) [080603_MM9_WG_CGH_HX3] 713,358 University of Southern California 2010-09-28 Roche NimbleGen Inc. Mus musculus
Mus musculus		 Tiling Array in situ oligonucleotide, NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array (Build MM9) [080603_MM9_WG_CGH_HX3], Format: 3x720K Source: UCSC Build: NCBI37, MM9 Probe Length: 50-75mer Median Probe Spacing: 3537 NimbleGen description files linked below: 080603_MM9_WG_CGH_HX3.ndf 080603_MM9_WG_CGH_HX3.pos
18 GPL15225 NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array [100718_MM9_WG_CGH] 713,358 Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences 2012-02-13 Roche NimbleGen Inc. Mus musculus
Mus musculus		 Tiling Array in situ oligonucleotide, NimbleGen Mouse CGH 3x720K Whole-Genome Tiling Array [100718_MM9_WG_CGH], Build: MM9
19 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.
20 GPL7685 UNC Celegans 2.1mil HX1 (C elegans ChIP HX1) 1,973,075 University of North Carolina-Chapel Hill 2008-11-20 Roche Nimblegen Caenorhabditis elegans
Caenorhabditis elegans		 Tiling Array in situ oligonucleotide, UNC Celegans 2.1mil HX1 (C elegans ChIP HX1), C. elegans whole genome tiling array at 50bp resolution, 2.1 million features per array Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR,Cerrina F. Maskless fabrication of light-directed oligonuc leotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697
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