Gene Expression Omnibus (GEO) Overview Version：2013-06-15Japanese 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
(129)		   Primates
(2)		   Rodents
(67)		   Mammals
(8)		   Vertebrates
(14)		   Invertebrates
(24)		   Plants
(99)		   Bacteria
(32)		   Viruses
(1)		   Phages
(1)		   Unclassified
(8)		   All
(385)		  
  SAGE NlaIII
(0)		   SAGE RsaI
(0)		   SAGE Sau3A
(0)		   MPSS
(0)		   GeneChip
(21)		   Tiling Array
(52)		   cDNA Array
(92)		   Oligo Array
(211)		   Bead Array
(1)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(5)		   HT-Seq
(1)		   Other
(2)		   All
(385)		  
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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 GPL9967 3D-Gene Mouse miRNA Oligo chip v13.0 728 Toray Industries,Inc. 2010-01-24 TORAY Industreies, Inc. Mus musculus
Mus musculus		 Oligo Array spotted oligonucleotide, 3D-Gene Mouse miRNA Oligo chip v13.0,
2 GPL9962 MRC Human IIR 37 v1 37 Mitsubishi Rayon Co.,LTD 2010-01-21 Mitsubishi Rayon Co., Ltd Homo sapiens
Homo sapiens		 Oligo Array spotted oligonucleotide, MRC Human IIR 37 v1, Oligo nucleotide probes were covalently attached to hydrophilic gel which bond to inner wall of plastic hollow fiber.
3 GPL9960 MRC Human IIR 0.2K v1 200 Mitsubishi Rayon Co.,LTD 2010-01-21 Mitsubishi Rayon Co., Ltd Homo sapiens
Homo sapiens		 Oligo Array spotted oligonucleotide, MRC Human IIR 0.2K v1, Oligo nucleotide probes were covalently attached to hydrophilic gel which bond to inner wall of plastic hollow fiber.
4 GPL9948 Agilent Human 0.6K miRNA Microarray G4471A 600 Cancer Insitute 2010-01-19 Agilent Technologies Homo sapiens
Homo sapiens		 Oligo Array in situ oligonucleotide, Agilent Human 0.6K miRNA Microarray G4471A,
5 GPL9862 University of Alberta Bovine 24K long oligo array 49,152 National Institute of Agrobiological Sciences 2010-01-08 Oligo design: Bovine Oligo Microarray Consortium; Array preparation: University of Alberta, Agricultural Genomics and Proteomics Unit Bos taurus
Bos taurus		 Oligo Array spotted oligonucleotide, University of Alberta Bovine 24K long oligo array, UniGene ID of sequence used to design oligonucleotide probe, Gene symbol, GenBank accession number and gene description were annotated in the GeneSifter based on the UniGene ID. The oligonucleotide sequences are provided as a supplementary file.
6 GPL9829 NimbleGen/RIKEN Aspergillus fumigatus 4x72K array 9,887 RIKEN 2009-12-28 NimbleGen Aspergillus fumigatus Af293
Aspergillus fumigatus Af293		 Oligo Array in situ oligonucleotide, NimbleGen/RIKEN Aspergillus fumigatus 4x72K array, Species: Aspergillus fumigatus Strain: Af293 Type of array: Eukaryotic Expression(4plex) Number of targets: 9,887 Length of probes: 60-mer Number of probes per target: 7 pairs Replicate: 1 Oligonucleotide sequences are available in the '2009-01-07_RDKK143_Afum_60mer_expr.ndf' supplementary file.
7 GPL9806 NimbleGen_Ppu_pSL1_5.3k array v1.0 5,346 National Institute for Agro-Environmental Sciences 2009-12-16 NimbleGen Pseudomonas putida KT2440
Pseudomonas putida KT2440		 Oligo Array in situ oligonucleotide, NimbleGen_Ppu_pSL1_5.3k array v1.0, NimbleGen design name 2007-08-09_GFC234_Pput_60mer_expr, NimbleGen design ID 6223. Sample species Pseudomonas putida KT2440. The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files.
8 GPL9805 Agilent-015520 Custom wheat 38k array 39,243 Kihara Institute for Biological Research, Yokohama City University 2009-12-16 Agilent Technologies Triticum aestivum
Triticum aestivum		 Oligo Array in situ oligonucleotide, Agilent-015520 Custom wheat 38k array,
9 GPL9729 Mouse custom CGH oligo array 15K (024443) 15,744 National Institute of Radiological Sciences 2009-11-30 Agilent Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Mouse custom CGH oligo array 15K (024443), Chromosome coordinates correspond to mouse genome build mm9 (NCBI Build 37).
10 GPL9727 Mouse custom CGH oligo array 44K (022188) 45,220 National Institute of Radiological Sciences 2009-11-30 Agilent Mus musculus
Mus musculus		 Oligo Array in situ oligonucleotide, Mouse custom CGH oligo array 44K (022188), Chromosome coordinates correspond to mouse genome build mm9 (NCBI Build 37).
11 GPL962 CHUGAI 41K 40,368 Cancer Insitute 2004-01-24 Homo sapiens
Homo sapiens		 cDNA Array spotted DNA/cDNA, CHUGAI 41K, Patients and Sample Preparation. We analyzed NT samples from 38 patients undergoing surgery at the Cancer Institute Hospital, Tokyo, during May 1996 – May 2001. All samples were collected with informed consent and ethical committee approval and were grossly dissected, snap-frozen in liquid nitrogen within 20 minutes of removal. Initial diagnosis of each sample from frozen section was later confirmed by detailed analysis of paraffin sections and immunohistochemistry. Following WHO guidelines,1 17 tumours were classified as SCLC including two combined SCLC with adenocarcinoma (SCLC-AD), 8 as LCNEC, including 2 combined LCNEC with AD (LCNEC-AD), 12 as TC and 1 as AC. The prevalence of LCNEC as a percentage all lung cancer resected at the Cancer Institute during the period was 2.7%. Since LCNEC is described as a variant of large cell carcinoma MAGE(LCC), we also analyzed thirteen LCC samples. Twelve well differentiated AD samples were included to aid interpretation of expression profiles for the SCLC-AD and LCNEC-AD samples, and to allow identification of markers that distinguish NT from non-small cell lung cancer. We included thirty normal lung samples from unrelated individuals. Finally 11 SCLC cell lines were incorporated into the analysis. Full clinical details of all tumour samples and cell lines are provided in supplementary table 1. Reference RNA, a mixture of lung cancer cell lines and normal lung, is exactly as described previously.5 Cell lines were obtained from the American Type Culture Collection. the Japanese Collection of Research Bioresources, or The RIKEN cell bank. cDNA microarray Each microarray contains 40,368 elements, of which 39,936 are derived from IMAGE cDNA clones purchased from Research Genetics (Huntsville, Alabama). This clone set was supplemented with 384 proprietary clones and 48 control elements. According to our latest estimate, the array represents 29,487 unique UNIGENE clusters accounting for 9,085 named genes, 15,276 ESTs and 5126 other un-named genes (for example, clones described as hypothetical proteins). Clones were purchased as sequence verified, but we estimate an error rate of at least 10%. Genes mentioned by name in this paper have been re-sequenced. cDNA PCR products were resuspended in 50% DMSO and printed at a pitch of 150 µm onto CMT-GAPS slides (Corning, Corning, NY) using a MicroGrid II spotting robot fitted with 10K pins (BioRobotics, Cambridge, UK). Relative humidity was controlled within the range 40-50% and temperature between 20-25°C. cDNA derived from 2µg of cRNA, essentially as described,7 was aminoallyl labeled8 with Cy5 (sample) or Cy3 (reference), hybridized overnight at 42ºC in a buffer containing 50% formamide, 5xSSC, 0.1% SDS, 0.25µg/µl human cot1 DNA and 0.125µg/µl poly dT and washed to a final stringency of 1x SSC at 42°C. After washing, slides were immediately scanned using an Axon GenePix 4000B scanner and quantified using Axon GenePix Pro software (Axon, Union city, CA). Raw data for all 40,386 elements across all 105 samples assayed here is deposited with
12 GPL9539 Agilent_MIE Plasmodium berghei 4X44k Microarray 44,407 mie university 2009-11-05 Agilent Plasmodium berghei
Plasmodium berghei		 Oligo Array in situ oligonucleotide, Agilent_MIE Plasmodium berghei 4X44k Microarray,
13 GPL9476 National Institute of Fruit Tree Science/Fruit Genome Research Team -Pyrus pyrifolia-18,862-ver017286 18,932 National Institutes of Fruit Tree Science 2009-10-21 Agilent Pyrus pyrifolia
Pyrus pyrifolia		 Oligo Array spotted oligonucleotide, National Institute of Fruit Tree Science/Fruit Genome Research Team -Pyrus pyrifolia-18,862-ver017286,
14 GPL9448 NimbleGen Human HG18 RefSeq Promoter 385K tiling array 386,230 Tokyo Medical and Dental University 2009-10-14 NimbleGen Homo sapiens
Homo sapiens		 Tiling Array in situ oligonucleotide, NimbleGen Human HG18 RefSeq Promoter 385K tiling array, Source: UCSC Build: HG18, NCBI 36 Probe Length: 50-75mer Median Probe Spacing: 100bp Design Name: Human ChIP 385K RefSeq Prom Arr Ser Native NimbleGen files (ndf, ngd, pos) linked below as supplementary files.
15 GPL9400 3D-Gene Human miRNA Oligo chip v12 935 TORAY Industries, Inc. 2009-10-08 TORAY Industries, inc. Homo sapiens
Homo sapiens		 Oligo Array spotted oligonucleotide, 3D-Gene Human miRNA Oligo chip v12,
16 GPL9398 Nimblegen/Affymetrix Bifidobacterium longum 2.7K Oligo Array 2,669 RIKEN 2009-10-08 Roche Nimblegen Bifidobacterium longum
Bifidobacterium longum		 GeneChip in situ oligonucleotide, Nimblegen/Affymetrix Bifidobacterium longum 2.7K Oligo Array,
17 GPL9284 NIAS Designed Custom Agilent Bovine 15K Oligo DNA Microarray 15,744 National Institute of Agrobiological Sciences 2009-09-24 Agilent Bos taurus
Bos taurus		 Oligo Array in situ oligonucleotide, NIAS Designed Custom Agilent Bovine 15K Oligo DNA Microarray,
18 GPL9283 Genopal Human 216 Autoimmunity Array v.1 219 RIMD, Osaka univ. 2009-09-24 Mitxubishi Rayon Co., Ltd Homo sapiens
Homo sapiens		 Oligo Array spotted oligonucleotide, Genopal Human 216 Autoimmunity Array v.1,
19 GPL9279 Frankia alni ACN14a whole genome microarray [2007-06-20_Frankia_expr] 6,723 Kagoshima University 2009-09-23 Roche NimbleGen Frankia alni ACN14a
Frankia alni ACN14a		 Oligo Array in situ oligonucleotide, Frankia alni ACN14a whole genome microarray [2007-06-20_Frankia_expr],
20 GPL9241 Frankia alni ACN14a whole genome microarray [2008-05-19_RDKK060_Faln_60mer_expr] 6,721 Kagoshima University 2009-09-21 Roche NimbleGen Frankia alni ACN14a
Frankia alni ACN14a		 Oligo Array in situ oligonucleotide, Frankia alni ACN14a whole genome microarray [2008-05-19_RDKK060_Faln_60mer_expr],
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