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
(37)		   SAGE RsaI
(0)		   SAGE Sau3A
(1)		   MPSS
(9)		   GeneChip
(78)		   Tiling Array
(226)		   cDNA Array
(558)		   Oligo Array
(799)		   Bead Array
(0)		   Protein Array
(0)		   Antibody
(0)		   RT-PCR
(0)		   HT-Seq
(432)		   Other
(26)		   All
(2,170)		  
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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.
61 GPL6331 NIBS-Arabidopsis-solexa-AGO sRNAs 586,511 National Institute Of Biological Sciences, Beijing (NIBS) 2007-12-27 Arabidopsis thaliana
Arabidopsis thaliana		 HT Sequencing other, NIBS-Arabidopsis-solexa-AGO sRNAs, Solexa, CSHL
62 GPL7176 Axtell_Physco_rdr6_Linker3 (Solexa sequencing) 582,688 Pennsylvania State University 2008-08-17 Physcomitrella patens
Physcomitrella patens		 HT Sequencing other, Axtell_Physco_rdr6_Linker3 (Solexa sequencing), Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all small RNA sequences from two technical replicates from 10 day old rdr6-19 plants. See Cho et al. for details.
63 GPL7175 Axtell_Physco_dcl3_Linker2 (Solexa sequencing) 522,668 Pennsylvania State University 2008-08-17 Physcomitrella patens
Physcomitrella patens		 HT Sequencing other, Axtell_Physco_dcl3_Linker2 (Solexa sequencing), Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all small RNA sequences from 10 day old dcl3 samples (line 5 and 10). See Cho et al. for details.
64 GPL7029 Carrington-Arabidopsis-Illumina-miRNA-AGO-high-throughput sequencing 515,462 Donald Danforth Plant Science Center 2008-07-08 Center for Genome Research and Biocomputing, Oregon State University Arabidopsis thaliana
Arabidopsis thaliana		 HT Sequencing other, Carrington-Arabidopsis-Illumina-miRNA-AGO-high-throughput sequencing, Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets. Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome were included in the analysis.
65 GPL9893 ENS SGDB Trichoderma virens Tv10_Tiling93_1 415,372 École Normale Supérieure 2010-01-11 Agilent Technologies Hypocrea virens
Hypocrea virens		 Tiling Array in situ oligonucleotide, ENS SGDB Trichoderma virens Tv10_Tiling93_1, Trichoderma virens Tiling array. One probe has been design every 93 base every other strand. The probe design has been done according to T. virens v1.0 genome assembly from the DOE JGI available here: http://genome.jgi-psf.org/Trive1/Trive1.home.html The probe ID is a code to find genome localisation of each probe: Scaffold_Start_Strand. The first number merge to Tv suffix indicates the scaffold number The second number is the start position of the probe The third number is the strand FWD or REV
66 GPL428 Arabidopsis Pilot Genome Tiling Array 1A 409,600 Stanford Genome Technology Center 2003-08-20 Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis Pilot Genome Tiling Array 1A, This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap using in situ synthesized 25 bp oligonucleotides. Perfect match and central position mismatch probes were made for these arrays. The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array. This chip tiles the first half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 1 that was chosen for these pilot arrays. Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.
67 GPL429 Arabidopsis Pilot Genome Tiling Array 1B 409,600 Stanford Genome Technology Center 2003-08-20 Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis Pilot Genome Tiling Array 1B, This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap using in situ synthesized 25 bp oligonucleotides. Perfect match and central position mismatch probes were made for these arrays. The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array. This chip tiles the second half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 1 that was chosen for these pilot arrays. Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.
68 GPL430 Arabidopsis Pilot Genome Tiling Array 1C 409,600 Stanford Genome Technology Center 2003-08-20 Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis Pilot Genome Tiling Array 1C, This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap using in situ synthesized 25 bp oligonucleotides. Perfect match and central position mismatch probes were made for these arrays. The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array. This chip tiles the first half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 2 that was chosen for these pilot arrays. Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.
69 GPL431 Arabidopsis Pilot Genome Tiling Array 1D 409,600 Stanford Genome Technology Center 2003-08-20 Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, Arabidopsis Pilot Genome Tiling Array 1D, This set of Affymetrix array tiles 5 Mb the Arabidopsis genome with a 12 bp overlap using in situ synthesized 25 bp oligonucleotides. Perfect match and central position mismatch probes were made for these arrays. The position coordinates in the table refer to the begining of the 2.5 Mb chromosomal fragment that was tiled on the array. This chip tiles the second half (1.25 MB) of both strands of the 2.5 Mb sequence of Chromosome 2 that was chosen for these pilot arrays. Features that have no sequence information represent positioning grids/checkerboards or random sequence controls.
70 GPL10634 NimbleGen/SNU Rice 3'-tiling 385K array 392,714 Seoul National University 2010-06-29 NimbleGen Oryza sativa
Oryza sativa		 Tiling Array in situ oligonucleotide, NimbleGen/SNU Rice 3'-tiling 385K array, The profiling was conducted with the Rice 3'Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene. Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, 270,000 probes were designed with the average size of probe is 60-nt long to have its Tm value 75 to 85 °C.
71 GPL3371 FHCRC Arabidopsis Tiling Array 391,015 Fred Hutchinson Cancer Research Center 2006-01-18 NimbleGen Systems Inc. Arabidopsis thaliana
Arabidopsis thaliana		 Tiling Array in situ oligonucleotide, FHCRC Arabidopsis Tiling Array, Arabidopsis tiling array using NimbleGen platform (DesignID=2482). TIGR release 5.0, 1/22/2004 (ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/). Entire genome, isothermal probes averaging 50 base pairs at 300 base pair intervals.
72 GPL1796 Chlamy 36mer array 390,886 NASA Ames Research Center 2005-01-14 Chlamydomonas reinhardtii
Chlamydomonas reinhardtii		 Oligo Array spotted oligonucleotide, Chlamy 36mer array, 389,285 different 36-mer oligonucleotide probes were selected from the V2 genome sequence of Chlamydomonas reinhardtii that was available from the JGI website (ftp://ftp.jgi-psf.org/pub/JGI_data/Chlamy/chlre2/) in February 2004. The probes are covering predicted proteins and intergenic regions. The selected oligonucleotides were synthesized on a glass-based array using an in situ maskless photolithographic synthesis device.
73 GPL7344 Rice NimbleGen 390K tiling array (2006-11-14_ggb_rap1_3tile_101706) 390,811 GGBIO 2008-09-19 Greengene Biotech Oryza sativa
Oryza sativa		 Tiling Array in situ oligonucleotide, Rice NimbleGen 390K tiling array (2006-11-14_ggb_rap1_3tile_101706), Rice genome build information requested but not provided.
74 GPL1842 ATH Whole genome chip 3 390,734 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH Whole genome chip 3, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
75 GPL1851 ATH whole genome chip 11 390,734 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH whole genome chip 11, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
76 GPL1840 ATH Whole genome chip 1 390,732 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH Whole genome chip 1, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
77 GPL1841 ATH Whole genome chip 2 390,732 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH Whole genome chip 2, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
78 GPL1849 ATH whole genome chip 9 390,732 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH whole genome chip 9, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
79 GPL1850 ATH whole genome chip 10 390,732 NASA Ames Research Center 2005-02-04 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH whole genome chip 10, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
80 GPL1853 ATH whole genome chip 13 390,732 NASA Ames Research Center 2005-02-05 Arabidopsis thaliana
Arabidopsis thaliana		 Oligo Array in situ oligonucleotide, ATH whole genome chip 13, 36-mer probes covering about every 10 bps of Arabidopsis Thaliana genome
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