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
(165)
  Primates
(0)
  Rodents
(23)
  Mammals
(3)
  Vertebrates
(8)
  Invertebrates
(3)
  Plants
(14)
  Bacteria
(3)
  Viruses
(0)
  Phages
(0)
  Unclassified
(3)
  All
(222)
 
  SAGE NlaIII
(1)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(0)
  Tiling Array
(0)
  cDNA Array
(9)
  Oligo Array
(4)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(0)
  HT-Seq
(0)
  Other
(0)
  All
(14)
 
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 GPL1676 SAGE:17:NlaIII:Magnaporthe grisea 70-15 51,925 2004-11-01 Magnaporthe oryzae 70-15
Magnaporthe oryzae 70-15
SAGE NlaIII SAGE NlaIII, SAGE:17:NlaIII:Magnaporthe grisea 70-15, This is a virtual platform for longSAGE 17 libraries generated for Magnaporthe grisea (stain 70-15) using NlaIII as an anchor enzyme. Platform_anchor: NlaIII
2 GPL1713 GBC_FOAR03_0001 28,800 University of British Columbia 2004-11-18 Arabidopsis thaliana
Arabidopsis thaliana
Oligo Array spotted oligonucleotide, GBC_FOAR03_0001, The Arabidopsis Genome Oligo Set Version 1.0 (Operon Biotechnologies, Huntsville, AL, USA) consists of 26090 70mer oligonucleotides (http://operon.com/arrays/oligosets_arabidopsis.php). As positive controls, we included oligos for twelve housekeeping genes (Operon). As negative controls, we synthesized four oligonucleotides specific for human genes with no similarity to any Arabidopsis gene and included twelve oligonucleotides with no similarity to any Arabidopsis gene (Operon). We used a PCR amplified green fluorescent protein (GFP) cDNA (Invitrogen, Carlsbad, CA, USA) as an orientation marker. Oligonucleotides were resuspended in 384 well flat bottom plates (Nunc, Rochester, NY, USA) to a concentration of 100 mM in 3 x SSC. Oligos were printed on MicroGrid II robots using Microspot 10k pins (Biorobotics, Huntington, UK) depositing approximately 0.5 nl (0.0075 pmole) of each oligo onto EZ rays aminosilane slides (Apogent Discoveries, Hudson, NH, USA). The pitch of the grid used for this library was 0.2 mm. Oligos were UV cross linked at 3000 x 100 μJ using a UV Stratalinker 2400 (Stratagene, La Jolla, CA, USA). We spotted single spots for 25,792 of the 26090 target oligonucleotides (due to software problems the print run was terminated shortly before completion); in addition, each subgrid contained six replicate spots of each of the four human negative controls, three spots of equally distributed Operon negative controls, a single spot of each of the twelve house keeping controls, and GFP marker on each corner of the s Keywords = GenomeBC-Forestry Keywords = 26k array v.1
3 GPL1722 Rice Chromosome 4 Tilling-Path 14,554 California Institute of Technology 2004-11-29 Oryza sativa
Oryza sativa
cDNA Array spotted DNA/cDNA, Rice Chromosome 4 Tilling-Path, The array represent a minimal tilling-path coving rice chromosome 4. This tilling-path was assembled using 14,742 randomly sheared shotgun subclone fragments. All subclone fragments were PCR amplified using universal primers and plasmids containing the genomic DNA fragment as the template. DNA gel analysis was performed for all fragments and poor amplification were not included here. In the final count by comparing with the TIGR version 2.0 sequence, 95.5% of the sequence of this chromosome is covered by the array. Keywords = rice Keywords = chromosome 4 Keywords = tilling-path
4 GPL1519 Soll albicans 14,112 The University of Iowa 2004-10-19 Candida albicans
Candida albicans
Oligo Array spotted oligonucleotide, Soll albicans, C. albicans Array-Ready Genome Oligo Set Version 1.1 (Qiagen, Valencia, CA) was resuspended at a concentration of 20uM in 150mM sodium phosphate buffer (pH 8.5). Oligos were printed in duplicate blocks on Code Link slides (Amersham Biosciences) at Microarray, Inc. DNA coupling and post-coupling processing of printed microarray slides were done according to the manufacturere's instructions (Amersham Biosciences).
5 GPL1508 Pinus taeda cDNA 9,204 North Carolina State University 2004-10-13 Pinus taeda
Pinus taeda
cDNA Array spotted DNA/cDNA, Pinus taeda cDNA, The microarray contains ESTs selected from 6 Xylem libraries: 1. NXCI - ESTs from juvenile compression wood of Pinus taeda (loblolly pine) 2. NXLV - ESTs from transitional/mature late wood of Pinus taeda (loblolly pine) 3. NXNV - ESTs from mature normal wood of Pinus taeda (loblolly pine) 4. NXPV - ESTs from transitional planings wood of Pinus taeda (loblolly pine) 5. NXRV - ESTs from root wood of Pinus taeda (loblolly pine) 6. NXSI - ESTs from juvenile side wood of Pinus taeda (loblolly pine) , a Pollen Cone library, and a Shoot tip library. The ESTs were PCR amplified, purified, denatured in 50% DMSO and printed on Corning GapsII amino-silane coated slides.
6 GPL1531 CEA_SGF:AIW 6,912 CEA 2004-10-25 Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, CEA_SGF:AIW, Chip contains 6912 features (probes and controls): 6528 PCR products from Research Genetics ORF collection 384 controls features
7 GPL1695 yeast intergenic array 6,814 University of Geneva 2004-11-08 Saccharomyces cerevisiae
Saccharomyces cerevisiae
Oligo Array spotted oligonucleotide, yeast intergenic array, -Platform: amino-silane coated glass slides (GAPS II, Corning) -S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic). -The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)
8 GPL1689 Struhl Lab Yeast Double Intergenic Array 6,438 Harvard Medical School 2004-11-04 Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, Struhl Lab Yeast Double Intergenic Array, All Saccharomyces cerevisiae intergenic regions
9 GPL1535 Custom Yeast Genomic 70-mer Oligonucleotide Microarray 5,617 University of Illinois at Urbana-Champaign 2004-10-25 Saccharomyces cerevisiae
Saccharomyces cerevisiae
Oligo Array spotted oligonucleotide, Custom Yeast Genomic 70-mer Oligonucleotide Microarray, The custom microarrays consisted of Operon’s Yeast Genomic 70-mer Oligonucleotide Set (Qiagen, Valencia, CA, v. 1.1) spotted in duplicate at a concentration of 20 mM in 150 mM sodium phosphate (pH 8.5), Arabidopsis oligonucleotide spike controls (Stratagene SpotReport, La Jolla, CA) spotted in quadruplicate, and 10 human and 10 yeast oligonucleotide negative controls spotted in duplicate. The oligonucleotides were printed on Codelink slides (Amersham, Piscataway, NJ) by Microarrays, Inc. (Nashville, TN). Post-print processing was conducted according to the manufacturer’s recommendations.
10 GPL1756 Emericella nidulans EST-based chip primary data 4,352 University of Debrecen 2004-12-21 Emericella nidulans
Emericella nidulans
cDNA Array spotted DNA/cDNA, Emericella nidulans EST-based chip primary data, Double printed Emericella nidulans chips containing 3533 unique EST sequences in 4352 spots.
11 GPL1752 Emericella nidulans EST-based chip normalized data 3,533 University of Debrecen 2004-12-17 Emericella nidulans
Emericella nidulans
cDNA Array spotted DNA/cDNA, Emericella nidulans EST-based chip normalized data, Double printed Emericella nidulans chips containing 3533 unique EST sequences in 4352 spots.
12 GPL1533 CEA_SGF:ABO 3,360 CEA 2004-10-25 Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, CEA_SGF:ABO, Chip contains 3360 features (probes and controls): 3264 PCR products from Research Genetics ORF collection 96 controls features
13 GPL1534 CEA_SGF:ABP 3,264 CEA 2004-10-25 Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, CEA_SGF:ABP, Chip contains 3264 features (probes and controls): 3168 PCR products from Research Genetics ORF collection 96 controls features
14 GPL1730 coffee nylon arrays 3,072 UNICAMP 2004-12-06 Coffea hybrid cultivar
Coffea hybrid cultivar
cDNA Array spotted DNA/cDNA, coffee nylon arrays, Nylon membranes containing coffee ESTs from subtracted cDNA librares. Plasmid clones were used. A set of sixteen 96-well plates was spotted on two nylon filters (85 mm x 125 mm) in a 4 x 4 array configuration, with a 96 pins hand-held array tool