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
(79)
  Primates
(3)
  Rodents
(90)
  Mammals
(14)
  Vertebrates
(19)
  Invertebrates
(20)
  Plants
(93)
  Bacteria
(43)
  Viruses
(0)
  Phages
(0)
  Unclassified
(15)
  All
(378)
 
  SAGE NlaIII
(4)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(18)
  Tiling Array
(20)
  cDNA Array
(22)
  Oligo Array
(210)
  Bead Array
(9)
  Protein Array
(0)
  Antibody
(1)
  RT-PCR
(6)
  HT-Seq
(84)
  Other
(3)
  All
(378)
 
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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 GPL13482 SMD Print_1561 (hoag) 49,152 Universitätsspital Basel 2011-05-03 Stanford Functional Genomics Facility, Stanford School of Medicine Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, SMD Print_1561 (hoag),
2 GPL13623 Umea Lucidea array 21,168 Umeå University 2011-05-19 Clinical bacteriology, Umeå university Pinus sylvestris,Mus musculus
Pinus sylvestris,Mus musculus
cDNA Array spotted DNA/cDNA, Umea Lucidea array, The in-house produced cDNA-array contains 44 clones: 19 clones from mice, 4 clones from Pine (involved in photosynthesis) and 21 artificial clones from the Lucidea Universal ScoreCard (Amersham Bioscienses), where each clone was printed 480 times in 48 identically designed sub-grids.
3 GPL13758 New Zealand White Rabbit Heart 15K cDNA array 15,488 BIDMC/Harvard Medical School 2011-06-22 Harvard FAS Center for Systems Biology Oryctolagus cuniculus
Oryctolagus cuniculus
cDNA Array spotted DNA/cDNA, New Zealand White Rabbit Heart 15K cDNA array, New Zealand White Rabbit Heart; male, new born- 3 week recovery
4 GPL13737 BiostarH-140s 14,112 Guangzhou University of Chinese Medicine 2011-06-16 Biostargene, Shanghai Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, BiostarH-140s,
5 GPL13739 CGEP TOM1 Tomato 13.4k cDNA microarray 13,440 CNB-CSIC 2011-06-17 Center for Gene Expression Profiling (CGEP) at the Boyce Thompson Institute (BTI) Solanum lycopersicum
Solanum lycopersicum
cDNA Array spotted DNA/cDNA, CGEP TOM1 Tomato 13.4k cDNA microarray,
6 GPL13666 Human 11k cDNA arrays 11,070 ULB 2011-05-31 Libert Frédérick Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, Human 11k cDNA arrays, The cDNAs used for the slides were isolated from cDNA libraries of CP64-MEL melanoma cell line, normal melanocyte, leukocytes and fetal brain (Invitrogen Carlsbad, CA). Slides containing 25K spots with 11K identified cDNA by sequencing were printed.
7 GPL13536 Kanazawa Univ. Human Liver chip 10k 9,643 Kanazawa University 2011-05-15 First Department of Internal Medmme, Kanazawa University Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, Kanazawa Univ. Human Liver chip 10k, In addition to in-house cDNA microarray slides consisting 1080 cDNA clones as previously described(Gastroenterology. 2001 Mar;120(4):955-66, we made a new cDNA microarray slide for detailed analysis of the signaling pathway of metabolism and enzyme function in liver disease. Besides cDNA microarray analysis, a total of 256 550 tags were obtained from hepatic SAGE libraries (derived from normal liver, CH-C, CH-C related HCC, CH-B, CH-B related HCC respectively), including 52 149 unique tags. Among these, 16 916 tags expressing more than two hits were selected to avoid the effect of sequencing errors in the libraries. From these candidate genes, 9,614 non-redundant clones were obtained from Incyte Genomics (Incyte Corporation, Beverly, MA, USA), Clontech (Nippon Becton Dickinson, Tokyo, Japan), and Invitrogen (Invitrogen Japan K.K., Tokyo, Japan). Each clone was sequence validated and PCR amplified by Dragon Genomics (Takara Bio, Otsu, Japan), and the cDNA microarray slides (Liver chip 10k) were constructed using SPBIO 2000 (Hitachi Software, Fukuoka, Japan) as described previously.
8 GPL13609 SALSA 2 IFR Salmonella 8K Arrays 8,064 Institute of Food Research 2011-05-18 Institute of Food research, Norwich, UK Salmonella typhimurium DT104,Salmonella enterica subsp. enterica serovar Typhimurium str. LT2,Salmonella enterica subsp. enterica serovar Enteritidis,Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344,Salmonella enterica subsp. enterica s
Salmonella typhimurium DT104,Salmonella enterica subsp. enterica serovar Typhimurium str. LT2,Salmonella enterica subsp. enterica serovar Enteritidis,Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344,Salmonella enterica subsp. enterica s
cDNA Array spotted DNA/cDNA, SALSA 2 IFR Salmonella 8K Arrays,
9 GPL13722 Saccharomyces cerevisiae 6.4K array (Y6.4K), version 4 [ORF-centered] 6,218 Gothenburg University 2011-06-14 UHN Microarray Center Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, Saccharomyces cerevisiae 6.4K array (Y6.4K), version 4 [ORF-centered], This is an ORF-centered version of Platform GPL4462
10 GPL13619 Valencia yeast v9 6,144 Universitat de Valencia 2011-05-19 Seccion de Chips de DNA-SCSIE (University of Valencia) Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, Valencia yeast v9, Nylon macroarray (7 x 11 cm) with 6144 positions: 6026 single spotted yeast ORF/non-ORF gene probes; 45 probes for rRNA controls and 15 probes for B. subtilis genes as spiked controls. Probes are PCR fragments comprising the whole ORF (5558 cases) or a 1000-bp fragment from the ORF 3' end (451 cases).
11 GPL13620 Valencia yeast v10 6,144 Universitat de Valencia 2011-05-19 Seccion de Chips de DNA-SCSIE (University of Valencia) Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, Valencia yeast v10, Nylon macroarray (7 x 11 cm) with 6144 positions: 6035 single spotted yeast ORF/non-ORF gene probes; 45 probes for rRNA controls and 15 probes for B. subtilis genes as spiked controls. Probes are PCR fragments comprising the whole ORF (5558 cases) or a 1000 bp-fragment from the ORF 3' end (451 cases).
12 GPL13727 Scsie_Univ Valencia_Saccaromyces cerevisiae_ver.4 5,985 Universidad de A Coruña 2011-06-15 DNA-Chips Services from Univ. Valencia. Spain Saccharomyces cerevisiae
Saccharomyces cerevisiae
cDNA Array spotted DNA/cDNA, Scsie_Univ Valencia_Saccaromyces cerevisiae_ver.4,
13 GPL13683 ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.3 4,992 Duke University 2011-06-02 Institute for Systems Biology Halobacterium sp. NRC-1
Halobacterium sp. NRC-1
cDNA Array spotted DNA/cDNA, ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.3,
14 GPL13392 3.7k LUMC BAC array 3,670 LUMC 2011-04-08 LUMC, dept of Molecular Cell Biology Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, 3.7k LUMC BAC array,
15 GPL13378 Plant Systems Biology Lab, Vitis vinifera 3.4K cDNA microarray 3,456 ICAT/FCUL 2011-04-06 Plant Systems Biology Lab Vitis vinifera
Vitis vinifera
cDNA Array spotted DNA/cDNA, Plant Systems Biology Lab, Vitis vinifera 3.4K cDNA microarray, Each clone was printed twice in the same sub-grid.
16 GPL13655 NCSU_Thermotoga species 2,583 North Carolina State University 2011-05-26 NCSU Kelly Group Thermotoga maritima,Thermotoga neapolitana,Thermotoga petrophila,Thermotoga sp. RQ2
Thermotoga maritima,Thermotoga neapolitana,Thermotoga petrophila,Thermotoga sp. RQ2
cDNA Array spotted DNA/cDNA, NCSU_Thermotoga species, Because some probes were designed based on SSH results, some probes duplicate the same ORF or cover intergenic DNA. Here is a key for the notation used for probe names: TRQ2_0171a means there is more than one probe for this ORF, TRQ2_1842-1843 means this probe covers part of 1842 as well as part of 1843 and any intergenic DNA in between, TRQ2_1803-1820739-1820933 means that this probe covers the genome coordinates listed. The probe may cover part of the indicated ORF or it may only cover intergenic DNA in the vicinity of that ORF.
17 GPL13463 EBT UA_KUL Daphnia magna unique_1.9K microarray 1,916 University of Antwerp 2011-04-29 Laboratory for Ecophysiology,biochemistry and toxicology, University of Antwerp, Belgium and Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Belgium Daphnia magna
Daphnia magna
cDNA Array spotted DNA/cDNA, EBT UA_KUL Daphnia magna unique_1.9K microarray,
18 GPL13481 miRXplore TM Microarray (867) 1,471 Miltenyi Biotec GmbH 2011-05-03 Miltenyi Biotec GmbH, Cologne, Germany Homo sapiens,Mus musculus,Rattus norvegicus
Homo sapiens,Mus musculus,Rattus norvegicus
cDNA Array spotted DNA/cDNA, miRXplore TM Microarray (867), The miRXplore TM Microarray is composed of 5892 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1374 miRNA sequences and 97 controls with all probes spotted in quadruplicates. The 1374 miRNA sequences covered sequence verified miRNAs of the species human (859) mouse (622) and rat (428) as well as viral miRNAs (129) as deposited in the miRBase sequence database version 12.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not be present in any of the human, mouse, rat or viral genome. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g. for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane / phenylendiisothiocyanate coated glass slides in quadruplicates using a customized piezoelectric spotter.
19 GPL13520 UCSF_MouseArray_1.0_972 [BAC array] 972 UCSF 2011-05-11 UCSF Array Core Mus musculus
Mus musculus
cDNA Array spotted DNA/cDNA, UCSF_MouseArray_1.0_972 [BAC array],
20 GPL13480 PIQOR (TM) Stem Cell Microarray, human AS (780) 936 Miltenyi Biotec GmbH 2011-05-03 Miltenyi Biotec GmbH, Cologne, Germany Homo sapiens
Homo sapiens
cDNA Array spotted DNA/cDNA, PIQOR (TM) Stem Cell Microarray, human AS (780), The PIQOR (TM) Stem Cell Microarray is composed of 946 human specific cDNAs. These cDNAs include for each array six house-keeping genes as positive controls. In addition four E. coli DNA fragments and the corresponding in vitro transcribed RNAs (spiking controls) provide a control for the labeling and hybridisation efficiency. Two negative controls are given by spotted herring sperm DNA and buffer, respectively. All features are spotted in quadruplicate. The Platform data table reflects a condensed representation of the quadruplicate features.
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