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
(3,985)
  Primates
(80)
  Rodents
(1,907)
  Mammals
(359)
  Vertebrates
(450)
  Invertebrates
(1,139)
  Plants
(2,490)
  Bacteria
(1,901)
  Viruses
(90)
  Phages
(11)
  Unclassified
(542)
  All
(13,032)
 
  SAGE NlaIII
(5)
  SAGE RsaI
(0)
  SAGE Sau3A
(1)
  MPSS
(2)
  GeneChip
(367)
  Tiling Array
(712)
  cDNA Array
(1,065)
  Oligo Array
(1,435)
  Bead Array
(138)
  Protein Array
(1)
  Antibody
(24)
  RT-PCR
(128)
  HT-Seq
(55)
  Other
(51)
  All
(3,985)
 
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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 GPL6314 NCI Human Solexa Platform 14814K 14,814,587 National Cancer Institute 2007-12-20 not applicable Homo sapiens
Homo sapiens
HT Sequencing other, NCI Human Solexa Platform 14814K,
2 GPL7003 MPIMG-Human-Solexa sequencing HEK PolIIa ChIP 12,814,371 Max Planck Institute for molecular genetics 2008-06-30 MPIMG Homo sapiens
Homo sapiens
HT Sequencing other, MPIMG-Human-Solexa sequencing HEK PolIIa ChIP, Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)
3 GPL7004 MPIMG-Human-Solexa sequencing-HEK and B cell RNA 12,004,594 Max Planck Institute for molecular genetics 2008-06-30 MPIMG Homo sapiens
Homo sapiens
HT Sequencing other, MPIMG-Human-Solexa sequencing-HEK and B cell RNA, Sequencing was carried out using the 1G Illumina Genome Analyser (Solexa)
4 GPL6300 NCI Human 454 Platform 2795K 2,795,975 National Cancer Institute 2007-12-19 not applicable Homo sapiens
Homo sapiens
HT Sequencing other, NCI Human 454 Platform 2795K,
5 GPL8267 HudsonAlpha Illumina Homo sapiens Methyl-seq 90,612 Stanford U 2009-03-09 NIH Homo sapiens
Homo sapiens
HT Sequencing other, HudsonAlpha Illumina Homo sapiens Methyl-seq, 1G Genome Analyzer sequencing machine
6 GPL8198 SNI_human_MPSS 29,953 Swedish Medical Center 2009-02-17 SOLEXA Homo sapiens
Homo sapiens
HT Sequencing MPSS, SNI_human_MPSS,
7 GPL7110 NCGR Human RefSeq 7 08 28,554 National Center for Genome Resources 2008-07-30 Homo sapiens
Homo sapiens
HT Sequencing other, NCGR Human RefSeq 7 08, Refseq Transcript Set. Sequencing-by-synthesis: Cerebellum samples were sequenced using Illumina Genome Analyzers with modifications for mRNA samples (Lister et al., 2008; Morin et al., 2008)(Mortazavi et al., 2008): Following quality assessment using a Bioanalyzer 2100 (Agilent Inc., Santa Clara, CA; Table 1), poly A+ RNA was isolated from 5 – 10 μg total RNA by two rounds of oligo-dT selection (Invitrogen Inc., Santa Clara, CA). mRNA was annealed to high concentrations of random hexamers and reverse transcribed. Following second strand synthesis, end repair, and A-tailing, adapters complementary to sequencing primers were ligated to cDNA fragment ends. Resultant cDNA libraries were size fractionated on agarose gels, 200 bp fragments excised, and amplified by 15 cycles of polymerase chain reaction. Following quality assessment using a Bioanalyzer 2100, single-stranded cDNA-adapter fragments were randomly annealed to the surface of a flow cell in a cluster station (Illumina Inc., San Diego, CA) via primers complementary to the adapters and incubated under conditions fostering annealing of the ends of cDNA-adapter fragments to adjacent complementary primers. Primers with annealed cDNA-adapter fragments were extended with DNA polymerase and unlabelled dNTPs in a solid-phase “bridge amplification”. Resultant double-stranded products were denatured, yielding 2 single stranded fragments. The latter steps were repeated for 35 cycles, generating ~40 million clusters of clonal amplicons. Subsequently, 32 – 36 cycles of sequencing-by-synthesis chemistry were performed in Illumina Genome Analyzer instruments with 4 dNTPs featuring cleavable dyes and reversible terminators. Following each base extension, 4 images (one for each nucleotide) are taken upon laser excitation. Incorporation of the next base occurred after removal of the blocked 3’ terminus and fluorescent tag of the previously incorporated nucleotide. Read Alignment-based gene expression profiling: Reads were aligned to the human genome and RefSeq transcript databases (Pruitt et al., 2005) using the algorithm GMAP (Wu and Watanabe, 2005) and the software system Alpheus (Sugarbaker et al., 2008), with adjustments for short SBS reads (oligomer overlap interval = 3nt, identities > 34/36 or 94%). Only the highest scoring alignment(s) was retained. Reads with a single best alignment or with equally good alignments to alternative transcripts of the same gene were considered uniquely aligned. Aligned read frequencies (per million aligned reads) were calculated for each sample and gene using Alpheus (Sugarbaker et al., 2008). Statistical Analysis: Array hybridization signals and read frequencies were log10 transformed prior to evaluation of inter-sample differences. Overlayed kernel density estimates, univariate distribution results, Mahalanobis distances, correlation coefficients of pairwise sample comparisons, unsupervised principal component analysis (by Pearson product-moment correlation) and Ward hierarchical clustering of Pearson product-moment correlations of read frequencies were performed with JMP Genomics, Version 3.2 (SAS Institute, Cary, NC). Decomposition of principal components of variance of array signals and read frequencies, FDR corrected analysis of variance (with inclusion of the non-diagnosis components of variance discussed above as fixed effects) and chi squared comparisons of GO annotations were also performed with JMP Genomics, Version 3.2. Patient, sample, and experimental parameters examined to quantify sources of variability in measurements were age, alignment percentage, brain pH, cause of death, cluster station, diagnosis, library creator, number of reads, post-mortem interval, psychotropic medication, race, read length, read quality score, RNA isolation date, RNA integrity number, sample storage duration, sequencing instrument and year sequenced.
8 GPL7564 Salk-Yeo-Solexa-ES,NP,NE cells 26,243 University of California, San Diego 2008-11-05 Illumina Homo sapiens
Homo sapiens
HT Sequencing other, Salk-Yeo-Solexa-ES,NP,NE cells,
9 GPL8664 LC Sciences Human 454 miRHuman_8.2 [condensed version] 503 "Sapienza" University of Rome 2009-06-05 LC sciences Homo sapiens
Homo sapiens
HT Sequencing in situ oligonucleotide, LC Sciences Human 454 miRHuman_8.2 [condensed version], This array represents a condensed version of full array which is linked as a supplementary file.
10 GPL10297 Illumina Genome analyzer II (Homo sapiens) 0 2010-04-07 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, Illumina Genome analyzer II (Homo sapiens),
11 GPL10400 454 GS (Homo sapiens) 0 2010-05-06 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, 454 GS (Homo sapiens),
12 GPL10999 Illumina Genome Analyzer IIx (Homo sapiens) 0 2010-09-29 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer IIx (Homo sapiens),
13 GPL11154 Illumina HiSeq 2000 (Homo sapiens) 0 2010-11-02 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, Illumina HiSeq 2000 (Homo sapiens),
14 GPL11255 AB SOLiD System 3 (Homo sapiens) 0 2010-11-30 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, AB SOLiD System 3 (Homo sapiens),
15 GPL11436 AB SOLiD 3 Plus (Homo sapiens) 0 2011-01-12 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, AB SOLiD 3 Plus (Homo sapiens),
16 GPL13317 Heliscope (Homo sapiens) 0 2011-03-23 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, Heliscope (Homo sapiens),
17 GPL13357 AB SOLiD System v3+ (Homo sapiens) 0 2011-03-31 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, AB SOLiD System v3+ (Homo sapiens),
18 GPL13393 AB SOLiD 4 System (Homo sapiens) 0 2011-04-08 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, AB SOLiD 4 System (Homo sapiens),
19 GPL13477 Illumina Genome Analyzer IIX (Homo sapiens) 0 2011-05-02 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, Illumina Genome Analyzer IIX (Homo sapiens),
20 GPL13484 454 Titanium (Homo sapiens) 0 2011-05-03 Homo sapiens
Homo sapiens
HT Sequencing high-throughput sequencing, 454 Titanium (Homo sapiens),
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