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
(33,137)
  Primates
(196)
  Rodents
(10,648)
  Mammals
(1,806)
  Vertebrates
(771)
  Invertebrates
(1,113)
  Plants
(7,693)
  Bacteria
(2,917)
  Viruses
(10)
  Phages
(0)
  Unclassified
(511)
  All
(58,828)
 
  SAGE NlaIII
(0)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(495)
  Tiling Array
(24)
  cDNA Array
(192)
  Oligo Array
(1,944)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(0)
  HT-Seq
(198)
  Other
(64)
  All
(2,917)
 
  brain
(0)
  blood
(24)
  connective
(75)
  reproductive
(8)
  muscular
(0)
  digestive
(40)
  liver
(6)
  lung
(8)
  urinary
(3)
  endo/exo-crine
(6)
  embryo
(1)
  adult aerial structure
(0)
  young aerial structure
(0)
  root
(0)
  meristem/growing tissue
(0)
  flower/sexual organ
(0)
  seed/fruit/grain
(0)
  pooled
(8)
  unclassified
(2,738)
  all
(2,917)
 
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Sample ID Title Number of Data Institute Submission date Platform Sample type Species Organ class Reasoning of the classification
Keywords used for the classification are shown with bold font.
1 GSM1087235 Neisseria lactamica 020-06 WT minus TEX 0 University of Würzburg 2013-02-22 [HT Sequencing] Illumina Genome Analyzer IIx (Neisseria lactamica 020-06) (GPL16715) SRA Neisseria lactamica 020-06
Neisseria lactamica 020-06
unclassified source_name:no treatment title:Neisseria lactamica 020-06 WT minus TEX
2 GSM1087236 Neisseria lactamica 020-06 WT plus TEX 0 University of Würzburg 2013-02-22 [HT Sequencing] Illumina Genome Analyzer IIx (Neisseria lactamica 020-06) (GPL16715) SRA Neisseria lactamica 020-06
Neisseria lactamica 020-06
unclassified source_name:terminator exonuclease (TEX) title:Neisseria lactamica 020-06 WT plus TEX
3 GSM1095213 M. kandleri sRNAs control 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
unclassified source_name:Cultured organism title:M. kandleri sRNAs control description:total small RNA (<200 bases) Sample 1 no additional treatment
4 GSM1095214 M. kandleri sRNAs +T4PNK -ATP 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
unclassified source_name:Cultured organism title:M. kandleri sRNAs +T4PNK -ATP description:total small RNA (<200 bases) Sample 2 The protocol for sample 4 was followed but the final addition of 2 mM ATP was omitted.
5 GSM1095215 M. kandleri sRNAs +T4PNK +ATP 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
unclassified source_name:Cultured organism title:M. kandleri sRNAs +T4PNK +ATP description:total small RNA (<200 bases) Sample 3 The protocol for sample 4 was followed but 2 mM ATP was added from the beginning.
6 GSM1095216 M. kandleri sRNAs +T4PNK/ATP 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
unclassified source_name:Cultured organism title:M. kandleri sRNAs +T4PNK/ATP description:total small RNA (<200 bases) Sample 4 10 μg of small RNA was incubated at 37°C for 6 hours with 20 units T4 PNK and 10 μl 5× T4 PNK buffer in a total volume of 50 μl. Subsequently, 2 mM ATP was added and the reaction mixture was incubated for 1 hour at 37°C to generate monophosphorylated 5’ termini.
7 GSM1095217 M. kandleri sRNAs + Tris-HCl pH8.8 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
embryo total small RNA (<200 bases) Sample 5 10 µg of M. kandleri sRNA was incubated in a buffer containing 170 mM Tris-HCl pH 8.8 37° C for 3 hours to facilitate deacetylation of tRNA molecules
8 GSM1095218 M. kandleri sRNAs + H2O2 0 MPI for terrestrial microbiology 2013-03-08 [HT Sequencing] Illumina HiSeq 2000 (Methanopyrus kandleri AV19) (GPL16769) SRA Methanopyrus kandleri AV19
Methanopyrus kandleri AV19
unclassified source_name:Cultured organism title:M. kandleri sRNAs + H2O2 description:total small RNA (<200 bases) Sample 6 10 µg of M. kandleri sRNA was incubated in a buffer containing 50 mM sodium phosphate, 1 mM EDTA and 0,36% H2O2 at 20°C for 3 hours to facilitate dethiolation of RNA
9 GSM1149845 R. sphaeroides 2.4.1 anaerob 0 Justus-Liebig University Gießen 2013-05-29 [HT Sequencing] Illumina HiSeq 2000 (Rhodobacter sphaeroides 2.4.1) (GPL17213) SRA Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1
unclassified source_name:bacterial cells title:R. sphaeroides 2.4.1 anaerob description:Note from submitter: R._sphaeroides_2.4.1_anaerob_forward.wig and R._sphaeroides_2.4.1_anaerob_div_by_4349519.0_multi_by_4349519.0_forward.wig are identical. They are the same files as for the mentioned file the normalization leads to the same outcome as without the normalizatoin- still I would keep it in the set as people usually load all normalized files together into a genome browser and might be confused if those are missing.
10 GSM1149846 R. sphaeroides 2.4.1 microaerob 0 Justus-Liebig University Gießen 2013-05-29 [HT Sequencing] Illumina HiSeq 2000 (Rhodobacter sphaeroides 2.4.1) (GPL17213) SRA Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1
unclassified source_name:bacterial cells title:R. sphaeroides 2.4.1 microaerob
11 GSM1149847 R. sphaeroides 2.4.1 iron depletion anaerob 0 Justus-Liebig University Gießen 2013-05-29 [HT Sequencing] Illumina HiSeq 2000 (Rhodobacter sphaeroides 2.4.1) (GPL17213) SRA Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1
unclassified source_name:bacterial cells title:R. sphaeroides 2.4.1 iron depletion anaerob
12 GSM1149848 R. sphaeroides 2.4.1 iron depletion microaerob 0 Justus-Liebig University Gießen 2013-05-29 [HT Sequencing] Illumina HiSeq 2000 (Rhodobacter sphaeroides 2.4.1) (GPL17213) SRA Rhodobacter sphaeroides 2.4.1
Rhodobacter sphaeroides 2.4.1
unclassified source_name:bacterial cells title:R. sphaeroides 2.4.1 iron depletion microaerob
13 GSM1232743 SigX_chip_sample1 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_chip_sample1 title:SigX_chip_sample1 description:ChIP-seq treated rep1 SigX_MACS_peaks_sample1.txt
14 GSM1232744 SigX_chip_sample2 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina HiSeq 2500 (Pseudomonas aeruginosa UCBPP-PA14) (GPL17739) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_chip_sample2 title:SigX_chip_sample2 description:ChIP-seq treated rep2 SigX_MACS_peaks_sample2.txt
15 GSM1232745 SigX_control_sample1 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_control_sample1 title:SigX_control_sample1 description:ChIP-seq control rep1
16 GSM1232746 SigX_control_sample2 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina HiSeq 2500 (Pseudomonas aeruginosa UCBPP-PA14) (GPL17739) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_control_sample2 title:SigX_control_sample2 description:ChIP-seq control rep2
17 GSM1232747 SigX_overexpressed_sample1 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_overexpressed_sample1 title:SigX_overexpressed_sample1 description:overexpressing wildtype rep1 SigX_differential_expression_overexpressed_vs_empty_vector.txt
18 GSM1232748 SigX_overexpressed_sample2 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_overexpressed_sample2 title:SigX_overexpressed_sample2 description:overexpressing wildtype rep2 SigX_differential_expression_overexpressed_vs_empty_vector.txt
19 GSM1232749 SigX_empty_vector_sample1 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_empty_vector_sample1 title:SigX_empty_vector_sample1 description:overexpressing control rep1 SigX_differential_expression_overexpressed_vs_empty_vector.txt
20 GSM1232750 SigX_empty_vector_sample2 0 Helmholtz Centre for Infection Research 2013-09-17 [HT Sequencing] Illumina Genome Analyzer IIx (Pseudomonas aeruginosa UCBPP-PA14) (GPL17738) SRA Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa UCBPP-PA14
unclassified source_name:SigX_empty_vector_sample2 title:SigX_empty_vector_sample2 description:overexpressing control rep2 SigX_differential_expression_overexpressed_vs_empty_vector.txt
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