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
(2,851)
  Primates
(60)
  Rodents
(2,564)
  Mammals
(41)
  Vertebrates
(39)
  Invertebrates
(59)
  Plants
(464)
  Bacteria
(78)
  Viruses
(0)
  Phages
(0)
  Unclassified
(146)
  All
(6,302)
 
  SAGE NlaIII
(24)
  SAGE RsaI
(0)
  SAGE Sau3A
(5)
  MPSS
(32)
  GeneChip
(2,621)
  Tiling Array
(155)
  cDNA Array
(1,964)
  Oligo Array
(1,212)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(9)
  RT-PCR
(15)
  HT-Seq
(0)
  Other
(265)
  All
(6,302)
 
  brain
(27)
  blood
(167)
  connective
(25)
  reproductive
(38)
  muscular
(116)
  digestive
(9)
  liver
(306)
  lung
(8)
  urinary
(13)
  endo/exo-crine
(152)
  embryo
(8)
  adult aerial structure
(0)
  young aerial structure
(0)
  root
(0)
  meristem/growing tissue
(0)
  flower/sexual organ
(0)
  seed/fruit/grain
(0)
  pooled
(190)
  unclassified
(153)
  all
(1,212)
 
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 GSM37570 Sprague Dawley Diabetic 2 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Sprague Dawley diabetic kidney total RNA Reference kidney total RNA
2 GSM37571 Sprague Dawley Diabetic 1 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Reference kidney total RNA Sprague Dawley diabetic kidney total RNA
3 GSM37572 Sprague Dawley Control 2 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Sprague Dawley control kidney total RNA Reference kidney total RNA
4 GSM37569 Sprague Dawley Control 1 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Reference kidney total RNA Sprague Dawley control kidney total RNA
5 GSM36125 Six4 target genes in mk4 cells 21,500 Jichi Medical School 2004-11-24 [Oligo Array] Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version) (GPL922) RNA Mus musculus
Mus musculus
kidney To identify Six4 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six4wt or VP16-Six4W263R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30 <super> latex beads (TaKaRa). Poly A+ RNA (20 µg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six4wt infected sample) or Cy5 (AxCAwt VP16-Six4W263R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.
6 GSM36124 Six1 target genes in mk4 cells 21,500 Jichi Medical School 2004-11-24 [Oligo Array] Agilent-011472 Mouse Development Oligo Microarray G4120A (Feature Number version) (GPL922) RNA Mus musculus
Mus musculus
kidney To identify Six1 target genes, we chose the mK4 cell line that represents later metanephric mesenchyme of the embryonic kidney. The cells were infected with adenovirus vectors (AxCAwt) overexpressing VP16-Six1wt or VP16-Six1W171R and cultured for 24h. Total RNA was extracted using Isogen reagent (Nippon Gene), treated with RNase-free DNase (Roche Diagnostics) and purified with RNeasy Midi Kit (QIAGEN). Poly A+ RNA was selected using Oligotex-dT30 <super> latex beads (TaKaRa). Poly A+ RNA (20 µg) was reverse transcribed using an oligo(dT) primer in the presence of aminoallyl dUTP without the addition of spike-in controls. Then, single-stranded cDNAs were coupled with Cy3 (AxCAwt VP16-Six1wt infected sample) or Cy5 (AxCAwt VP16-Six1W171R infected sample) dyes, and the labeled probes were purified with QIAquick PCR Purification kit (QIAGEN). Hybridization to the microarray was carried out at 65°C for 17h according to the manufacturer's instruction. The arrays were washed, dried and scanned using ScanArray 5000 (GSI Lumonics) at two different PMT voltage settings (high and low) to avoid signal saturation. Cy3 and Cy5 intensities for each spot on the array were determined by QuantArray software (Version 3.0.0.0, GSI Lumonics). The raw data thus obtained was processed and the Cy3 to Cy5 ratios were calculated as follows: 1) subtraction of the fluorescence intensity of negative control spots as background from the intensity of each of the Cy3 and Cy5 spots, 2) normalization of the entire data set using the global normalization method, 3) elimination of spots with high background intensity for either dye, and 4) determination of the Cy3 to Cy5 ratios.
7 GSM37576 Ren-2 Diabetic 2 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Ren-2 diabetic kidney total RNA Reference kidney total RNA
8 GSM37575 Ren-2 Diabetic 1 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Reference kidney total RNA Ren-2 diabetic kidney total RNA
9 GSM37574 Ren-2 Control 2 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Ren-2 control kidney total RNA Reference kidney total RNA
10 GSM37573 Ren-2 Control 1 23,040 St Vincents Institute 2004-12-14 [Oligo Array] Ramaciotti Centre 10k combined Rat Oligo (GPL1747) RNA Rattus norvegicus
Rattus norvegicus
kidney Reference kidney total RNA Ren-2 control kidney total RNA
11 GSM33977 Kidney 39,309 University of Toronto 2004-10-28 [Oligo Array] Mouse XM microarray set (GPL1537) RNA Mus musculus
Mus musculus
kidney Kidney
12 GSM37454 CD1 strain kidney 21,882 University of Toronto 2004-12-09 [Oligo Array] Agilent Custom Mouse Alternative Splicing Oligo Microarray (GPL1738) RNA Mus musculus
Mus musculus
kidney Pooled mouse CD1 strain kidney
13 GSM33957 Bladder 39,309 University of Toronto 2004-10-28 [Oligo Array] Mouse XM microarray set (GPL1537) RNA Mus musculus
Mus musculus
bladder Bladder