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.
RSS
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
(4,712)
  Primates
(41)
  Rodents
(1,963)
  Mammals
(85)
  Vertebrates
(71)
  Invertebrates
(162)
  Plants
(837)
  Bacteria
(313)
  Viruses
(0)
  Phages
(18)
  Unclassified
(320)
  All
(8,522)
 
  SAGE NlaIII
(4)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(43)
  Tiling Array
(0)
  cDNA Array
(115)
  Oligo Array
(0)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(0)
  HT-Seq
(0)
  Other
(0)
  All
(162)
 
  brain
(0)
  blood
(0)
  connective
(0)
  reproductive
(27)
  muscular
(0)
  digestive
(56)
  liver
(0)
  lung
(0)
  urinary
(0)
  endo/exo-crine
(3)
  embryo
(20)
  adult aerial structure
(0)
  young aerial structure
(0)
  root
(0)
  meristem/growing tissue
(0)
  flower/sexual organ
(0)
  seed/fruit/grain
(0)
  pooled
(2)
  unclassified
(54)
  all
(162)
 
1   |   2   |   3   |   4   |   5      »      [9]
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 GSM47073 Egg differentially expressed gene compare to adult worm 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-02 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Egg Adult worm
2 GSM47074 Male differentilly expressed gene compare to egg 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-02 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Male Egg
3 GSM47075 Cercariae differentially expressed gene compare to adult worm 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-02 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
pooled Adult worm were obtained by perfusion of the hepatic portal system of infected rabbits (7 weeks post-infection), and cercariae were released from infected snails and concentrated by centrifugation.Adult worm and cercariae were ground into a fine powder in a 10 cm ceramic mortar (RNase-free). Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China). After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase. The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from adult worm RNA and cercariae RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP. The two color probes were then mixed and diluted to 500uL with TE, and concentrated using Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried. !Sample_description = The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr. Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3 median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69. Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis. Keywords = adult worm Keywords = cercariae Keywords = differentially expressed gene
4 GSM47076 Cercariae differentially expressed gene compare to egg 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-02 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Egg Cercariae
5 GSM48311 Egg differentially expressed gene compare to adult worm 1 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-18 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Egg Adult worm
6 GSM48312 Schistosoma japonicum adult worm 1 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-18 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Male Egg
7 GSM48313 Cercariae differentially expressed gene compare to adult worm 1 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-18 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
pooled Adult worm were obtained by perfusion of the hepatic portal system of infected rabbits (7 weeks post-infection), and cercariae were released from infected snails and concentrated by centrifugation.Adult worm and cercariae were ground into a fine powder in a 10 cm ceramic mortar (RNase-free). Ground tissue was homogenized in TRIzol (Biostar, Shanghai, China). After centrifugation, the supernatant was extracted with an equal volume of chloroform. After centrifugation, supernatant was taken from the organic phase. The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The cDNA from adult worm RNA and cercariae RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, 5 ug of oligo(dT) 18 was added and annealed to 50ug of total RNA by heating the reaction to 70°C for 10 min, and then chilling on ice. The final reaction buffer mixture contained dNTPs(200uM dATP, dCTP,dGTP, 60 uM dTTP, and 60uM Cy3- or Cry5-dUTP) , 2uL of Superscript II reverse transcriptase(Invitrogen), and 1 X reaction buffer. Reactions were carried out at 42°C for 2 hrs,.Then RNA was hydrolyzed by adding 4 uL of 2.5 M NaOH and incubating at 65 for 10 min and then neutralized with 4uL of 2.5 M HCl. The RNA samples from egg were labeled with Cy3-dUTP and those from male worm with Cy5-dUTP. The two color probes were then mixed and diluted to 500uL with TE, and concentrated using Microcon YM-30 filter(Millipore, Bedford, MA) to 10uL, The sample was then vacuum dried.The probe was dissolved in 20 μl of Hybridization Solution [5X SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide. Microarrays were pre-hybridized with Hybridization Solution containing 0.5 mg/ml denatured salmon sperm DNA at 42oC for 6hr. Fluorescent probe mixtures were denatured at 95oC for 5 minutes, and the denatured probe mixtures were applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42oC for 15-17 hours. The hybridized chips were then washed at 60°C for 10 min each in solutions of 2X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS and 0.1X SSC, then dried at room temperature. Fluorescent array images were collected with a ScanArray5000 fluorescent scanner at two wavelengths to detect emission from both Cy3 and Cy5. and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP, Ratios of Cy3 to Cy5 was computed using the GenePix Pro 3 median of ratio method, Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged Bad or Not Found by GenePix software were removed from the final data. Genes were identified as differentially expressed if the absolute value of the natural logarithm of the ratios was >0.69. Only genes with raw intensity values for both Cy3 and Cy5 of >200 counts were chosen for differential analysis. Keywords = adult worm Keywords = cercariae Keywords = differentially expressed gene
8 GSM48314 Cercariae differentially expressed gene compare to egg 1 3,136 shanghai research institute of domestic animal parasitolgy 2005-04-18 [cDNA Array] Schistosoma japonicum 3.1K (GPL1944) RNA Schistosoma japonicum
Schistosoma japonicum
ovary Egg Cercariae
9 GSM50791 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 1 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut) Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae)
10 GSM50792 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 2 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae) Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut)
11 GSM50793 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 3 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut) Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae)
12 GSM50794 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 4 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae) Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut)
13 GSM50795 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 5 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut) Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae)
14 GSM50796 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 6 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae) Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut)
15 GSM50797 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 7 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae) Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut)
16 GSM50798 Drosophila yakuba strain 14021-0261.0 blue gut larvae vs. white prepupae, replicate 8 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Dec03_r40 (GPL1782) RNA Drosophila yakuba
Drosophila yakuba
intestine Drosophila yakuba strain 14021-0261.0 late 3rd instar larvae (blue gut) Drosophila yakuba strain 14021-0261.0 start of pupariation (white prepupae)
17 GSM50470 Drosophila simulans strain 14021-0251.167 blue gut larvae vs. white prepupae, replicate 1 20,000 Harvard University 2005-05-04 [cDNA Array] DmelWhiteLab2003Jul30_r40 (GPL1783) RNA Drosophila simulans
Drosophila simulans
intestine Drosophila simulans strain 14021-0251.167 start of pupariation (white prepupae) Drosophila simulans strain 14021-0251.167 late 3rd instar larvae (blue gut)
18 GSM50471 Drosophila simulans strain 14021-0251.167 blue gut larvae vs. white prepupae, replicate 2 20,000 Harvard University 2005-05-04 [cDNA Array] DmelWhiteLab2003Aug19_r40 (GPL1780) RNA Drosophila simulans
Drosophila simulans
intestine Drosophila simulans strain 14021-0251.167 start of pupariation (white prepupae) Drosophila simulans strain 14021-0251.167 late 3rd instar larvae (blue gut)
19 GSM50785 Drosophila simulans strain 14021-0251.167 blue gut larvae vs. white prepupae, replicate 3 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Jul30_r40 (GPL1783) RNA Drosophila simulans
Drosophila simulans
intestine Drosophila simulans strain 14021-0251.167 late 3rd instar larvae (blue gut) Drosophila simulans strain 14021-0251.167 start of pupariation (white prepupae)
20 GSM50786 Drosophila simulans strain 14021-0251.167 blue gut larvae vs. white prepupae, replicate 4 20,000 Harvard University 2005-05-10 [cDNA Array] DmelWhiteLab2003Jul30_r40 (GPL1783) RNA Drosophila simulans
Drosophila simulans
intestine Drosophila simulans strain 14021-0251.167 late 3rd instar larvae (blue gut) Drosophila simulans strain 14021-0251.167 start of pupariation (white prepupae)
1   |   2   |   3   |   4   |   5      »      [9]