Gene Expression Omnibus (GEO) Overview Version´╝Ü2014-04-12Japanese 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
(615,734)
  Primates
(5,814)
  Rodents
(225,055)
  Mammals
(20,968)
  Vertebrates
(22,581)
  Invertebrates
(46,584)
  Plants
(107,706)
  Bacteria
(45,091)
  Viruses
(1,432)
  Phages
(112)
  Unclassified
(6,986)
  All
(1,101,311)
 
  SAGE NlaIII
(0)
  SAGE RsaI
(0)
  SAGE Sau3A
(0)
  MPSS
(0)
  GeneChip
(8,349)
  Tiling Array
(1,464)
  cDNA Array
(10,807)
  Oligo Array
(21,920)
  Bead Array
(0)
  Protein Array
(0)
  Antibody
(0)
  RT-PCR
(51)
  HT-Seq
(2,336)
  Other
(164)
  All
(45,091)
 
  brain
(90)
  blood
(355)
  connective
(131)
  reproductive
(78)
  muscular
(90)
  digestive
(223)
  liver
(65)
  lung
(199)
  urinary
(5)
  endo/exo-crine
(69)
  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
(143)
  unclassified
(20,452)
  all
(21,920)
 
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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 GSM832329 Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #1 4,829 Stony Brook University 2011-11-13 [Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199) genomic Yersinia pestis
Yersinia pestis
peripheral blood Yersinia pestis KIM6+ transposon library unselected input Yersinia pestis KIM6+ transposon library output after selection inside macrophage
2 GSM832330 Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy3) vs Input (Cy5) #2 4,829 Stony Brook University 2011-11-13 [Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199) genomic Yersinia pestis
Yersinia pestis
peripheral blood Yersinia pestis KIM6+ transposon library unselected input Yersinia pestis KIM6+ transposon library output after selection inside macrophage
3 GSM832337 Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#1 4,829 Stony Brook University 2011-11-13 [Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199) genomic Yersinia pestis
Yersinia pestis
peripheral blood Yersinia pestis KIM6+ transposon library output after selection inside macrophage Yersinia pestis KIM6+ transposon library unselected input
4 GSM832338 Yersinia pestis KIM6+ TraSH Microarry Analysis Output (Cy5) vs Input (Cy3)#2 4,829 Stony Brook University 2011-11-13 [Oligo Array] JCVI PFGRC Yersinia pestis 30K v2 array designed primarily based on strain KIM (GPL4199) genomic Yersinia pestis
Yersinia pestis
peripheral blood Yersinia pestis KIM6+ transposon library output after selection inside macrophage Yersinia pestis KIM6+ transposon library unselected input
5 GSM885543 HC1 5,925 University of South Florida 2012-03-04 [Oligo Array] Combimatrix Thiomicrospira crunogena array (GPL15301) RNA Thiomicrospira crunogena
Thiomicrospira crunogena
peripheral blood HC1
6 GSM38212 LL2-Cy3+LL14-Cy5 (expt 1) 5,408 Nagoya University 2004-12-28 [Oligo Array] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1
Thermosynechococcus elongatus BP-1
peripheral blood Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
7 GSM38213 LL2-Cy5+LL14-Cy3 (expt 1, dye swap) 5,408 Nagoya University 2004-12-28 [Oligo Array] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1
Thermosynechococcus elongatus BP-1
peripheral blood Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
8 GSM38214 LL2-Cy3+LL14-Cy5 (expt 2) 5,408 Nagoya University 2004-12-28 [Oligo Array] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1
Thermosynechococcus elongatus BP-1
peripheral blood Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
9 GSM38215 LL2-Cy5+LL14-Cy3 (expt 2, dye swap) 5,408 Nagoya University 2004-12-28 [Oligo Array] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1
Thermosynechococcus elongatus BP-1
peripheral blood Strain and culture conditions. We grew wild-type T. elongatus (Yamaoka et al., Plant Cell Physiol. 19, 943-954) at 50oC under constant light from white fluorescent lamps at 38 micromol m-2 sec-1 (hereafter called LL conditions) in BG-11 liquid medium (Rippka et al., J. Gen. Microbiol. 111, 1-61) with bubbling of air containing 5% (v/v) CO2. We subjected the cells to 12 h of darkness to synchronize the circadian clock, and transferred them back to LL. We collected cells for RNA isolation at 2 h (LL2) and 14 h (LL14) after the transfer. Microarray experiments. We isolated total RNAs from two independent cultures by the hot-phenol method (Kucho et al., Genes Genet. Syst. 79, 189-197) and purified them using the SV total RNA isolation system (Promega, WI, USA). We used a mixture of the total RNAs from the two cultures for labeling reactions. We synthesized fluorescence-labeled cDNA by direct incorporation of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience, NJ, USA) during random-primed reverse transcription, using 5.9 microgram total RNA and an RNA fluorescence labeling core kit (M-MLV version 2.0, TaKaRa, Japan). We prehybridized the microarray for 1 h at 42oC in a solution containing 5 X SSC (1 X SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% sodium lauryl sulfate (SDS), and 10 mg/ml bovine serum albumin. We washed the microarray at room temperature in distilled water 3 times for 1 min, rinsed it in 2-propanol, and dried it by centrifugation at 150 X g for 2 min. We performed hybridization for 16 h at 42oC in 12-mL solution containing 5 X SSC, 0.1% SDS, 30% formamide, and heat-denatured labeled cDNA. We then washed the microarray at room temperature with 2 X SSC containing 0.1% SDS for 4 min, with 0.1 X SSC containing 0.1% SDS for 4 min, and 3 times with 0.1 X SSC for 1 min. We dried the microarray by centrifugation. We obtained fluorescence images of Cy3 and Cy5 dye channels using a GenePix 4000B scanner (Axon Instruments, CA, USA). Data analysis. We used GenePix Pro 5.0 software (Axon Instruments) to determine the signal intensity of each spot and its local background. We calculated net signal intensity by subtracting the median signal intensity of all pixels within the local background area from the median signal intensity of all pixels within the spot area. We visually confirmed the correct recognition of all spot areas by the automatic alignment function of the GenePix Pro. We flagged spots and did not use them for data analysis when any of following occurred: (i) the GenePix Pro did not find the spot area automatically, (ii) the net signal intensity was <= 0, (iii) the percentage of saturated pixels in the spot area was >= 25, and (iv) severe noise was present. We normalized biases in signal intensity between the two fluorescent dye channels in a microarray by locally weighted linear regression analysis (lowess normalization) (Yang et al., Nucleic Acids Res. 30, e15) using MIDAS software (http://www.tigr.org/software/tm4/midas.html). For all normalization, we set the smoothing parameter to 0.33. Keywords = circadian clock Keywords = thermophilic cyanobacteria
10 GSM348486 WH8102_bsy89255d0025_copper-shock_rep4 19,200 Macquarie University 2008-12-08 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode CD44r(2)-WH8102 in normal SOW-CuEDTA shock CD43r(2)-WH8102 in normal SOW- Control of CD44r(2)
11 GSM348542 WH8102_bsy89280d0056_copper-shock_rep5 19,200 Macquarie University 2008-12-08 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode CD44r(2)-WH8102 in normal SOW-CuEDTA shock CD43r(2)-WH8102 in normal SOW-Control of CD44r(2)
12 GSM348544 WH8102_bsy89280d0057_copper-shock_rep6 19,200 Macquarie University 2008-12-08 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode CD43r(2)-WH8102 in normal SOW-Control of CD44r(2) CD44r(2)-WH8102 in normal SOW-CuEDTA shock
13 GSM329374 Early_log_phase_phosphate_stress_bsy89255d0021_rep1 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 5 micromolar phosphate SOW medium, early log phase CD39r wild type in 87 micromolar phosphate SOW medium, early log phase CD40r
14 GSM329375 Early_log_phase_phosphate_stress_bsy89255d0022_rep4 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 5 micromolar phosphate SOW medium, early log phase CD43r wild type in 87 micromolar phosphate SOW medium, early log phase CD44r
15 GSM329376 Early_log_phase_phosphate_stress_bsy89280d0048_rep2 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 5 micromolar phosphate SOW medium, early log phase CD39r wild type in 87 micromolar phosphate SOW medium, early log phase CD40r
16 GSM329378 Early_log_phase_phosphate_stress_bsy89280d0049_rep3 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 87 micromolar phosphate SOW medium, early log phase CD40r wild type in 5 micromolar phosphate SOW medium, early log phase CD39r
17 GSM329379 Early_log_phase_phosphate_stress_bsy89280d0050_rep5 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 5 micromolar phosphate SOW medium, early log phase CD43r wild type in 87 micromolar phosphate SOW medium, early log phase CD44r
18 GSM329380 Early_log_phase_phosphate_stress_bsy89280d0051_rep6 15,156 Macquarie University 2008-10-10 [Oligo Array] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102
Synechococcus sp. WH 8102
lymphnode wild type in 87 micromolar phosphate SOW medium, early log phase CD44r wild type in 5 micromolar phosphate SOW medium, early log phase CD43r
19 GSM532754 UH328 7,103 John A Burns School of Medicine 2010-04-12 [Oligo Array] NimbleGen/Yamaga Streptococcus pyogenes 7k ID_2222 (GPL10318) RNA Streptococcus pyogenes
Streptococcus pyogenes
peripheral blood Streptococcus pyogenes (blood)
20 GSM660483 Streptococcus pneumoniae ParB-GFP_ChIP-on-chip 1,332 University of Groningen 2011-01-24 [Oligo Array] Streptococcus pneumoniae D39 Multiplatform 1909k array (GPL11484) genomic Streptococcus pneumoniae
Streptococcus pneumoniae
lymphnode Strain MT2 ChIP eluate Strain MT2 ChIP input
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