遺伝子発現バンク(GEO)目次バージョン：2013-06-15English page

NCBI Gene Expression Omnibus (GEO) に登録されているデータを、測定技術と材料の属性に基づいて整理しました。

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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 [オリゴアレイ] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1 末梢血 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 [オリゴアレイ] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1 末梢血 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 [オリゴアレイ] T. elongatus 2.5k oligoarray (GPL1771) RNA Thermosynechococcus elongatus BP-1 末梢血 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v1.0 (GPL7448) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] JCVI Synechococcus sp. WH 8102 19K v2.0 (GPL7449) RNA Synechococcus sp. WH 8102 リンパ節 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 [オリゴアレイ] NimbleGen/Yamaga Streptococcus pyogenes 7k ID_2222 (GPL10318) RNA 化膿レンサ球菌(Streptococcus pyogenes) 末梢血 Streptococcus pyogenes (blood) 20 GSM660483 Streptococcus pneumoniae ParB-GFP_ChIP-on-chip 1,332 University of Groningen 2011-01-24 [オリゴアレイ] Streptococcus pneumoniae D39 Multiplatform 1909k array (GPL11484) genomic 肺炎球菌(Streptococcus pneumoniae) リンパ節 Strain MT2 ChIP eluate Strain MT2 ChIP input 1   |   2   |   3   |   4   |   5      »      [16]