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Sample GSM67033 Query DataSets for GSM67033
Status Public on Aug 02, 2006
Title CtrXM_96hr.2_m
Sample type RNA
 
Channel 1
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Zebrafish liver tissue exposed to arsenic
Growth protocol Zebrafish were reared at room temperature (27 ± 2°C)
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy5
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were
reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and
resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
Channel 2
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues
of wild-type zebrafish.
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy3
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse
transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in
DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
 
Scan protocol The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
Description Fish were treated with arsenic [As(V)] acid (Na2HAsO4.7H2O; Sigma, USA) at 60 mg/L in a static condition for 96 hours (h) whereby less than 10% mortality occurred in arsenic-treated group within the experiment duration. No mortality was observed in the control group. The concentration was chosen based on an initial survival versus concentration experiment. Fish livers were sampled at 8 h, 24 h, 48 h and 96 h, and 12 fish livers were separated into 3 pooled-samples (each pooled samples consist of 4 livers) at each time point.
Three biological replicates are performed for each time point (8,24,48,96 hrs). Test and control samples are hybridized against a reference. No dye swap experiment has been performed.
Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2
 
Submission date Aug 03, 2005
Last update date Aug 03, 2005
Contact name Siew Hong Lam
E-mail(s) [email protected]
Phone (65)- 68742860
Fax (65)-67792486
Organization name National University of Singapore
Department Biological Sciences
Street address 14 Science Drive 4
City Singapore
ZIP/Postal code 117543
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE3048 Trancriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver.

Data table header descriptions
ID_REF Unique ID
VALUE log2 of PRE_VALUE
CH1_Median CH1(F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median CH1 (F635) background median fluorescence intensity
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD CH1 (F635) background fluorescence intensity standard deviation
%>CH1_BKD_+2SD % of feature pixels greater than two standard deviations over the background
CH2_Median CH2(F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
%>CH2_BKD_+2SD % of feature pixels greater than two standard deviations over the background
Ratio_of_Means Unnormalized ratio of means defined by CH1/CH2
AREA Number of feature pixels
BKD_AREA Number of feature background pixels
CH1_Median-CH1_BKD Channel 1 median signal
CH2_Median-CH2_BKD Channel 2 median signal
CH1_Mean-CH1_BKD Channel 1 mean signal
CH2_Mean-CH2_BKD Channel 2 mean signal
PRE_VALUE Normalized ratio of means defined by CH1/CH2

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD %>CH1_BKD_+2SD CH2_Median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD %>CH2_BKD_+2SD Ratio_of_Means AREA BKD_AREA CH1_Median-CH1_BKD CH2_Median-CH2_BKD CH1_Mean-CH1_BKD CH2_Mean-CH2_BKD PRE_VALUE
5269516 -0.4302 1090 1227 560 124 133 63 98 1573 1611 476 141 149 63 100 .75 80 644 966 1432 1094 1462 .74217619787776612
5269517 0.2891 4196 4825 2803 127 140 70 100 4052 3957 1318 154 159 65 100 1.2350000000000001 80 560 4069 3898 4685 3798 1.2218996247691378
5269518 -0.3933 231 245 110 138 155 80 25 274 282 138 143 150 63 50 .77000000000000002 120 790 93 131 90 132 .76140867721253236
5269519 -0.7925 273 293 116 150 168 88 36 367 404 174 159 161 62 75 .58399999999999996 80 650 123 208 125 243 .57732291729748264
5269520 -0.3735 616 622 196 160 169 75 96 695 735 221 143 151 66 100 .78000000000000003 52 420 456 552 453 584 .77191434758200306
5269521 -0.0772 166 174 80 151 165 96 3 155 162 60 138 147 61 5 .95799999999999996 156 1080 15 17 9 15 .94790636333663014
5269522 0.3771 302 317 119 145 161 82 46 255 274 108 143 152 65 45 1.3129999999999999 80 536 157 112 156 122 1.2986914928156685
5269523 -0.7003 281 293 111 153 171 84 36 373 370 114 145 153 62 76 .622 52 420 128 228 122 217 .61545224749972505
5269524 -0.0486 287 307 128 133 144 68 53 304 314 114 136 145 57 71 .97799999999999998 80 560 154 168 163 169 .96689227486413465
5269525 -1.3470 186 191 92 160 176 92 6 217 231 101 153 162 66 27 .39700000000000002 156 1140 26 64 15 69 .3931116690760606
5269526 -0.4434 590 618 214 160 171 79 92 746 765 210 149 155 58 100 .74399999999999999 80 560 430 597 447 610 .73541690752373223
5269527 0.3186 164 180 79 151 165 77 8 154 161 73 138 145 62 9 1.2609999999999999 156 1198 13 16 15 16 1.247150905259536
5269528 -0.4028 250 263 100 120 130 57 57 328 330 118 143 152 67 63 .76500000000000001 80 628 130 185 133 178 .75638564030953603
5269529 -1.1269 368 381 146 125 135 64 78 721 697 263 144 151 61 92 .46300000000000002 80 546 243 577 246 546 .45789265636765902
5269530 0.2955 571 545 164 138 160 110 85 478 471 164 143 157 75 85 1.2410000000000001 80 642 433 335 385 314 1.227352777978818
5269531 1.0244 441 511 243 147 163 83 80 328 322 123 145 151 63 62 2.056 80 549 294 183 348 171 2.0341218349567187
5269532 -1.0069 277 319 134 156 169 79 43 465 467 140 143 150 62 93 .503 80 560 121 322 150 317 .49761268027011502
5269533 -1.8738 147 161 79 153 169 101 3 167 173 69 144 151 64 8 .27600000000000002 156 1058 -6 23 -8 22 .2728606023397796
5269534 -0.9089 154 167 85 146 158 77 6 174 185 73 146 158 73 7 .53800000000000003 156 938 8 28 9 27 .53260290649014663
5269535 -1.9227 141 163 76 151 165 78 4 184 189 76 144 153 64 12 .26700000000000002 156 1111 -10 40 -2 36 .2637652489284536

Total number of rows: 16512

Table truncated, full table size 2012 Kbytes.




Supplementary data files not provided
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