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Sample GSM67016 Query DataSets for GSM67016
Status Public on Aug 02, 2006
Title As_48h.3_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 0.9469 11307 10964 1967 152 176 125 100 5478 5390 1075 158 164 75 100 2.0670000000000002 80 560 11155 5320 10788 5226 1.9277180610707922
5269517 0.9602 16738 15965 3227 237 346 640 100 8061 7699 1602 158 207 335 100 2.0859999999999999 52 420 16501 7903 15619 7492 1.945583051457999
5269518 0.1863 440 441 102 169 180 69 90 346 366 135 143 157 77 65 1.22 80 560 271 203 261 209 1.1378087142761524
5269519 0.2668 743 732 171 189 204 84 98 567 566 177 145 155 69 94 1.29 52 420 554 422 528 411 1.203158790371184
5269520 -0.1613 1498 1493 248 126 152 133 100 1519 1537 308 111 138 101 100 .95899999999999996 52 420 1372 1408 1341 1399 .89424022942789516
5269521 -0.2973 431 453 119 166 188 98 71 515 516 173 187 197 88 81 .872 32 176 265 328 265 319 .81375039695141282
5269522 0.1533 461 467 121 132 150 78 96 422 445 177 164 179 88 76 1.1919999999999999 52 340 329 258 317 266 1.1120996441281135
5269523 -0.3644 584 591 191 133 149 69 97 692 719 278 169 179 81 97 .83299999999999996 80 560 451 523 442 540 .77679782903663475
5269524 -0.6723 451 457 110 159 174 72 96 584 607 221 164 176 92 92 .67300000000000004 52 420 292 420 283 431 .6275058117987935
5269525 -0.2742 326 352 128 149 163 70 67 357 376 157 147 153 65 70 .88600000000000001 80 560 177 210 189 223 .82692433031349766
5269526 -0.5471 747 757 158 173 184 69 100 925 949 281 153 168 85 100 .73399999999999999 52 420 574 772 573 781 .68439210980274467
5269527 -0.8519 250 256 58 158 169 62 33 327 329 132 164 173 83 50 .59399999999999997 12 104 92 163 87 156 .55404794210764341
5269528 0.4187 666 707 231 151 164 74 100 497 539 227 151 168 194 42 1.4330000000000001 80 560 515 346 543 371 1.3367441144791501
5269529 0.8162 1971 1946 261 183 200 79 100 1043 1088 250 154 165 77 100 1.8879999999999999 52 420 1788 889 1746 923 1.7608025184569649
5269530 0.0987 761 792 164 179 200 109 100 695 690 212 156 171 91 96 1.1479999999999999 80 644 582 539 592 519 1.0708396221141478
5269531 -0.4954 751 749 142 184 200 82 98 899 901 232 158 164 82 100 .76000000000000001 52 420 567 741 549 737 .70935698358811561
5269532 -1.0049 456 450 120 161 175 67 88 705 695 204 154 170 87 93 .53400000000000003 80 560 295 551 275 525 .49831710210500157
5269533 -0.7855 329 339 73 163 177 82 50 438 452 153 169 178 81 71 .622 32 236 166 269 162 274 .58013817836611969
5269534 -0.5496 235 244 59 140 155 74 28 333 323 125 181 202 104 31 .73199999999999998 32 176 95 152 89 121 .68320369981080487
5269535 -0.6422 244 269 101 133 150 79 33 342 369 126 171 182 85 50 .68700000000000006 80 560 111 171 119 187 .64073571536258078

Total number of rows: 16512

Table truncated, full table size 2058 Kbytes.




Supplementary data files not provided
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