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Sample GSM67032 Query DataSets for GSM67032
Status Public on Aug 02, 2006
Title CtrXM_96hr.1_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) dbslsh@nus.edu.sg
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 -0.2921 1944 1912 346 145 176 164 100 2490 2466 408 147 180 230 100 .76200000000000001 52 420 1799 2343 1736 2286 .81668420665854247
5269517 -0.3799 2477 2478 448 180 202 135 100 3265 3363 589 158 178 125 100 .71699999999999997 52 420 2297 3107 2276 3185 .76849376225852994
5269518 -0.0017 407 426 155 166 181 81 69 409 412 148 133 147 73 76 .93200000000000005 52 420 241 276 245 265 .9988206233409026
5269519 0.0402 534 538 188 184 200 87 86 496 512 168 143 149 55 94 .95899999999999996 52 420 350 353 338 363 1.0282417936719572
5269520 0.0290 781 815 233 181 193 90 98 800 802 221 136 144 56 96 .95199999999999996 80 560 600 664 622 658 1.020312917419028
5269521 0.5701 340 363 120 158 174 90 50 281 298 109 150 152 59 50 1.385 32 176 182 131 189 146 1.4846035746357309
5269522 0.4877 735 719 217 180 187 82 98 520 559 207 147 155 71 92 1.3080000000000001 52 340 555 373 532 404 1.4021998147743491
5269523 -0.2280 529 543 151 167 188 88 92 594 610 167 138 149 72 98 .79700000000000004 52 420 362 456 355 461 .85381583010881712
5269524 0.2788 417 424 110 158 176 84 78 379 382 115 147 155 68 80 1.1319999999999999 52 340 259 232 248 227 1.2131992428906997
5269525 -0.0375 359 373 150 163 172 72 61 370 379 145 148 153 67 73 .90900000000000003 52 340 196 222 201 226 .97437396472766369
5269526 0.0886 1066 1052 209 170 190 90 100 1073 1017 239 128 137 65 100 .99199999999999999 52 420 896 945 862 880 1.0633719016634189
5269527 -0.3115 248 279 111 176 181 75 31 256 270 91 133 137 53 59 .752 32 236 72 123 98 133 .80581438104849845
5269528 0.2878 597 599 175 140 155 74 98 550 545 185 142 151 58 96 1.139 52 420 457 408 444 394 1.2207479275210853
5269529 -0.5615 467 482 150 164 174 78 84 662 643 159 140 145 59 100 .63200000000000001 52 420 303 522 308 498 .67760638739907897
5269530 0.3507 635 646 183 157 178 91 95 538 552 138 141 150 62 97 1.1899999999999999 80 554 478 397 468 402 1.2752208166107306
5269531 0.3987 1237 1189 301 173 190 86 98 953 966 279 140 152 62 98 1.23 52 420 1064 813 999 814 1.3183539261254684
5269532 -0.0693 694 703 182 173 193 92 98 718 731 164 135 142 54 100 .88900000000000001 52 420 521 583 510 589 .95312084133595287
5269533 0.2663 308 310 108 163 175 81 37 255 273 120 142 152 63 46 1.1220000000000001 32 236 145 113 135 121 1.2027196190569711
5269534 0.0502 413 423 135 167 178 71 78 395 407 153 142 149 59 88 .96599999999999997 52 340 246 253 245 258 1.0354102206313589
5269535 -0.0355 297 296 100 164 182 85 32 283 288 84 143 151 61 59 .91000000000000003 52 420 133 140 114 137 .9757179288169433

Total number of rows: 16512

Table truncated, full table size 2027 Kbytes.




Supplementary data files not provided
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