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Sample GSM67021 Query DataSets for GSM67021
Status Public on Aug 02, 2006
Title As_96h.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 0.3557 10340 10702 2408 117 134 136 100 10802 10574 3071 156 166 77 100 1.016 80 426 10223 10646 10568 10408 1.2796346954239777
5269517 0.4182 13740 14478 3684 141 153 65 100 13107 13669 4926 156 165 82 100 1.0609999999999999 80 560 13599 12951 14325 13504 1.336244731959769
5269518 -0.0207 492 511 122 176 189 74 94 611 603 213 175 187 87 82 .78300000000000003 52 414 316 436 322 416 .98578120953883441
5269519 -0.0992 486 489 94 214 227 90 84 525 551 186 180 196 93 82 .74099999999999999 52 420 272 345 262 355 .93355150149029109
5269520 -0.0729 1055 1065 197 135 151 67 100 1401 1401 379 169 181 83 97 .755 80 560 920 1232 914 1220 .95071804769538115
5269521 -0.0946 139 151 57 122 134 59 8 184 200 105 161 173 80 12 .74399999999999999 156 1175 17 23 17 27 .9365110120777661
5269522 -0.1697 246 250 52 106 116 57 71 332 365 159 161 174 85 50 .70599999999999996 32 228 140 171 134 191 .88902059564380231
5269523 -0.7932 426 436 130 151 166 69 90 773 789 249 167 180 84 98 .45800000000000002 80 560 275 606 270 609 .5770772757093009
5269524 -1.2041 207 205 50 144 156 62 9 323 338 122 161 175 76 55 .34499999999999997 52 340 63 162 49 163 .43404630776018033
5269525 -1.1317 302 297 66 193 199 63 37 421 452 175 165 177 83 75 .36199999999999999 32 236 109 256 98 275 .45638455664873478
5269526 -0.7067 561 558 111 198 208 68 98 896 899 260 159 175 86 100 .48599999999999999 52 420 363 737 350 724 .61270338348424214
5269527 -4.7965 141 155 63 200 208 65 0 187 200 97 165 181 84 7 -1.286 156 1121 -59 22 -53 19 .035984166966534857
5269528 0.2884 870 884 229 116 126 51 100 890 943 348 151 162 78 96 .96999999999999997 80 432 754 739 758 781 1.2212808182581527
5269529 0.3516 1857 1907 494 129 137 51 100 1983 1903 781 148 163 77 93 1.0129999999999999 80 560 1728 1835 1770 1740 1.275951401895991
5269530 0.9638 1394 1391 246 166 216 201 100 974 961 358 170 193 129 92 1.5489999999999999 80 547 1228 804 1175 768 1.9504692271683715
5269531 -0.0164 846 833 188 172 184 79 98 1023 1002 276 160 169 75 100 .78500000000000003 52 420 674 863 649 833 .98870986077290235
5269532 -0.6378 550 559 148 138 147 57 98 937 992 250 167 180 79 100 .51000000000000001 52 420 412 770 412 812 .64269903060835276
5269533 -1.0002 177 188 57 136 143 54 21 334 316 123 185 193 80 46 .39700000000000002 32 176 41 149 45 123 .49993270136712548
5269534 -1.1647 103 118 49 101 110 45 5 204 216 95 168 241 256 0 .35399999999999998 156 985 2 36 8 -25 .44605373635600498
5269535 -0.8948 215 219 57 140 152 63 21 345 360 125 175 181 77 51 .42699999999999999 52 340 75 170 67 179 .5378174143917237

Total number of rows: 16512

Table truncated, full table size 2081 Kbytes.




Supplementary data files not provided
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