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Sample GSM67012 Query DataSets for GSM67012
Status Public on Aug 02, 2006
Title As_24hr.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) [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 1.1469 7427 6638 2398 122 167 321 93 3960 3354 1747 138 179 302 83 2.0259999999999998 80 631 7305 3822 6471 3175 2.2143381453388837
5269517 0.9860 15243 14397 3245 127 138 59 100 8607 7999 2868 125 130 44 96 1.8120000000000001 80 560 15116 8482 14259 7869 1.9806487700407134
5269518 0.2471 379 371 104 131 143 59 92 351 360 95 139 151 51 93 1.0860000000000001 80 546 248 212 228 209 1.1868555745122786
5269519 0.2910 447 443 143 115 124 48 92 404 414 116 121 127 39 97 1.119 80 656 332 283 319 287 1.2234469124750578
5269520 0.2608 1054 1062 212 106 119 62 100 1035 1001 286 129 138 49 95 1.0960000000000001 80 642 948 906 943 863 1.1981751641850928
5269521 -0.7383 255 259 80 112 125 59 61 403 407 127 139 147 50 94 .54900000000000004 52 420 143 264 134 260 .59946170785417285
5269522 0.2783 1043 1053 255 112 121 55 100 1150 1057 419 209 262 164 90 1.1100000000000001 52 406 931 941 932 795 1.2127538921538328
5269523 0.0270 634 639 146 102 112 49 100 711 707 225 131 140 47 96 .93200000000000005 80 560 532 580 527 567 1.0188979963570146
5269524 -0.4488 279 287 87 106 114 49 82 370 390 130 120 125 40 93 .67000000000000004 80 560 173 250 173 265 .73264521351953193
5269525 0.0518 277 294 92 110 119 51 86 310 318 106 124 128 43 86 .94799999999999995 52 420 167 186 175 190 1.0365613204889885
5269526 -0.3687 705 682 194 125 134 50 96 927 914 188 128 135 44 100 .70899999999999996 80 552 580 799 548 779 .7744824038154049
5269527 -0.9626 205 207 71 130 139 51 32 271 284 92 120 128 46 75 .46999999999999997 52 420 75 151 68 156 .5131280821004941
5269528 0.5218 649 674 193 117 126 50 100 573 557 219 133 142 47 90 1.3140000000000001 80 546 532 440 548 415 1.4357150221672363
5269529 1.2466 2275 2296 520 127 133 48 100 1224 1129 384 130 136 44 95 2.1709999999999998 80 560 2148 1094 2163 993 2.3728646679466396
5269530 0.1783 769 724 261 138 157 118 88 740 710 271 144 179 186 79 1.0349999999999999 120 757 631 596 567 531 1.1315144142578561
5269531 -0.5556 444 433 133 118 126 51 90 665 633 195 127 132 37 96 .623 80 554 326 538 307 501 .68036026696041074
5269532 -1.0503 381 381 126 100 110 47 91 776 765 162 129 136 41 100 .442 80 560 281 647 271 629 .48286764958586892
5269533 -0.1587 232 255 106 105 115 48 59 317 322 115 139 144 46 75 .81999999999999995 52 340 127 178 140 178 .89581653677327056
5269534 -1.0994 169 194 97 115 126 57 33 355 384 186 199 283 212 7 .42699999999999999 156 1050 54 156 68 101 .46669620440112336
5269535 -0.0462 277 282 109 103 112 49 73 346 335 110 133 142 48 77 .88600000000000001 80 560 174 213 170 193 .96845750148785559

Total number of rows: 16511

Table truncated, full table size 2063 Kbytes.




Supplementary data files not provided
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