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Sample GSM67017 Query DataSets for GSM67017
Status Public on Aug 02, 2006
Title As_8hr.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 0.9613 5323 5171 667 85 112 215 100 3000 2853 693 83 95 100 97 1.8360000000000001 80 644 5238 2917 5059 2758 1.9470849236823939
5269517 0.7957 9418 9296 1155 101 123 109 100 5923 5706 1454 89 99 78 100 1.637 52 420 9317 5834 9173 5607 1.7359436236496941
5269518 0.1786 784 783 228 117 127 58 100 747 721 279 97 109 45 100 1.0669999999999999 52 420 667 650 656 612 1.1318215188840892
5269519 0.4122 851 777 350 63 76 50 93 641 615 298 46 61 41 88 1.2549999999999999 80 656 788 595 701 554 1.3306819092489897
5269520 0.4644 1657 1654 206 94 111 75 100 1338 1300 368 101 116 82 96 1.3009999999999999 52 420 1563 1237 1543 1184 1.3797287771623097
5269521 -0.0521 408 453 179 101 114 55 98 476 489 233 102 107 34 92 .91000000000000003 52 420 307 374 339 382 .96453947350393976
5269522 0.3034 587 619 224 93 104 50 97 437 553 290 101 108 37 100 1.1639999999999999 80 560 494 336 515 445 1.2340581274223712
5269523 -0.1159 726 726 194 89 99 47 100 830 829 273 97 104 37 98 .87 80 650 637 733 627 725 .92281927808587039
5269524 -0.1419 363 372 138 78 86 43 96 420 435 166 91 94 27 98 .85499999999999998 80 560 285 329 286 341 .90631088312905694
5269525 -0.0718 358 402 188 79 88 41 97 376 448 226 88 95 33 98 .89700000000000002 80 560 279 288 314 353 .95145516672558372
5269526 0.2993 1139 1230 325 94 102 42 100 1077 1073 431 94 101 35 95 1.1599999999999999 80 560 1045 983 1128 972 1.2305065982666799
5269527 -0.5897 223 257 89 111 117 42 81 303 355 212 122 147 133 31 .627 32 176 112 181 140 208 .66448509232246877
5269528 0.5369 557 582 211 84 93 50 97 425 447 177 83 86 23 100 1.3680000000000001 80 560 473 342 489 361 1.450829128453736
5269529 0.9789 1592 1491 465 97 108 49 100 847 836 289 86 91 30 98 1.859 80 560 1495 761 1383 745 1.9710144927536302
5269530 0.1519 1118 1054 465 110 151 232 83 1029 997 512 96 148 290 73 1.048 120 775 1008 933 903 849 1.1110548783430259
5269531 -0.1967 1171 1189 261 84 98 58 100 1405 1430 485 87 87 43 100 .82299999999999995 52 420 1087 1318 1091 1343 .87251835644388687
5269532 -0.4796 880 864 130 93 105 50 100 1232 1239 195 99 108 43 100 .67600000000000005 52 420 787 1133 759 1131 .71719595914494871
5269533 -0.1080 210 267 175 99 112 53 51 216 293 183 101 108 40 62 .875 80 560 111 115 155 185 .92788971367974882
5269534 -0.0934 356 378 162 104 129 80 68 410 440 176 130 161 92 67 .88400000000000001 80 560 252 280 249 279 .93729689050046516
5269535 0.3023 324 339 135 89 98 44 88 289 313 126 98 101 28 96 1.163 52 420 235 191 241 212 1.2330760314681048

Total number of rows: 16512

Table truncated, full table size 2010 Kbytes.




Supplementary data files not provided
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