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Sample GSM67011 Query DataSets for GSM67011
Status Public on Aug 02, 2006
Title AS_24hr.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 1.3052 11367 11138 1912 138 153 97 100 5654 5340 1849 140 152 84 93 2.1150000000000002 80 546 11229 5514 10985 5188 2.4712437095614654
5269517 1.1538 13399 12129 3712 153 163 63 100 7128 6419 2646 131 138 47 96 1.905 80 560 13246 6997 11966 6281 2.2249768138688721
5269518 0.1490 367 366 93 142 150 60 84 361 370 100 134 145 56 90 .94899999999999995 52 420 225 227 216 225 1.1088230635197207
5269519 0.4896 650 658 162 140 148 60 100 571 569 220 138 142 42 93 1.202 80 650 510 433 510 427 1.404037556649391
5269520 0.6974 1385 1391 275 114 128 58 100 1070 1046 356 126 132 43 93 1.3879999999999999 80 560 1271 944 1263 914 1.6215461194636316
5269521 -0.5126 234 251 87 116 126 57 53 347 364 92 139 144 46 94 .59999999999999998 52 420 118 208 125 220 .70093457943925197
5269522 -0.0811 500 506 181 120 129 58 96 492 622 509 145 152 48 98 .80900000000000005 52 420 380 347 377 470 .94535551245126226
5269523 -0.0475 617 617 159 125 136 60 100 767 730 226 136 141 42 97 .82799999999999996 80 645 492 631 481 589 .96762012649863061
5269524 -0.8343 331 343 98 162 168 65 66 509 515 154 138 144 43 96 .47999999999999998 80 560 169 371 175 371 .56087161307915379
5269525 0.0602 374 409 140 160 171 69 83 405 413 113 134 140 43 98 .89200000000000002 80 560 214 271 238 273 1.0426087830368802
5269526 -0.4251 811 796 234 161 171 72 95 1133 1129 213 133 141 48 100 .63800000000000001 80 552 650 1000 625 988 .74480163645235109
5269527 -0.4104 247 258 80 144 154 65 30 303 304 96 127 134 44 78 .64400000000000002 52 420 103 176 104 170 .75241565024552459
5269528 0.8888 808 829 237 130 142 62 100 583 579 231 138 147 53 91 1.585 80 538 678 445 687 432 1.8516752495390669
5269529 1.2881 1637 1580 424 146 156 59 100 830 818 247 132 137 41 100 2.0899999999999999 80 555 1491 698 1424 681 2.4420315522737788
5269530 0.5797 721 742 163 142 171 129 100 600 602 196 133 149 73 91 1.2789999999999999 80 640 579 467 571 453 1.4945300201263367
5269531 -0.7613 530 495 167 143 151 60 85 850 829 223 132 138 38 97 .505 80 560 387 718 344 691 .58997841215355495
5269532 -0.7155 375 382 90 125 137 61 92 622 628 137 135 146 56 100 .52100000000000002 52 420 250 487 245 482 .6089931944418111
5269533 -0.1967 228 236 81 115 124 55 51 285 296 99 134 140 40 73 .747 80 554 113 151 112 156 .87256259374639389
5269534 -0.3480 220 226 69 111 123 56 46 305 319 91 148 166 73 58 .67300000000000004 80 555 109 157 103 153 .7856479204241128
5269535 0.3323 331 340 134 132 144 65 72 305 333 138 140 147 45 75 1.0780000000000001 80 560 199 165 196 186 1.2590189337078102

Total number of rows: 16512

Table truncated, full table size 2049 Kbytes.




Supplementary data files not provided
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