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Sample GSM67015 Query DataSets for GSM67015
Status Public on Aug 02, 2006
Title As_48h.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) 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 1.4199 18805 18354 1994 344 376 156 100 5689 5620 903 205 220 111 100 3.3260000000000001 80 540 18461 5484 17978 5400 2.675741307369282
5269517 1.0917 8501 8473 1179 173 198 173 100 3184 3307 620 174 188 92 100 2.649 52 420 8328 3010 8275 3119 2.1313097360539794
5269518 -0.1212 365 379 138 91 107 65 86 467 450 177 198 211 96 57 1.143 52 420 274 269 272 239 .91943454775313138
5269519 0.6214 459 473 118 81 92 55 100 360 400 156 195 210 98 43 1.9119999999999999 80 560 378 165 381 190 1.538370975021093
5269520 -0.1243 834 806 164 91 110 126 100 778 830 268 203 255 533 3 1.1399999999999999 52 420 743 575 696 575 .91741824392033955
5269521 -0.2279 276 276 81 103 117 66 59 340 366 145 203 216 98 37 1.0609999999999999 32 236 173 137 159 150 .85386137831981768
5269522 -0.2902 328 345 140 99 113 59 78 387 443 209 201 216 94 50 1.0169999999999999 52 340 229 186 232 227 .81780283637959317
5269523 -0.0887 603 625 168 99 112 63 100 593 648 234 198 209 103 86 1.169 52 420 504 395 513 439 .94037722356306386
5269524 -0.3575 365 355 109 95 107 57 92 451 470 188 202 214 102 59 .96999999999999997 52 340 270 249 248 256 .78049014781282622
5269525 0.2404 347 380 142 101 118 64 88 360 384 153 194 211 112 36 1.468 52 420 246 166 262 173 1.1813524156328064
5269526 -0.2672 824 834 306 111 126 65 100 850 905 299 205 220 106 98 1.0329999999999999 80 560 713 645 708 685 .83093897253189264
5269527 -1.4422 175 192 81 149 161 76 12 250 279 126 185 211 115 21 .45700000000000002 32 236 26 65 31 68 .36801834956608054
5269528 0.4168 771 854 361 328 347 128 76 479 515 242 198 215 112 57 1.659 80 546 443 281 507 300 1.3349203489065575
5269529 0.9740 1189 1208 235 141 152 66 100 643 620 185 183 191 91 88 2.4420000000000002 52 420 1048 460 1056 429 1.9643182600595364
5269530 -0.8184 405 393 115 104 124 80 88 570 615 292 205 217 104 75 .70499999999999996 52 420 301 365 269 398 .56707807625139783
5269531 -0.2862 660 666 141 86 92 43 100 767 760 201 191 200 91 96 1.0189999999999999 52 420 574 576 574 560 .82005805445468227
5269532 -0.4589 428 463 134 85 102 123 82 607 621 219 203 242 479 0 .90400000000000003 52 420 343 404 361 379 .72751908294102441
5269533 -0.7144 186 208 84 108 117 60 37 319 342 142 210 219 106 28 .75800000000000001 32 176 78 109 91 123 .60947365854847735
5269534 -0.3224 274 285 90 117 129 72 56 388 387 175 218 234 106 37 .99399999999999999 32 170 157 170 156 153 .79974484331189544
5269535 0.0017 263 270 86 102 116 65 59 310 334 158 199 211 92 34 1.244 32 236 161 111 154 123 1.0011620631089655

Total number of rows: 16512

Table truncated, full table size 2029 Kbytes.




Supplementary data files not provided
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