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Sample GSM67014 Query DataSets for GSM67014
Status Public on Aug 02, 2006
Title As_48h.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 1.4027 19330 18883 2744 89 113 275 100 5923 6001 1180 136 149 74 100 3.2040000000000002 80 552 19241 5787 18770 5852 2.6439216811706743
5269517 1.2114 37534 35044 11329 141 184 132 100 13750 12593 4232 157 174 97 100 2.8069999999999999 80 560 37393 13593 34860 12419 2.3156846884431124
5269518 0.2393 573 576 120 91 106 55 100 497 491 162 152 164 78 87 1.431 80 560 482 345 470 327 1.1804277772910032
5269519 0.3780 830 825 176 80 89 43 100 590 616 207 143 154 72 98 1.575 80 560 750 447 736 462 1.2995485595071135
5269520 -0.0081 1302 1322 178 83 110 101 100 1187 1170 258 142 157 82 100 1.2050000000000001 52 420 1219 1045 1212 1013 .99443310089763826
5269521 -0.1102 268 282 96 81 92 44 88 346 342 147 163 167 69 53 1.123 52 420 187 183 190 175 .92648929697438998
5269522 -0.2018 343 366 135 72 83 40 98 434 452 164 173 181 82 76 1.054 52 420 271 261 283 271 .86944178288796603
5269523 -0.1424 640 647 240 76 85 39 100 632 680 305 160 169 74 93 1.0980000000000001 80 643 564 472 562 511 .90600406194465599
5269524 -0.5711 414 409 88 99 112 57 100 523 533 169 153 163 78 90 .81599999999999995 52 420 315 370 297 370 .67309362515198878
5269525 -0.1365 287 324 147 109 117 49 80 311 340 172 145 153 74 58 1.103 80 656 178 166 207 187 .90970635525090959
5269526 -0.6884 499 545 173 96 107 43 98 738 736 221 139 150 69 98 .752 80 560 403 599 438 586 .62053944087876112
5269527 -0.6924 175 189 60 102 109 44 40 241 255 100 139 146 75 28 .75 52 340 73 102 80 109 .6188118811881187
5269528 1.0313 888 943 270 76 84 35 100 474 489 217 139 148 66 88 2.4769999999999999 80 552 812 335 859 341 2.0438472418670437
5269529 1.1345 6153 6230 631 102 132 109 100 2431 2458 404 155 167 79 100 2.661 52 420 6051 2276 6098 2291 2.1954431656800066
5269530 0.3069 1140 1181 272 115 158 170 100 861 877 265 166 193 110 98 1.4990000000000001 80 634 1025 695 1023 684 1.2370435355771863
5269531 -0.2129 777 743 203 80 88 41 100 774 786 287 152 165 85 91 1.046 80 560 697 622 655 621 .86282287534747149
5269532 -0.6417 361 357 78 82 95 49 100 491 503 143 149 159 77 94 .77700000000000002 52 420 279 342 262 344 .64095392590106459
5269533 -0.0205 219 223 88 82 91 43 71 267 293 97 175 185 86 25 1.1950000000000001 32 176 137 92 132 108 .98590367511327381
5269534 -0.3255 242 245 97 68 77 35 82 312 354 158 171 178 78 42 .96699999999999997 52 340 174 141 168 176 .79803062273440439
5269535 -0.1860 216 239 97 76 85 38 83 300 314 118 161 174 78 46 1.0649999999999999 80 554 140 139 154 140 .87900946957440829

Total number of rows: 16512

Table truncated, full table size 2027 Kbytes.




Supplementary data files not provided
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