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Sample GSM67018 Query DataSets for GSM67018
Status Public on Aug 02, 2006
Title As_8hr.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 0.8290 4390 4321 772 87 96 49 100 3295 3123 1004 140 149 68 96 1.419 80 560 4303 3155 4225 2974 1.7764411347237996
5269517 0.5433 7444 6830 2295 114 122 45 100 6225 5916 1815 148 153 46 100 1.1639999999999999 80 560 7330 6077 6708 5763 1.4572654097788649
5269518 -0.3703 266 264 66 107 113 42 86 397 397 97 143 152 50 94 .61799999999999999 52 420 159 254 151 245 .773604801277186
5269519 0.2386 404 398 125 102 109 43 92 462 459 146 145 152 53 91 .94299999999999995 80 560 302 317 289 307 1.179818722447644
5269520 -0.2649 755 749 117 102 111 46 100 1164 1133 277 160 167 55 100 .66500000000000004 52 420 653 1004 638 966 .83223247970548897
5269521 -0.7386 163 167 53 99 107 46 27 302 306 109 164 169 47 65 .47899999999999998 80 560 64 138 60 137 .59934072520227666
5269522 -0.0882 328 338 89 102 109 47 96 485 490 145 176 186 61 92 .752 52 420 226 309 229 304 .9406662787082567
5269523 -0.4680 394 402 104 97 106 47 94 674 691 178 163 178 65 98 .57799999999999996 52 420 297 511 296 513 .72296810406947976
5269524 -0.8641 238 248 68 97 105 40 86 466 501 142 157 163 49 100 .439 52 420 141 309 143 338 .54937858369473391
5269525 -0.1392 293 303 79 118 128 50 88 406 413 122 158 166 57 88 .72499999999999998 52 420 175 248 175 247 .9079977422758827
5269526 -0.3989 510 505 129 99 108 47 98 807 808 268 138 146 52 95 .60599999999999998 80 560 411 669 397 662 .75841069994209076
5269527 -0.2767 144 154 51 92 100 38 33 217 226 80 132 136 43 50 .66000000000000003 80 560 52 85 54 90 .82549996005645232
5269528 0.3340 362 366 117 83 90 40 97 428 420 158 139 147 86 72 1.0069999999999999 80 560 279 289 276 273 1.2604723876375701
5269529 0.9540 1139 1125 177 105 111 40 100 806 798 185 139 142 42 100 1.548 52 420 1034 667 1014 656 1.9371710844929428
5269530 0.2395 808 779 207 114 127 66 97 834 859 209 154 164 57 100 .94299999999999995 80 656 694 680 652 695 1.1805537063172922
5269531 -0.4817 426 430 71 113 123 61 100 700 704 182 150 218 1140 0 .57199999999999995 52 420 313 550 307 486 .71614789244678489
5269532 -1.3599 304 314 73 102 109 44 94 797 840 178 159 169 66 100 .311 52 420 202 638 205 671 .38962065283513292
5269533 -0.5075 177 179 61 102 112 49 26 291 304 92 167 171 46 69 .56200000000000006 52 340 75 124 67 133 .70343403707188623
5269534 -0.4096 175 180 57 100 110 47 34 301 315 81 182 191 62 48 .60199999999999998 52 420 75 119 70 124 .75282072515456244
5269535 -0.2243 213 221 71 89 96 45 71 332 350 106 157 163 47 84 .68400000000000005 52 340 124 175 125 187 .85599227013040791

Total number of rows: 16512

Table truncated, full table size 2037 Kbytes.




Supplementary data files not provided
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