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Sample GSM67020 Query DataSets for GSM67020
Status Public on Aug 02, 2006
Title As_96h.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 0.8230 14312 14499 2163 148 292 863 100 8337 8360 1520 174 247 493 100 1.7529999999999999 52 420 14164 8163 14207 8113 1.7690364021367073
5269517 0.5634 13735 13259 3720 157 205 443 100 9347 9145 1181 198 228 176 100 1.464 52 414 13578 9149 13054 8917 1.4777007823964423
5269518 -0.2300 282 268 87 50 52 14 98 314 320 130 62 70 38 95 .84499999999999997 80 560 232 252 216 250 .85263495490421937
5269519 -0.7336 256 258 64 50 51 13 98 388 407 109 58 66 37 100 .59599999999999997 52 420 206 330 207 341 .60140114902315966
5269520 -0.2663 742 739 135 51 53 15 100 845 898 281 63 72 45 100 .82399999999999995 52 420 691 782 686 826 .83143501090654592
5269521 -1.0580 159 153 55 54 54 14 84 259 269 103 61 72 44 88 .47599999999999998 52 340 105 198 99 197 .48028409531941535
5269522 -0.8973 220 219 92 53 55 18 91 308 373 231 61 73 46 88 .53200000000000003 80 560 167 247 164 300 .53688323113146774
5269523 -0.6480 277 275 99 115 129 59 67 399 438 202 185 192 83 61 .63200000000000001 80 546 162 214 146 246 .63815445730946396
5269524 -0.8887 216 220 69 53 55 16 96 345 375 158 63 74 43 95 .53500000000000003 80 650 163 282 165 301 .54011746746358491
5269525 -2.0530 210 223 79 191 194 86 6 281 300 172 166 174 89 27 .23899999999999999 156 1106 19 115 29 126 .24097474283476772
5269526 -0.4181 679 689 161 198 208 67 97 831 839 270 177 186 88 97 .74199999999999999 80 560 481 654 481 653 .74842769212947069
5269527 -5.9177 173 183 78 191 199 77 5 222 227 100 166 173 87 10 -.13100000000000001 156 1036 -18 56 -16 54 .016542323534763769
5269528 0.7691 877 926 237 139 152 76 100 592 624 206 158 178 100 92 1.6890000000000001 52 420 738 434 774 446 1.7041788110158891
5269529 0.2231 1208 1106 433 58 87 78 93 1040 988 407 82 127 161 87 1.157 80 507 1150 958 1019 861 1.1672380341394901
5269530 0.1641 582 574 110 51 61 65 100 535 536 155 65 79 69 98 1.1100000000000001 52 420 531 470 513 457 1.1204877871116103
5269531 -0.8199 295 297 87 50 54 22 100 517 500 192 60 71 45 98 .56100000000000005 52 420 245 457 243 429 .56646179249610396
5269532 -1.0508 262 260 57 50 52 15 100 462 501 201 62 68 37 100 .47799999999999998 52 420 212 400 208 433 .4827042471077993
5269533 -1.3734 112 120 49 50 52 16 78 238 248 109 65 72 39 84 .38300000000000001 52 340 62 173 68 176 .38598754914448791
5269534 -0.7958 186 192 63 55 57 18 92 294 308 137 68 77 45 86 .57099999999999995 52 420 131 226 135 231 .57601749075008668
5269535 -2.4252 190 189 42 139 145 57 8 462 478 144 207 217 107 58 .185 12 104 51 255 44 261 .18617744199641881

Total number of rows: 16512

Table truncated, full table size 2029 Kbytes.




Supplementary data files not provided
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