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Sample GSM67029 Query DataSets for GSM67029
Status Public on Aug 02, 2006
Title CtrXM_8hr.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 0.1502 6252 6169 1126 80 95 58 100 5486 5099 1902 65 139 176 91 1.21 80 636 6172 5421 6074 4960 1.1097017346265572
5269517 0.0176 3812 4068 1091 108 126 76 100 3406 3771 1762 182 208 136 98 1.103 52 420 3704 3224 3942 3563 1.0122673510548279
5269518 -0.0869 246 261 107 105 120 64 57 297 337 136 185 201 76 36 1.026 80 656 141 112 141 136 .94157411878319608
5269519 -0.3312 350 358 122 105 117 63 90 445 472 146 180 187 59 92 .86599999999999999 80 552 245 265 241 285 .79489757446273679
5269520 0.4907 1149 1233 304 118 137 73 100 860 903 257 175 190 95 98 1.532 52 420 1031 685 1096 713 1.4051315656820238
5269521 -0.3349 186 187 72 117 129 57 16 247 242 70 161 172 54 41 .86399999999999999 12 104 69 86 58 70 .79284177143504309
5269522 0.1801 267 300 133 116 131 64 65 288 320 116 171 181 67 43 1.2350000000000001 80 624 151 117 169 139 1.1329351640908805
5269523 -0.2690 344 363 125 126 144 70 75 409 428 146 166 176 58 90 .90500000000000003 80 546 218 243 219 252 .82989004832271118
5269524 -0.3849 193 219 130 123 132 60 32 238 280 128 165 176 64 30 .83499999999999996 80 560 70 73 87 104 .76585560430793731
5269525 -1.1055 206 215 101 138 151 67 23 269 316 159 164 181 80 37 .50700000000000001 80 552 68 105 64 135 .46475132786093648
5269526 0.2938 1044 1055 256 133 149 82 100 823 868 331 178 188 63 92 1.3360000000000001 80 650 911 645 906 680 1.2259008110623579
5269527 -0.5983 131 141 66 105 120 59 11 196 210 74 160 175 63 17 .71999999999999997 52 320 26 36 21 35 .66055045871559592
5269528 -0.5817 474 526 244 81 94 58 91 698 675 223 64 122 148 92 .72799999999999998 80 546 393 634 432 553 .66817820087388657
5269529 0.3275 1413 1426 238 102 116 62 100 1239 1160 361 192 198 63 94 1.3680000000000001 52 420 1311 1047 1310 962 1.2548335734324052
5269530 1.1678 903 1017 361 106 124 70 100 531 554 218 182 196 69 92 2.4489999999999998 80 628 797 349 893 358 2.2467199368649489
5269531 -0.2165 576 574 188 104 117 55 95 691 683 201 182 193 66 98 .93799999999999994 80 552 472 509 457 490 .86066399311468766
5269532 0.3043 677 652 197 119 132 65 93 585 572 155 176 185 60 96 1.3460000000000001 80 560 558 409 520 387 1.2348253173941242
5269533 -0.3170 132 141 63 120 134 68 5 176 189 83 165 175 60 8 .875 156 1166 12 11 7 14 .80275229357798117
5269534 -0.1983 150 158 71 120 136 68 10 201 211 76 171 222 224 0 .94999999999999996 156 963 30 30 22 -11 .87155963302752237
5269535 -0.7344 206 209 75 133 145 73 13 286 285 103 169 183 64 44 .65500000000000003 52 420 73 117 64 102 .60107560898449819

Total number of rows: 16512

Table truncated, full table size 2007 Kbytes.




Supplementary data files not provided
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