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Sample GSM67023 Query DataSets for GSM67023
Status Public on Aug 02, 2006
Title CtrXM_24hr.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) 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 0.4000 5998 6048 488 97 127 199 100 5009 5005 760 124 171 435 100 1.2190000000000001 80 636 5901 4885 5921 4834 1.3194993219578317
5269517 0.2038 5547 5586 471 100 112 51 100 5343 5262 574 107 115 47 100 1.0640000000000001 52 420 5447 5236 5474 5147 1.1517418888902862
5269518 0.0203 215 225 68 91 101 48 68 255 255 58 112 117 35 90 .93700000000000006 80 645 124 143 124 138 1.0141373777737392
5269519 -0.0328 329 337 113 113 122 50 87 367 372 98 124 130 38 96 .90300000000000002 80 656 216 243 215 242 .97751710654936252
5269520 0.4861 1227 1233 234 98 108 48 100 1031 997 281 120 125 35 95 1.294 80 554 1129 911 1125 872 1.400632814543872
5269521 -0.1552 169 170 47 92 103 45 44 211 213 73 119 123 31 59 .82999999999999996 52 334 77 92 67 90 .89803813208068339
5269522 0.5429 238 238 69 98 108 47 72 243 259 66 155 165 61 35 1.3460000000000001 80 536 140 88 130 94 1.4568764568764541
5269523 0.1658 491 501 111 104 112 49 100 493 500 156 117 121 32 100 1.0369999999999999 80 656 387 376 389 379 1.1218111740304928
5269524 -0.6715 191 195 53 119 127 50 30 264 261 76 130 137 40 73 .57999999999999996 52 340 72 134 68 124 .62787085687848909
5269525 -0.3795 171 180 75 104 113 46 34 219 224 68 117 124 37 69 .70999999999999996 120 773 67 102 67 100 .76870170328114096
5269526 0.0391 680 670 152 126 138 53 100 707 708 136 135 142 41 100 .94899999999999995 80 656 554 572 532 566 1.0274774672680411
5269527 0.1140 95 101 43 85 93 43 7 122 125 30 109 113 30 8 1 156 1154 10 13 8 12 1.08225108225108
5269528 0.3508 602 582 157 93 100 41 100 501 534 154 119 125 33 97 1.1779999999999999 80 613 509 382 482 409 1.2752307933030798
5269529 0.1767 519 510 150 110 123 68 93 500 501 114 118 126 47 98 1.044 80 546 409 382 387 375 1.1302883365546528
5269530 0.5921 685 674 137 89 104 62 100 541 535 133 115 123 57 95 1.393 80 624 596 426 570 412 1.5074211502782899
5269531 -0.0921 412 435 128 116 127 58 98 501 496 135 128 134 41 98 .86699999999999999 52 340 296 373 308 362 .93814699792960476
5269532 0.2288 778 778 128 98 109 50 100 751 749 175 121 125 30 98 1.083 80 623 680 630 669 624 1.1718642291890675
5269533 -1.4265 97 105 38 94 104 46 3 147 149 40 117 121 35 14 .34399999999999997 156 1070 3 30 1 28 .37202380952380876
5269534 -1.4454 121 123 49 104 114 47 6 198 230 342 174 212 207 0 .33900000000000002 156 948 17 24 9 18 .36719233147804503
5269535 -0.0324 193 199 69 96 104 45 55 208 230 71 116 120 31 82 .90400000000000003 80 560 97 92 95 110 .97782334624439693

Total number of rows: 16512

Table truncated, full table size 2011 Kbytes.




Supplementary data files not provided
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