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Sample GSM67031 Query DataSets for GSM67031
Status Public on Aug 02, 2006
Title CtrXM_8hr.3_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 0.2559 4920 4900 782 116 129 61 100 4724 4597 1205 384 388 102 100 1.1359999999999999 80 544 4804 4340 4771 4209 1.194040877430351
5269517 0.3381 11395 11690 1545 159 184 101 100 10327 9978 3181 386 403 148 100 1.202 52 420 11236 9941 11506 9575 1.2640879316710592
5269518 -0.2408 380 397 119 195 233 133 32 610 643 205 392 423 161 33 .80500000000000005 80 536 185 218 164 220 .84624697843745567
5269519 -0.4322 375 393 125 159 177 83 72 667 668 204 336 360 136 61 .70499999999999996 80 656 216 331 216 308 .74113488654934878
5269520 0.6073 1399 1443 217 129 144 72 100 1171 1235 325 328 350 197 96 1.4490000000000001 52 420 1270 843 1299 885 1.5233775854813008
5269521 -0.2379 121 133 59 108 118 51 9 324 335 92 304 317 111 4 .80600000000000005 156 1097 13 20 15 18 .84800379905701606
5269522 1.0025 320 314 102 133 145 70 65 425 449 136 354 392 181 7 1.905 52 332 187 71 169 57 2.0034312911616494
5269523 -0.1847 504 526 165 116 127 63 96 782 820 308 330 335 102 82 .83699999999999997 80 560 388 452 399 485 .87984720702160613
5269524 -0.2597 337 339 92 115 129 59 90 537 609 206 327 339 106 48 .79400000000000004 52 420 222 210 210 270 .8352536710144568
5269525 -0.2243 319 323 125 126 141 66 68 577 577 178 335 343 98 62 .81399999999999995 32 236 193 242 182 234 .85599325633738799
5269526 0.7535 1085 1111 215 117 130 64 100 923 903 248 283 303 116 93 1.603 80 645 968 640 981 600 1.685831552525348
5269527 -1.7576 114 121 50 112 125 60 3 294 325 121 293 310 123 5 .28100000000000003 156 1214 2 1 -4 15 .29574132492113436
5269528 0.1253 573 587 160 114 127 59 100 817 831 260 375 391 118 81 1.0369999999999999 80 480 459 442 460 440 1.0907262899625463
5269529 0.2966 1690 1660 288 131 145 68 100 1611 1670 399 361 377 122 100 1.1679999999999999 52 420 1559 1250 1515 1293 1.2282515529871203
5269530 0.3757 707 716 154 162 197 119 98 792 824 284 375 398 141 71 1.234 80 555 545 417 519 426 1.2974269260583693
5269531 0.1494 530 521 134 155 176 89 94 666 690 185 343 356 117 69 1.0549999999999999 52 420 375 323 345 334 1.1091009918271937
5269532 -0.2189 500 487 136 134 149 75 91 755 761 214 329 352 177 65 .81699999999999995 80 560 366 426 338 409 .85923199750749324
5269533 -0.6194 113 124 57 111 123 58 5 318 328 101 307 316 106 4 .61899999999999999 156 1066 2 11 1 12 .65094386860948095
5269534 1.3720 143 158 62 126 139 64 7 364 382 138 369 451 268 0 2.4620000000000002 156 961 17 -5 19 -69 2.5883685189678771
5269535 0.0410 229 251 92 115 129 60 44 422 465 144 326 330 89 34 .97799999999999998 52 420 114 96 122 135 1.0288299328991022

Total number of rows: 16512

Table truncated, full table size 2025 Kbytes.




Supplementary data files not provided
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