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Sample GSM67028 Query DataSets for GSM67028
Status Public on Aug 02, 2006
Title CtrXM_48hr.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) 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 -1.3586 1669 1701 353 104 120 76 100 3212 3230 557 111 122 97 100 .51200000000000001 80 555 1565 3101 1581 3108 .38996426833350972
5269517 -1.3520 2384 2396 448 120 132 66 100 4563 4539 907 114 117 35 100 .51400000000000001 80 547 2264 4449 2264 4422 .39173669648581561
5269518 0.0807 476 523 201 112 127 77 93 405 408 89 112 120 50 100 1.389 80 560 364 293 396 288 1.0575121961260581
5269519 -0.2485 445 473 202 116 122 60 91 418 437 128 114 116 38 100 1.105 80 554 329 304 351 321 .84178458331663175
5269520 -0.4300 808 849 270 121 134 67 98 875 859 144 112 115 35 100 .97499999999999998 80 548 687 763 715 744 .74224289898869444
5269521 0.3039 499 524 207 135 139 65 92 340 372 139 132 138 43 90 1.621 52 420 364 208 385 234 1.2344503681137351
5269522 0.1437 1447 1429 706 125 137 67 98 1135 1036 556 137 139 38 97 1.4510000000000001 80 555 1322 998 1292 897 1.1047224342524957
5269523 -0.1790 1036 1039 313 139 151 72 98 903 912 230 136 139 45 100 1.1599999999999999 80 629 897 767 888 773 .88331592873799725
5269524 0.1788 693 684 220 143 154 71 97 492 489 144 125 128 36 97 1.486 80 554 550 367 530 361 1.1319601951742095
5269525 -0.2376 433 486 211 143 154 65 86 393 417 233 109 113 33 96 1.1140000000000001 52 420 290 284 332 304 .84816173925084848
5269526 -0.3988 1093 1099 335 133 139 59 100 1080 1086 223 116 120 39 100 .996 80 546 960 964 960 966 .75847394414302693
5269527 0.1477 476 474 157 138 152 75 84 344 340 100 109 113 34 94 1.4550000000000001 52 420 338 235 322 227 1.1078030880011085
5269528 -0.1045 358 392 167 105 118 70 80 319 341 117 106 112 40 93 1.2210000000000001 80 631 253 213 274 229 .93014211404773917
5269529 -1.2513 489 535 226 123 132 62 92 847 857 155 110 114 34 100 .55200000000000005 80 560 366 737 403 743 .42006054173536
5269530 0.3229 1254 1242 251 117 136 103 100 813 799 129 114 123 71 100 1.6419999999999999 80 554 1137 699 1106 676 1.2508269355851931
5269531 0.3138 1552 1543 406 115 129 97 96 1011 994 154 119 123 48 100 1.6319999999999999 80 645 1437 892 1414 871 1.2429550647372436
5269532 -0.1409 809 814 249 115 125 57 100 712 702 112 115 119 37 100 1.1910000000000001 80 631 694 597 689 583 .90693121205712535
5269533 0.3367 290 321 176 127 138 63 61 217 248 120 131 134 39 50 1.6579999999999999 52 340 163 86 183 114 1.2628481783089558
5269534 0.3653 804 825 262 140 150 72 100 532 543 136 138 139 42 100 1.6910000000000001 52 420 664 394 675 404 1.2881630043346222
5269535 0.0283 402 457 217 141 148 70 80 389 379 127 143 145 43 84 1.339 52 340 261 246 309 234 1.0197890714755966

Total number of rows: 16512

Table truncated, full table size 2013 Kbytes.




Supplementary data files not provided
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