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Sample GSM80324 Query DataSets for GSM80324
Status Public on Oct 28, 2005
Title ZFL T5+
Sample type RNA
 
Channel 1
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Zebrafish liver tumor tissue or normal liver tissue
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 Cy5-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
Channel 2
Source name Zebrafish normal liver tissue
Organism Danio rerio
Characteristics Reference RNA was obtained by pooling equal amount of male 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 (Amersham Inc.). 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 Zebrafish liver tumor tissue (induced by carcinogens) vs zebrafish normal liver tissue.
Data processing Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2
 
Submission date Oct 27, 2005
Last update date Oct 27, 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)
GSE3519 Molecular Conservation of Zebrafish and Human Liver Tumors.

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 2.2620 11778 11735 1059 117 121 42 100 2921 2941 412 98 102 36 100 4.0869999999999997 80 642 11661 2823 11614 2839 4.7963947361033217
5269517 2.2109 15665 14753 3427 111 118 43 100 3858 3800 860 88 93 31 99 3.9449999999999998 120 780 15554 3770 14635 3707 4.6296998947709103
5269518 0.5264 763 769 134 110 115 37 100 618 630 159 93 95 32 100 1.2270000000000001 120 874 653 525 654 535 1.440361598517232
5269519 0.3112 795 797 178 112 117 38 100 753 742 277 94 100 34 100 1.0569999999999999 80 642 683 659 680 642 1.2407262505071543
5269520 1.2086 2342 2327 209 94 99 32 100 1224 1231 224 97 103 34 100 1.9690000000000001 80 650 2248 1127 2228 1128 2.3111922564191669
5269521 -0.0674 699 691 184 95 102 40 100 889 840 252 107 115 49 100 .81299999999999994 80 626 604 782 589 725 .95433904015269133
5269522 -0.0490 1503 1408 362 87 91 29 100 1712 1708 504 104 108 36 100 .82399999999999995 80 642 1416 1608 1317 1600 .96662686007984444
5269523 -0.1536 1134 1148 157 91 96 32 100 1463 1480 244 100 102 31 100 .76600000000000001 80 650 1043 1363 1052 1378 .89899299176702463
5269524 0.0605 562 566 128 88 93 31 100 647 634 149 96 98 29 100 .88800000000000001 120 768 474 551 473 536 1.0428120145906385
5269525 -0.0020 437 397 159 89 93 31 93 478 455 162 93 95 32 100 .85099999999999998 80 560 348 385 304 360 .99862526911005334
5269526 0.4373 1181 1109 311 88 94 33 98 1024 969 312 84 89 32 98 1.1539999999999999 120 791 1093 940 1015 880 1.3540754887138233
5269527 0.0367 418 393 151 81 86 28 97 473 442 167 85 90 29 97 .874 80 644 337 388 307 352 1.0257624176431106
5269528 0.4447 572 595 233 101 107 34 96 492 524 241 98 102 36 90 1.1599999999999999 120 734 471 394 488 422 1.3610615177764513
5269529 1.4744 748 771 196 101 105 36 100 340 371 152 88 90 29 95 2.367 120 756 647 252 666 281 2.778745500091234
5269530 0.2390 848 842 125 110 114 36 100 823 821 138 93 96 32 100 1.0049999999999999 120 812 738 730 728 725 1.1801578702987119
5269531 0.0338 1060 1046 218 111 117 39 98 1206 1164 277 92 97 33 98 .872 120 735 949 1114 929 1067 1.0237106719921487
5269532 1.1497 2127 2144 250 93 99 34 100 1178 1184 196 99 103 33 100 1.8899999999999999 80 650 2034 1079 2045 1081 2.2186884749356288
5269533 -0.1442 524 679 355 90 96 32 97 650 870 506 106 111 40 95 .77100000000000002 120 746 434 544 583 759 .90486198166309983
5269534 -0.0346 1107 1094 299 85 89 29 100 1342 1317 370 104 108 35 100 .83199999999999996 120 744 1022 1238 1005 1209 .9763168181941303
5269535 -0.0298 700 649 296 94 102 36 100 792 766 341 101 104 34 100 .83499999999999996 80 644 606 691 547 662 .97956158000635096

Total number of rows: 16512

Table truncated, full table size 2083 Kbytes.




Supplementary data files not provided
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