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Sample GSM80327 Query DataSets for GSM80327
Status Public on Oct 28, 2005
Title ZFL T8+
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 2.7720 31417 31374 2534 83 92 39 100 4594 4527 735 101 107 42 100 7.0700000000000003 80 639 31334 4493 31282 4420 6.8307388706610688
5269517 2.6511 28641 26144 6909 106 117 54 100 4366 4113 1144 108 113 44 100 6.5010000000000003 120 754 28535 4258 26027 4000 6.281520080575608
5269518 0.4358 489 485 99 86 94 36 100 385 390 126 105 108 35 96 1.3999999999999999 120 764 403 280 391 282 1.3526570048309177
5269519 0.4400 698 700 108 85 91 41 100 543 544 165 106 109 39 100 1.4039999999999999 80 631 613 437 609 435 1.3566276222619285
5269520 0.8241 1628 1636 199 84 92 45 100 949 956 166 109 113 38 100 1.8320000000000001 80 638 1544 840 1544 843 1.7703859601092802
5269521 -0.1421 344 347 94 75 89 52 98 390 402 123 112 127 83 82 .93799999999999994 80 650 269 278 258 275 .90621355988672325
5269522 -0.0836 1243 1248 157 73 83 39 100 1339 1342 251 139 156 78 100 .97699999999999998 80 638 1170 1200 1165 1186 .94369551162351772
5269523 -0.2133 875 879 138 80 88 40 100 997 1007 190 112 119 43 100 .89300000000000002 80 637 795 885 791 888 .86254824170782385
5269524 -0.1276 676 662 141 86 94 38 100 698 714 190 106 113 39 100 .94699999999999995 80 637 590 592 568 601 .91533180778032031
5269525 -0.2371 806 780 214 81 87 32 100 897 903 248 107 112 39 100 .878 52 420 725 790 693 791 .84844512417158258
5269526 -0.0496 1874 1859 228 81 92 50 100 1886 1886 250 108 116 74 100 1 80 639 1793 1778 1767 1770 .96618357487922701
5269527 -0.1858 599 576 142 81 90 42 100 640 647 184 103 109 38 100 .91000000000000003 52 420 518 537 486 538 .87915601023017897
5269528 1.1428 849 868 222 75 82 33 100 444 451 135 104 108 38 100 2.2850000000000001 80 631 774 340 786 343 2.2080218296231324
5269529 1.8311 1205 1163 285 84 92 36 100 401 398 160 105 111 44 89 3.6829999999999998 120 716 1121 296 1071 287 3.558061697251488
5269530 0.1764 817 811 137 80 86 32 100 726 727 180 102 107 36 100 1.1699999999999999 120 706 737 624 725 620 1.1300483091787439
5269531 -0.3843 780 783 108 82 88 34 100 988 990 153 106 110 40 100 .79300000000000004 80 632 698 882 695 880 .76617045926508831
5269532 2.3992 3709 3731 433 84 93 50 100 772 777 139 109 113 39 100 5.46 80 630 3625 663 3638 664 5.2749573317133853
5269533 -0.6647 544 542 210 83 100 62 98 752 816 295 113 136 106 98 .65300000000000002 80 615 461 639 442 680 .63083678644319374
5269534 0.9527 713 700 104 73 83 41 100 528 528 148 215 361 359 0 2.0030000000000001 80 607 640 313 617 167 1.9354539982404961
5269535 -0.0254 451 437 148 77 84 34 100 459 467 195 113 117 37 98 1.0169999999999999 80 612 374 346 353 350 .98255956767379016

Total number of rows: 16512

Table truncated, full table size 2116 Kbytes.




Supplementary data files not provided
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