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Sample GSM80323 Query DataSets for GSM80323
Status Public on Oct 28, 2005
Title ZFL T4+
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 2.4210 9776 9759 1701 100 106 45 100 2512 2277 750 104 110 40 94 4.4450000000000003 120 778 9676 2408 9653 2167 5.3554300034930176
5269517 2.3171 11148 11264 1430 72 77 31 100 2742 2787 419 81 85 32 100 4.1360000000000001 120 772 11076 2661 11187 2702 4.9831254062814292
5269518 0.2957 847 817 197 60 64 22 100 857 823 268 80 85 28 100 1.0189999999999999 120 878 787 777 753 738 1.2275211208224517
5269519 0.3050 757 752 306 65 71 26 98 714 759 411 89 92 29 98 1.0249999999999999 120 771 692 625 681 667 1.2353893184678979
5269520 0.3720 2115 2021 574 65 75 89 100 1987 1916 775 95 100 40 99 1.0740000000000001 120 755 2050 1892 1946 1816 1.2941386633850025
5269521 -0.2010 1403 1287 466 118 131 88 99 1983 1769 744 150 170 114 99 .72199999999999998 120 768 1285 1833 1156 1599 .86994054041986091
5269522 0.0929 1248 1313 734 95 102 41 100 1468 1540 933 164 187 90 99 .88500000000000001 120 836 1153 1304 1211 1353 1.0664752031381306
5269523 -0.1253 2193 2075 491 127 133 44 100 2871 2705 718 145 153 54 100 .76100000000000001 120 768 2066 2726 1942 2552 .91679216867469604
5269524 -0.1963 2308 2223 374 99 110 51 100 3145 3047 615 115 128 65 100 .72399999999999998 80 621 2209 3030 2113 2919 .87279541083843981
5269525 -0.1183 1450 1381 395 88 95 36 100 1912 1795 542 104 110 40 100 .76500000000000001 80 548 1362 1808 1286 1685 .92124856611543471
5269526 -0.0167 1599 1544 318 77 84 32 100 1937 1882 405 94 100 37 100 .81999999999999995 120 744 1522 1843 1460 1782 .9885178297080911
5269527 -0.0524 499 475 101 86 92 35 100 619 591 165 105 113 44 98 .80000000000000004 52 420 413 514 383 478 .96435123208884621
5269528 0.4712 626 649 270 76 83 34 99 585 592 333 94 99 36 92 1.151 120 718 550 491 566 493 1.3862679634199406
5269529 1.2572 719 683 189 62 67 23 100 401 394 171 81 85 33 94 1.984 120 798 657 320 616 309 2.3903922398860544
5269530 0.1806 964 947 156 59 65 29 100 1009 1025 225 81 85 28 100 .94099999999999995 120 798 905 928 882 940 1.1333469471104725
5269531 -0.1053 1275 1209 323 64 68 24 96 1587 1571 332 87 90 29 100 .77200000000000002 120 704 1211 1500 1141 1481 .9295943883350084
5269532 1.2437 4885 4949 484 61 74 112 100 2612 2577 279 90 97 41 100 1.9650000000000001 80 612 4824 2522 4875 2480 2.3679761264599946
5269533 -0.3219 1583 1531 450 114 127 53 100 2470 2278 661 144 164 83 100 .66400000000000003 80 626 1469 2326 1404 2114 .80001354998249552
5269534 -0.0286 1955 1992 697 96 105 43 100 2337 2506 930 176 205 108 100 .81399999999999995 120 756 1859 2161 1887 2301 .98040229587879124
5269535 -0.0170 1541 1450 363 122 127 42 100 1831 1758 506 139 144 49 100 .81999999999999995 80 540 1419 1692 1323 1614 .9882643607164886

Total number of rows: 16512

Table truncated, full table size 2176 Kbytes.




Supplementary data files not provided
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