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Sample GSM80325 Query DataSets for GSM80325
Status Public on Oct 28, 2005
Title ZFL T6+
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 3.4780 17674 16360 3792 83 90 33 100 1557 1467 462 85 88 27 98 11.778 120 783 17591 1472 16270 1379 11.142722967413167
5269517 3.4873 25984 25041 3904 89 173 537 100 2202 2192 267 87 96 44 100 11.853999999999999 80 650 25895 2115 24868 2096 11.214457625557028
5269518 0.8033 891 850 209 79 82 24 99 505 501 196 83 87 30 94 1.8440000000000001 120 888 812 422 768 414 1.7450308492483468
5269519 0.6987 879 853 170 81 84 23 100 566 537 232 87 91 33 97 1.716 80 642 798 479 769 446 1.6230421528434775
5269520 1.1181 1740 1759 146 75 79 27 100 833 830 196 96 102 38 100 2.294 80 644 1665 737 1680 728 2.1705562243664271
5269521 -0.3157 515 518 132 73 76 24 100 613 616 178 92 96 30 100 .84899999999999998 80 636 442 521 442 520 .80344053095683465
5269522 -0.2532 863 943 238 73 77 24 100 1014 1084 351 103 114 54 100 .88700000000000001 80 560 790 911 866 970 .83902568865203297
5269523 -0.2259 912 897 200 70 75 25 100 1026 1008 272 93 98 32 99 .90400000000000003 120 744 842 933 822 910 .85508527588649197
5269524 -0.2554 869 848 183 67 71 25 100 979 974 267 92 95 32 100 .88500000000000001 80 656 802 887 777 879 .83773654526458963
5269525 -0.1769 706 629 307 68 70 20 100 772 689 329 89 94 34 96 .93500000000000005 80 554 638 683 559 595 .88457899716177879
5269526 0.1109 1614 1583 199 74 76 22 100 1420 1409 248 87 91 31 100 1.141 80 645 1540 1333 1507 1318 1.0798981503613259
5269527 -0.0911 824 716 330 68 71 21 100 841 737 364 84 89 34 98 .99199999999999999 80 560 756 757 645 648 .93882973714216178
5269528 0.6671 673 699 160 78 82 25 100 442 455 135 85 90 30 100 1.6779999999999999 80 629 595 357 617 365 1.5878697997903297
5269529 1.7559 1437 1400 313 72 91 119 100 467 458 188 86 91 33 98 3.5699999999999998 80 630 1365 381 1309 367 3.3773817153436894
5269530 0.5113 1010 988 169 75 79 23 100 687 688 145 82 86 28 100 1.5069999999999999 120 816 935 605 909 602 1.4253554021438097
5269531 -0.1187 866 819 195 83 86 24 98 851 846 203 90 92 31 100 .97399999999999998 120 758 783 761 733 754 .92104538651369305
5269532 2.6703 5112 5079 363 73 77 28 100 844 839 140 95 101 37 100 6.7279999999999998 80 631 5039 749 5002 738 6.3656524348684149
5269533 -0.2609 536 583 241 74 77 22 100 673 668 306 91 95 31 100 .88200000000000001 120 721 462 582 506 573 .83457809535833583
5269534 0.0335 1022 1013 118 74 79 28 100 981 980 198 112 135 85 100 1.0820000000000001 80 609 948 869 934 845 1.0234600142129058
5269535 -0.0831 527 533 262 69 73 22 100 545 560 318 95 99 31 96 .998 120 707 458 450 460 461 .94403922645751315

Total number of rows: 16512

Table truncated, full table size 2033 Kbytes.




Supplementary data files not provided
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