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Sample GSM80317 Query DataSets for GSM80317
Status Public on Oct 28, 2005
Title ZFL C9-
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 0.9495 5698 5465 1034 62 229 854 98 2996 2872 601 63 156 474 96 1.923 80 612 5636 2933 5236 2716 1.9311850463441556
5269517 0.8940 6423 6123 1007 63 153 603 100 3400 3337 654 63 114 340 100 1.851 80 622 6360 3337 5970 3223 1.858380375503238
5269518 -0.4624 115 115 34 55 56 17 77 134 140 33 57 58 12 98 .72299999999999998 80 608 60 77 59 82 .7257947452460457
5269519 -0.6274 102 102 30 53 55 16 66 134 132 34 56 57 11 97 .64500000000000002 80 550 49 78 47 75 .64732614669203248
5269520 1.0114 603 575 186 59 73 140 89 331 318 94 61 71 108 75 2.008 156 940 544 270 502 247 2.0158454830997177
5269521 -0.4536 89 94 32 54 56 17 50 111 113 27 58 60 13 82 .72699999999999998 80 600 35 53 38 53 .73019350127784
5269522 -0.3552 163 163 51 61 65 25 84 211 213 61 82 99 53 61 .77900000000000003 52 340 102 129 98 114 .7817529660627256
5269523 0.2809 197 201 56 57 62 29 94 178 179 41 60 64 23 98 1.21 156 904 140 118 139 115 1.2149438088488429
5269524 -0.7840 102 112 39 53 56 20 70 155 159 32 57 59 14 100 .57799999999999996 80 619 49 98 56 100 .58075439010945851
5269525 -0.7848 90 96 40 59 63 22 40 116 124 34 60 63 15 87 .57799999999999996 80 636 31 56 33 61 .58044678714859543
5269526 0.6344 261 270 78 52 54 19 98 194 196 48 55 56 13 98 1.546 156 906 209 139 216 140 1.5523085248796633
5269527 -0.5969 75 79 26 52 53 15 40 93 96 23 55 56 11 77 .65900000000000003 120 730 23 38 26 40 .661181310608288
5269528 0.1286 150 159 57 61 71 87 11 149 152 45 62 68 70 11 1.089 80 622 89 87 88 84 1.0932619366354326
5269529 -0.3504 99 107 37 57 60 20 55 119 123 32 59 61 12 90 .78100000000000003 80 541 42 60 47 62 .78438755020080464
5269530 1.1638 1274 1260 202 55 56 18 100 609 598 111 58 59 11 99 2.2309999999999999 120 794 1219 551 1204 539 2.2404432544994832
5269531 -0.1948 163 167 53 53 55 18 97 193 189 37 58 59 12 100 .87 80 598 110 135 112 130 .87372390324657567
5269532 1.1908 767 728 210 55 57 18 96 372 355 92 59 60 11 98 2.274 156 858 712 313 671 295 2.2827797677195307
5269533 -0.2458 89 94 33 52 55 16 60 108 108 26 58 59 12 81 .83999999999999997 80 611 37 50 39 49 .84337349397590511
5269534 -10.3496 54 58 20 69 81 45 0 1436 1436 679 126 3604 13860 0 -.0080000000000000002 80 320 -15 1310 -23 -2168 .0007664244765320839
5269535 0.5363 61 67 25 54 59 24 7 67 69 15 60 64 26 0 1.444 156 884 7 7 8 5 1.4502454261490432

Total number of rows: 16512

Table truncated, full table size 1915 Kbytes.




Supplementary data files not provided
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