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Sample GSM80315 Query DataSets for GSM80315
Status Public on Oct 28, 2005
Title ZFL C7-
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 1.3858 6490 6226 1356 79 95 132 97 2430 2328 526 77 82 55 97 2.7309999999999999 120 768 6411 2353 6131 2246 2.6131926480309646
5269517 1.1738 6673 6366 1181 123 151 250 99 2868 2752 586 104 114 109 98 2.3580000000000001 120 766 6550 2764 6215 2638 2.2561037309009953
5269518 0.1253 167 168 49 62 63 18 95 165 166 34 73 74 14 95 1.1399999999999999 120 731 105 92 105 92 1.0907032978340276
5269519 -0.1589 177 183 47 66 68 22 96 212 209 45 84 85 15 97 .93600000000000005 120 706 111 128 115 124 .8956937799043061
5269520 1.2177 837 827 213 76 94 189 94 408 398 98 89 93 34 97 2.4300000000000002 156 1055 761 319 733 305 2.3257614468651768
5269521 -0.0430 135 138 37 67 68 20 77 153 155 34 85 87 16 90 1.014 80 643 68 68 70 68 .97060833902939136
5269522 -0.1204 266 264 67 65 70 46 96 302 310 66 103 107 38 98 .96099999999999997 120 770 201 199 194 203 .9199546956984026
5269523 0.5475 312 324 73 72 80 39 99 259 257 53 92 96 28 98 1.5269999999999999 156 1062 240 167 244 161 1.4615050021748583
5269524 -0.4144 167 163 38 94 99 34 53 186 192 37 104 107 24 86 .78400000000000003 80 635 73 82 64 85 .75032622879512811
5269525 -0.2642 155 150 38 83 91 40 31 181 179 32 102 109 36 56 .87 32 236 72 79 59 70 .83266016280370325
5269526 0.9044 617 642 126 65 68 20 100 373 376 68 81 83 17 100 1.956 156 993 552 292 574 293 1.8717054577893111
5269527 -0.5565 81 83 31 56 58 19 30 93 98 26 60 63 18 46 .71099999999999997 52 332 25 33 25 35 .67992948879375459
5269528 0.6089 233 228 53 75 89 107 10 173 172 39 76 82 46 52 1.5940000000000001 80 612 158 97 139 90 1.52511961722488
5269529 -0.0255 177 179 54 102 113 49 32 177 175 45 100 104 27 67 1.0269999999999999 80 530 75 77 66 71 .98245614035087692
5269530 0.9685 1542 1521 204 63 68 28 100 809 787 148 74 78 23 99 2.0449999999999999 120 789 1479 735 1453 709 1.9568237180992769
5269531 0.0006 288 297 73 67 69 21 100 304 306 58 86 87 15 100 1.0449999999999999 120 665 221 218 228 219 1.0004349717268375
5269532 3.0080 3595 3573 294 76 104 250 100 501 507 65 91 96 40 100 8.4060000000000006 120 756 3519 410 3469 411 8.0442583732057393
5269533 -0.4131 122 128 42 66 68 20 66 166 167 38 88 89 16 92 .78500000000000003 80 626 56 78 60 78 .7510144751983524
5269534 -0.4355 129 129 31 78 85 32 21 165 182 54 116 120 26 46 .77300000000000002 32 170 51 49 44 62 .73945193562418421
5269535 -0.6485 83 88 28 76 85 39 1 109 112 23 94 102 31 4 .66700000000000004 156 995 7 15 3 10 .63795853269537461

Total number of rows: 16512

Table truncated, full table size 1940 Kbytes.




Supplementary data files not provided
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