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Sample GSM80309 Query DataSets for GSM80309
Status Public on Oct 28, 2005
Title ZFL C1-
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 2.0296 5471 5360 599 48 52 25 100 1247 1263 153 65 67 20 100 4.4340000000000002 120 836 5423 1182 5308 1196 4.082925194538471
5269517 2.0789 7441 7536 1130 48 75 305 100 1711 1696 258 64 71 74 100 4.5880000000000001 120 823 7393 1647 7461 1625 4.224894377640557
5269518 0.8229 112 120 42 47 49 15 85 96 101 32 63 65 19 42 1.921 156 960 65 33 71 36 1.7689250751187351
5269519 -0.0080 98 101 40 47 49 14 69 111 114 34 64 66 19 59 1.0800000000000001 208 1147 51 47 52 48 .99447513812154653
5269520 1.0133 437 436 98 48 50 21 100 235 242 59 65 68 21 100 2.1920000000000002 156 956 389 170 386 174 2.0184994433519563
5269521 0.3805 82 88 30 47 49 15 56 88 94 31 65 67 20 27 1.4139999999999999 80 552 35 23 39 27 1.3018352702101981
5269522 0.5466 90 94 36 48 50 14 63 87 91 29 62 64 19 36 1.5860000000000001 80 632 42 25 44 27 1.46059566901632
5269523 0.5784 173 171 53 51 57 23 92 136 142 45 68 72 26 64 1.6220000000000001 256 1597 122 68 114 70 1.4932059130954152
5269524 0.8435 258 276 114 48 50 15 100 169 182 63 65 66 18 95 1.9490000000000001 120 820 210 104 226 116 1.7943995844548322
5269525 1.3029 209 257 149 48 51 15 97 141 143 46 65 67 17 82 2.6789999999999998 120 730 161 76 206 76 2.467299428625394
5269526 1.4748 375 383 78 57 62 26 100 169 174 47 66 68 19 96 3.0190000000000001 156 1033 318 103 321 106 2.7794829820612494
5269527 1.4586 228 246 96 49 51 16 100 121 131 49 65 67 18 68 2.9849999999999999 80 596 179 56 195 64 2.748479267816283
5269528 1.3653 290 311 99 48 53 28 100 149 157 45 63 66 21 91 2.798 120 767 242 86 258 91 2.576309705732533
5269529 0.6445 117 121 43 48 49 14 88 100 106 29 63 65 18 51 1.698 120 790 69 37 72 41 1.5632361128956263
5269530 0.8260 539 535 109 46 48 13 100 317 318 72 64 66 18 99 1.925 156 842 493 253 487 252 1.7727411145430017
5269531 0.1123 183 182 52 47 51 24 96 177 180 53 65 70 33 82 1.1739999999999999 208 984 136 112 131 110 1.0809512370886376
5269532 1.5347 683 692 132 47 49 14 100 268 269 68 64 66 18 98 3.1459999999999999 156 892 636 204 643 203 2.8971836679692751
5269533 -0.0035 67 74 31 48 50 14 36 79 85 27 61 65 19 21 1.083 80 530 19 18 24 20 .9975445058317981
5269534 0.2289 106 106 31 50 52 16 75 104 108 35 64 68 20 49 1.2729999999999999 120 808 56 40 54 40 1.171940398459735
5269535 0.5117 92 97 36 49 53 17 58 93 96 31 65 68 19 35 1.548 156 759 43 28 44 28 1.4257708073427189

Total number of rows: 16512

Table truncated, full table size 1902 Kbytes.




Supplementary data files not provided
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