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Sample GSM80328 Query DataSets for GSM80328
Status Public on Oct 28, 2005
Title ZFL T9+
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 1.3405 7907 7455 1615 64 155 676 98 3066 2868 728 59 92 251 97 2.6309999999999998 120 762 7843 3007 7300 2776 2.5324210541463903
5269517 1.3392 377 2873 3345 68 83 49 84 140 1125 1303 58 62 16 81 2.629 316 1862 309 82 2790 1063 2.530188623081274
5269518 -0.1414 121 120 34 55 58 19 79 122 123 26 54 55 10 97 .94199999999999995 120 759 66 68 62 68 .90666889846703225
5269519 -0.3317 113 126 46 55 58 19 78 136 141 45 55 57 19 90 .82599999999999996 80 635 58 81 68 84 .79459229581216295
5269520 0.8530 600 594 207 61 101 453 3 347 341 94 57 69 138 58 1.877 156 940 539 290 493 272 1.8063143054670665
5269521 -0.3130 99 104 38 58 61 21 48 108 110 21 55 57 19 77 .83599999999999997 80 645 41 53 43 53 .80496981363198883
5269522 -0.1021 178 178 61 57 64 51 63 194 191 47 66 78 56 60 .96799999999999997 120 745 121 128 114 113 .93166506256015413
5269523 -0.1850 130 140 54 55 58 21 79 143 146 29 53 55 15 100 .91400000000000003 156 1027 75 90 82 91 .87967131340101634
5269524 0.0658 131 142 53 55 60 38 49 134 133 28 53 54 18 95 1.087 120 719 76 81 82 79 1.046679499518768
5269525 -0.1096 108 112 40 60 64 25 46 114 112 27 58 60 14 82 .96299999999999997 120 735 48 56 48 52 .92681709621074404
5269526 -0.0002 271 271 81 57 59 20 99 261 259 57 53 55 21 98 1.0389999999999999 156 1042 214 208 212 204 .99984114673369662
5269527 -0.4178 83 91 32 56 59 19 36 95 100 23 55 55 11 85 .77800000000000002 80 608 27 40 32 45 .74858303924713943
5269528 -0.0207 177 193 74 66 84 119 8 182 184 46 60 65 34 87 1.024 80 535 111 122 109 119 .98574932472290366
5269529 -0.0552 121 122 37 66 74 35 30 110 112 30 56 58 13 82 1 80 570 55 54 48 54 .96246390760346501
5269530 -0.3062 515 518 119 55 58 20 100 616 605 99 54 54 10 100 .83999999999999997 120 788 460 562 460 551 .80874916373939076
5269531 -0.3447 160 164 53 56 59 20 90 185 185 36 53 54 16 100 .81799999999999995 80 623 104 132 105 131 .78747046985738056
5269532 2.1628 1926 1799 526 59 62 22 98 454 430 124 56 56 10 96 4.6520000000000001 156 954 1867 398 1737 374 4.4777732599733397
5269533 0.0341 96 106 43 56 59 20 47 103 103 22 56 57 11 88 1.0640000000000001 80 636 40 47 47 46 1.0238977740462394
5269534 0.8662 176 184 64 59 64 30 83 138 136 31 70 116 122 0 1.8939999999999999 120 716 117 68 120 20 1.8228483098550474
5269535 0.1672 57 60 19 53 58 23 2 57 59 11 53 57 22 0 1.167 156 872 4 4 2 2 1.1228745588707092

Total number of rows: 16512

Table truncated, full table size 1904 Kbytes.




Supplementary data files not provided
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