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Sample GSM80310 Query DataSets for GSM80310
Status Public on Oct 28, 2005
Title ZFL C2-
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 1.9817 2465 2506 450 43 46 14 100 625 643 144 58 60 20 100 4.21 120 746 2422 567 2460 583 3.9495838745369682
5269517 1.5976 4048 4035 643 141 142 34 100 1286 1276 288 69 72 25 100 3.226 120 821 3907 1217 3893 1204 3.0264358471766459
5269518 0.4454 180 183 38 48 49 14 100 147 153 49 60 64 25 77 1.452 120 806 132 87 134 89 1.3617381831386546
5269519 0.2639 243 244 53 52 55 16 99 211 212 73 62 65 25 90 1.28 120 746 191 149 189 147 1.2007504690431514
5269520 1.2067 767 763 97 47 50 17 100 351 353 74 62 64 23 100 2.46 80 608 720 289 713 289 2.3081436206907657
5269521 -0.1217 145 147 34 50 52 16 97 162 166 50 67 70 26 83 .97999999999999998 80 637 95 95 95 96 .91913506547652835
5269522 -0.1048 504 509 74 52 54 16 100 534 538 129 77 81 30 100 .99099999999999999 120 836 452 457 455 457 .92994672646542875
5269523 -0.1576 368 357 71 55 57 18 98 390 383 105 67 70 24 97 .95599999999999996 120 755 313 323 300 313 .89652551832236871
5269524 -0.0390 195 195 47 57 61 19 96 201 204 69 71 77 32 85 1.038 120 758 138 130 134 127 .97335270634371995
5269525 -0.2578 120 128 35 54 57 16 88 142 147 45 64 67 25 75 .89200000000000002 80 636 66 78 71 80 .83636610230791786
5269526 1.0996 813 792 153 61 66 51 100 401 399 119 79 87 72 92 2.2839999999999998 120 755 752 322 726 312 2.1429409005628504
5269527 -0.1536 118 122 33 53 56 16 85 134 138 41 66 71 32 51 .95799999999999996 80 538 65 68 66 67 .89899937460913026
5269528 0.7249 147 152 41 41 43 11 99 117 120 43 57 59 21 68 1.762 120 704 106 60 109 61 1.6528187259894567
5269529 0.9510 361 369 68 132 136 39 100 187 186 55 71 74 34 78 2.0609999999999999 120 720 229 116 233 112 1.933273513337139
5269530 0.5941 324 328 70 48 50 14 99 229 234 72 60 63 25 96 1.609 156 877 276 169 278 171 1.5095641672597089
5269531 0.1664 371 379 71 50 53 16 100 332 339 105 64 68 27 96 1.196 120 728 321 268 326 271 1.1222923418045363
5269532 1.2597 693 679 145 46 49 15 99 314 311 78 63 66 26 99 2.552 120 748 647 251 630 245 2.3943896386854671
5269533 -0.4507 195 204 79 48 51 16 96 273 265 91 65 67 25 95 .78000000000000003 120 730 147 208 153 198 .73170731707317038
5269534 0.1791 192 192 46 52 55 17 100 198 202 58 86 98 51 58 1.2070000000000001 120 787 140 112 137 104 1.1321731254447815
5269535 0.2155 204 204 65 53 56 20 97 186 190 71 68 72 28 80 1.238 120 721 151 118 148 118 1.1610740319256905

Total number of rows: 16512

Table truncated, full table size 1928 Kbytes.




Supplementary data files not provided

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