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Sample GSM80326 Query DataSets for GSM80326
Status Public on Oct 28, 2005
Title ZFL T7+
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 2.4967 15603 15415 1746 78 89 45 100 2724 2709 449 96 100 41 100 5.8689999999999998 80 650 15525 2628 15326 2609 5.6437487120609937
5269517 2.2558 22490 20526 6343 96 109 54 100 4443 4217 1344 104 109 37 100 4.9669999999999996 120 768 22394 4339 20417 4108 4.7761319643157689
5269518 0.0937 375 358 127 75 78 21 96 297 299 121 44 47 16 95 1.1100000000000001 120 768 300 253 280 252 1.067119155354449
5269519 0.8439 604 607 118 75 86 43 100 369 381 110 96 100 34 98 1.867 80 650 529 273 521 281 1.7948717948717938
5269520 0.6280 1267 1282 186 75 85 43 100 844 853 147 102 105 37 100 1.607 80 644 1192 742 1197 748 1.5453753969066877
5269521 0.1774 267 259 75 72 84 42 87 269 268 88 109 113 49 71 1.1759999999999999 32 176 195 160 175 155 1.1308659893565547
5269522 -0.6283 329 320 117 65 69 21 92 426 437 184 58 73 56 90 .67300000000000004 80 646 264 368 251 364 .64694540288207802
5269523 -0.7654 253 267 72 81 84 21 100 343 355 94 51 62 37 100 .61199999999999999 80 638 172 292 183 293 .58830971659918996
5269524 1.0964 561 570 116 63 71 35 100 330 326 80 98 102 37 98 2.2240000000000002 80 650 498 232 499 224 2.1381578947368411
5269525 0.1414 242 258 102 63 70 33 93 241 264 97 94 99 34 90 1.147 80 554 179 147 188 165 1.1029411764705876
5269526 -0.0789 637 637 109 59 66 29 100 674 676 134 89 94 34 100 .98499999999999999 80 646 578 585 571 582 .94679596383173847
5269527 -0.9137 156 167 75 45 47 14 87 245 263 123 42 46 20 97 .55200000000000005 80 650 111 203 120 217 .53080403759136763
5269528 0.9117 416 436 118 76 85 39 100 266 278 104 94 97 33 87 1.9570000000000001 80 633 340 172 351 181 1.8812709030100325
5269529 1.5965 678 706 241 77 89 45 98 298 302 109 102 107 36 91 3.145 120 720 601 196 617 195 3.0240384615384599
5269530 0.2842 757 750 195 75 78 21 100 592 576 200 43 48 19 95 1.266 120 723 682 549 672 528 1.2177081829989891
5269531 0.0083 523 531 99 76 89 47 100 515 529 114 94 98 33 100 1.046 80 632 447 421 442 431 1.005747126436781
5269532 1.8900 1841 1886 246 82 93 46 100 579 573 124 105 108 36 100 3.855 80 632 1759 474 1793 465 3.7064431295200508
5269533 0.0347 660 642 230 71 82 48 100 652 641 196 105 109 40 100 1.0649999999999999 80 638 589 547 560 532 1.0243254879448904
5269534 0.1042 313 317 89 61 64 23 98 255 284 113 55 65 42 92 1.1180000000000001 80 640 252 200 253 219 1.074907625125965
5269535 -0.9046 186 200 75 85 87 25 78 244 256 101 49 58 35 93 .55600000000000005 80 625 101 195 113 198 .53418803418803396

Total number of rows: 16512

Table truncated, full table size 2051 Kbytes.




Supplementary data files not provided
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