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Sample GSM80318 Query DataSets for GSM80318
Status Public on Oct 28, 2005
Title ZFL T1+
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 2.2177 18033 18029 2111 48 60 34 100 3584 3562 412 70 73 22 100 5.149 120 734 17985 3514 17969 3489 4.6514888592948553
5269517 2.4417 23228 22788 2114 49 67 40 100 3899 3851 428 70 73 23 100 6.0140000000000002 156 974 23179 3829 22721 3778 5.4327167621495489
5269518 -0.4720 211 209 48 39 41 11 99 284 284 76 71 73 23 98 .79800000000000004 156 930 172 213 168 211 .7209774758154468
5269519 -0.5026 231 231 42 38 42 25 99 302 318 88 71 78 54 97 .78100000000000003 208 1260 193 231 189 240 .70585051329595627
5269520 -0.4679 483 487 69 38 40 16 100 646 632 130 71 74 27 100 .80000000000000004 120 836 445 575 447 558 .72299594059517547
5269521 -0.8312 90 93 26 37 37 8 95 154 158 48 68 70 21 83 .622 156 963 53 86 56 88 .56207969487102283
5269522 -0.4480 304 292 77 38 39 11 98 396 387 131 74 82 34 95 .81200000000000006 156 981 266 322 253 305 .73306377366223086
5269523 0.1404 428 425 64 37 39 9 100 389 386 91 68 71 23 99 1.22 256 1427 391 321 386 315 1.1021913154142025
5269524 -0.1404 266 269 50 39 43 20 100 299 298 71 69 73 27 99 1.004 120 838 227 230 226 225 .9072870932493895
5269525 -0.4136 220 220 40 38 52 76 77 283 287 76 68 94 177 3 .83099999999999996 156 1042 182 215 168 193 .75072288013595512
5269526 -0.6071 298 286 73 36 37 8 100 406 410 105 66 69 21 99 .72699999999999998 156 980 262 340 249 341 .65649881305014601
5269527 -0.1838 147 151 34 36 37 8 100 174 182 52 64 66 20 96 .97499999999999998 120 822 111 110 114 116 .88037603539877207
5269528 1.1061 945 975 212 48 54 26 100 448 461 102 72 74 27 100 2.383 120 783 897 376 921 387 2.1526950488013878
5269529 0.9334 354 354 60 39 43 16 100 207 217 67 68 71 21 98 2.1139999999999999 156 840 315 139 311 146 1.9097506411305725
5269530 -0.6068 1031 977 254 40 44 15 98 1391 1361 275 72 74 24 100 .72699999999999998 156 838 991 1319 933 1287 .65665771734003875
5269531 -0.8367 308 307 49 38 44 33 100 499 506 113 72 84 82 99 .62 208 966 270 427 263 422 .55990575266735776
5269532 3.5018 8279 7726 1801 39 42 17 100 699 677 188 64 68 34 98 12.539999999999999 156 893 8240 635 7684 609 11.32788380629864
5269533 -0.4278 116 117 28 38 40 12 96 158 163 51 67 70 21 87 .82299999999999995 156 857 78 91 77 93 .74337548931044872
5269534 2.7542 1010 994 161 38 40 13 100 209 207 61 79 122 119 4 7.4690000000000003 120 770 972 130 954 85 6.7468383017163509
5269535 -0.1991 201 200 39 38 42 23 100 234 238 63 70 77 48 88 .96399999999999997 256 962 163 164 158 161 .87108013937282236

Total number of rows: 16512

Table truncated, full table size 2001 Kbytes.




Supplementary data files not provided
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