NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM80314 Query DataSets for GSM80314
Status Public on Oct 28, 2005
Title ZFL C6-
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 1.4602 3770 3589 647 63 69 93 100 1328 1266 309 65 70 54 98 2.9359999999999999 80 643 3707 1263 3520 1196 2.7515339840979127
5269517 1.5348 4272 4282 755 65 73 31 100 1449 1432 281 68 70 16 100 3.0920000000000001 120 735 4207 1381 4209 1362 2.8975091178434891
5269518 -0.4588 100 103 25 44 44 10 95 129 132 32 56 56 10 97 .77600000000000002 120 756 56 73 59 76 .72756868741676106
5269519 0.2456 146 147 39 42 45 20 97 135 137 40 54 57 19 88 1.2649999999999999 120 758 104 81 102 80 1.1856234685696863
5269520 1.3061 651 641 151 50 52 12 99 284 281 66 57 58 11 97 2.6379999999999999 120 721 601 227 589 223 2.4727205783906814
5269521 -0.3317 81 81 16 42 42 10 85 99 98 21 52 54 12 87 .84799999999999998 80 622 39 47 39 44 .79458864756937364
5269522 2.8699 124 123 51 45 46 11 80 170 186 79 176 323 289 0 7.7999999999999998 156 1053 79 -6 77 -137 7.3102155576382373
5269523 -0.2862 146 151 35 46 47 10 100 173 178 36 58 58 12 100 .875 208 1319 100 115 104 120 .82005623242736636
5269524 -0.0425 160 164 39 49 50 13 100 167 170 30 59 60 11 100 1.036 80 619 111 108 114 110 .97098035242365133
5269525 -0.7854 85 84 20 58 59 14 45 104 107 24 65 65 13 71 .61899999999999999 80 532 27 39 25 42 .58017583790779659
5269526 0.1172 252 253 49 47 48 11 99 238 237 53 59 60 11 97 1.157 156 959 205 179 205 177 1.0846329623116371
5269527 -0.2862 103 101 24 45 46 9 91 120 121 27 57 58 11 93 .875 80 600 58 63 55 63 .82005623242736636
5269528 0.5335 191 201 44 62 64 19 100 155 155 37 65 67 15 97 1.544 80 540 129 90 137 88 1.4474643340622722
5269529 -0.1409 78 81 31 51 58 24 23 86 94 31 63 65 14 45 .96799999999999997 156 945 27 23 23 29 .90697463494270936
5269530 0.1842 767 754 118 46 47 12 100 653 643 102 59 60 12 100 1.212 120 696 721 594 707 583 1.1362031556919283
5269531 -0.0019 235 239 36 44 47 23 100 238 239 35 56 58 20 100 1.0660000000000001 80 612 191 182 192 181 .99866332754620735
5269532 2.5251 1973 1907 336 46 48 16 100 361 358 82 55 56 11 97 6.1420000000000003 120 697 1927 306 1859 302 5.756245727665549
5269533 -0.0936 80 81 20 44 45 10 77 94 94 19 57 57 10 77 1 80 606 36 37 36 37 .93720712277413298
5269534 4.2988 91 89 33 47 48 12 67 116 169 133 167 625 859 0 21 156 911 44 -51 41 -456 19.681349578256793
5269535 -0.1275 89 89 23 47 48 10 81 104 102 24 59 60 12 75 .97699999999999998 120 628 42 45 41 42 .91541160829101353

Total number of rows: 16512

Table truncated, full table size 1905 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap