NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM80312 Query DataSets for GSM80312
Status Public on Oct 28, 2005
Title ZFL C4-
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 1.0198 9987 8603 3138 135 148 77 100 4382 3849 1334 100 107 37 98 2.2589999999999999 120 763 9852 4282 8455 3742 2.0275903616188726
5269517 1.0709 10907 10265 2296 66 73 30 100 4709 4429 1031 71 74 19 100 2.3399999999999999 120 751 10841 4638 10192 4355 2.1008022555765282
5269518 0.0809 164 171 50 52 55 17 98 162 165 37 64 66 15 98 1.1779999999999999 120 770 112 98 116 99 1.0576461595890285
5269519 0.4566 168 185 73 52 55 18 92 140 151 49 64 66 15 90 1.5289999999999999 120 759 116 76 130 85 1.3722941042943515
5269520 0.6032 806 794 153 68 74 28 100 503 509 96 80 84 25 100 1.6919999999999999 80 637 738 423 720 425 1.5191271923767431
5269521 0.2228 137 143 46 65 71 27 70 141 146 34 86 91 27 50 1.3 120 872 72 55 72 55 1.1669658886894072
5269522 0.4391 276 270 105 51 54 18 98 216 220 86 75 79 23 89 1.51 120 762 225 141 216 141 1.3557853030396827
5269523 -0.1482 242 249 86 58 62 21 98 248 261 73 71 73 18 100 1.0049999999999999 156 1076 184 177 187 188 .90239062647642421
5269524 0.7418 294 295 77 64 70 28 100 193 195 49 71 74 21 95 1.863 80 560 230 122 225 121 1.6722650141889148
5269525 -0.8303 108 115 42 63 69 25 42 143 157 86 74 77 19 77 .627 80 548 45 69 46 80 .56239319936838905
5269526 0.4862 524 528 149 63 67 24 99 375 373 104 75 80 25 96 1.5600000000000001 156 977 461 300 461 293 1.4007205426963716
5269527 0.1904 142 140 45 65 69 25 68 131 134 40 75 79 22 57 1.2709999999999999 80 616 77 56 71 55 1.1411009341812979
5269528 0.1999 251 252 68 133 145 76 28 181 192 39 99 107 36 65 1.28 32 220 118 82 107 85 1.148626474392386
5269529 0.5082 168 183 71 61 67 29 86 139 145 42 68 73 21 75 1.5840000000000001 80 614 107 71 116 72 1.422276108092984
5269530 0.0863 970 966 177 53 58 21 100 828 838 131 66 69 20 100 1.1830000000000001 120 711 917 762 908 769 1.0616180314601722
5269531 0.2375 338 336 96 51 53 17 99 287 283 85 66 67 14 95 1.3129999999999999 120 736 287 221 283 216 1.1789623476656543
5269532 0.8558 1204 1190 166 61 65 24 100 656 636 123 76 80 23 100 2.016 80 639 1143 580 1125 556 1.8097589125416771
5269533 0.1876 143 151 57 66 72 29 60 148 153 48 86 90 23 60 1.2689999999999999 80 540 77 62 79 63 1.1388300865510863
5269534 0.1392 162 171 48 52 54 17 97 180 182 43 85 106 73 12 1.2270000000000001 80 612 110 95 117 76 1.1012604342112566
5269535 0.2936 127 130 50 59 64 24 64 123 126 33 74 77 20 63 1.365 120 732 68 49 66 49 1.2256594393039633

Total number of rows: 16512

Table truncated, full table size 1919 Kbytes.




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