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Sample GSM80319 Query DataSets for GSM80319
Status Public on Oct 28, 2005
Title ZFL C10-
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 0.8042 4199 3988 1149 63 97 293 97 2277 2166 546 75 93 163 97 1.877 120 774 4136 2202 3891 2073 1.7461323724044358
5269517 1.0372 7681 7590 1244 65 266 1093 100 3592 3482 612 71 171 544 100 2.206 80 631 7616 3521 7324 3311 2.0521841102316039
5269518 -0.3079 114 121 39 55 58 20 71 136 140 38 64 66 12 95 .86799999999999999 120 840 59 72 63 74 .80783353733170149
5269519 -0.3906 131 136 40 54 57 20 82 161 165 42 65 67 14 97 .81999999999999995 80 544 77 96 79 98 .76279069767441865
5269520 0.3707 516 498 174 56 59 22 96 394 387 120 69 71 21 96 1.3899999999999999 156 1018 460 325 439 316 1.2929647506216178
5269521 -0.1559 109 111 37 56 60 21 56 121 128 34 71 72 16 77 .96499999999999997 80 600 53 50 51 56 .89759281925744605
5269522 -0.0203 212 219 62 60 64 28 96 217 226 51 76 80 23 100 1.0600000000000001 80 608 152 141 155 146 .98604651162790713
5269523 -0.3607 163 164 55 56 59 24 85 188 196 51 67 70 20 98 .83699999999999997 156 926 107 121 105 126 .77879935100054098
5269524 -0.4771 127 134 46 56 58 19 82 164 168 45 67 68 13 97 .77200000000000002 120 700 71 97 76 100 .71839742113746263
5269525 -0.5486 119 125 44 64 83 372 0 158 157 39 74 88 237 0 .73499999999999999 80 618 55 84 42 69 .68366489212664627
5269526 0.3362 325 322 98 56 58 19 99 263 262 78 66 68 24 96 1.357 156 943 269 197 264 194 1.2624584717607976
5269527 -0.1360 95 103 43 58 60 19 48 109 114 33 68 70 16 60 .97799999999999998 120 730 37 41 43 44 .9100101112234581
5269528 -0.0112 158 169 60 57 65 43 61 175 177 53 72 82 62 33 1.0669999999999999 80 614 101 103 104 95 .99224806201550397
5269529 0.0067 131 139 51 58 61 21 77 134 141 43 66 68 13 87 1.0800000000000001 80 623 73 68 78 73 1.0046511627906978
5269530 0.5944 1023 1025 212 56 60 29 100 680 663 132 66 67 14 100 1.623 120 808 967 614 965 596 1.5098749561762301
5269531 0.1057 198 209 76 54 57 20 97 195 200 50 66 67 13 100 1.157 80 608 144 129 152 133 1.0760152724748351
5269532 0.6219 696 684 196 57 60 20 96 461 449 116 70 71 13 97 1.6539999999999999 156 876 639 391 624 378 1.5389335460514206
5269533 -0.0519 107 114 45 58 61 23 52 122 127 36 73 75 15 70 1.0369999999999999 80 621 49 49 53 52 .96468561584840662
5269534 -0.4696 108 117 43 58 62 24 51 154 156 41 80 619 5404 0 .77600000000000002 120 860 50 74 55 -463 .72215422276621788
5269535 -0.0801 110 117 42 57 61 26 50 129 127 34 68 74 28 55 1.0169999999999999 120 704 53 61 56 53 .9459992116673237

Total number of rows: 16512

Table truncated, full table size 1919 Kbytes.




Supplementary data files not provided
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