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Sample GSM211595 Query DataSets for GSM211595
Status Public on Feb 29, 2008
Title mibm132 48h (AH_WT48hVsm13248h_BRI_TR1_139)
Sample type RNA
 
Channel 1
Source name mib mutant embryos
Organism Danio rerio
Characteristics mib mutant embryos
Extracted molecule total RNA
Extraction protocol Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
Label Cy-5 d-UTP
Label protocol 20ug of total RNA was reverse transcribed to produce Cy-5 d-UTP (Sample) cDNA targets
 
Channel 2
Source name wild type embryos
Organism Danio rerio
Characteristics wild type siblings
Extracted molecule total RNA
Extraction protocol Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
Label Cy3 d-UTP
Label protocol 20ug of total RNA was reverse transcribed to produce Cy3 d-UTP (Reference) cDNA targets
 
 
Hybridization protocol Standard procedure (Mathavan et al., 2005)
Scan protocol GenePix 4000B microarray scanner (Axon Instruments)
Description RNA from mib mutant embryos and their wild type siblings at three different time points
Data processing The intensity-based log ratio median method (Yang et al./, 2003)
 
Submission date Jul 19, 2007
Last update date Oct 26, 2007
Contact name Govindarajan Kunde Ramamoorthy
E-mail(s) mathavans@gis.a-star.edu.sg
Phone +65-64788059
Fax +65-64789058
Organization name Genome Institute of Singapore
Department Research Computing Group
Street address 60, Biopolis Street, Genome
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE8522 RNA from 3 d and 2 d old embryos of mibta52b, mibm132 and mibtfi91, and RNA from 3 d, 2d and 1 d old embryos of mibta52b

Data table header descriptions
ID_REF Unique ID
VALUE Normalized log2 ratio of means defined by CH1/CH2
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

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
5269516 0.8398 23662 24270 8193 81 86 35 100 27604 26501 9431 100 104 29 100 .916 156 945 23581 27504 24184 26397
5269517 0.9728 39880 35495 12647 90 106 143 100 37439 33487 11153 129 181 897 93 1.061 156 944 39790 37310 35389 33306
5269518 0.5217 909 860 263 70 73 26 95 1553 1491 349 103 106 24 99 .569 156 922 839 1450 787 1385
5269519 0.8504 12867 12398 1869 86 91 37 100 14457 13409 3147 139 147 108 99 .928 120 793 12781 14318 12307 13262
5269520 1.2603 848 846 157 65 68 25 100 663 662 112 94 95 24 99 1.375 120 703 783 569 778 567
5269521 0.6151 157 166 52 64 69 31 80 244 252 64 100 106 33 93 .671 120 808 93 144 97 146
5269522 1.1409 1869 1846 447 66 88 142 95 1583 1527 369 97 118 125 95 1.245 120 724 1803 1486 1758 1409
5269523 0.7655 222 219 72 62 65 22 94 270 270 70 82 83 15 96 .835 120 730 160 188 154 187
5269524 1.0233 648 632 116 66 93 113 100 588 594 96 87 111 104 100 1.116 80 595 582 501 539 483
5269525 1.1680 666 667 143 63 67 31 100 585 554 137 80 83 30 98 1.274 120 778 603 505 600 471
5269526 0.9094 324 315 91 63 66 24 95 334 335 63 81 82 16 100 .992 120 822 261 253 249 253
5269527 0.9029 196 195 55 63 66 23 96 206 212 46 78 79 15 99 .985 120 822 133 128 129 133
5269528 0.7775 1052 1120 294 69 75 42 100 1233 1326 333 87 95 117 99 .848 120 725 983 1146 1045 1231
5269529 0.8968 1042 895 460 80 89 51 87 1107 955 426 122 131 48 92 .978 156 846 962 985 806 824
5269530 1.0187 1387 1348 307 71 74 26 100 1299 1254 333 105 107 27 96 1.111 156 786 1316 1194 1274 1147
5269531 1.4798 1526 1504 238 80 84 30 100 1080 1017 257 135 136 26 96 1.615 120 740 1446 945 1420 881
5269532 0.7110 141 149 54 66 69 25 70 203 204 45 97 98 22 93 .776 120 679 75 106 80 106
5269533 0.8465 204 208 58 63 72 80 35 249 255 55 98 113 113 11 .924 120 727 141 151 136 142
5269534 0.5070 186 193 56 63 68 27 95 317 328 69 93 99 35 100 .553 80 572 123 224 125 229
5269535 0.7264 139 145 56 61 64 23 72 189 190 51 84 85 15 93 .792 120 692 78 105 81 105

Total number of rows: 16512

Table truncated, full table size 1497 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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