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Sample GSM211579 Query DataSets for GSM211579
Status Public on Feb 29, 2008
Title mibm132 72h (AH_WT72hVsm13272h_BRI_TR3_40)
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 1.3450 31333 32010 8782 137 149 82 100 25396 25727 6505 136 136 28 100 1.245 120 723 31196 25260 31861 25591
5269517 1.3215 37777 38012 6767 137 150 120 100 31580 31083 7177 131 140 148 100 1.224 120 796 37640 31449 37862 30943
5269518 0.7071 602 609 213 133 139 69 94 879 852 212 125 127 28 100 .655 156 866 469 754 470 725
5269519 0.2577 776 809 200 129 136 74 100 2934 2979 392 129 149 201 100 .239 80 611 647 2805 673 2830
5269520 1.1256 721 746 209 130 164 158 95 676 644 161 53 74 108 95 1.042 80 620 591 623 582 570
5269521 0.9710 336 346 147 132 141 70 67 373 367 74 129 133 35 100 .899 120 703 204 244 205 234
5269522 1.3072 1109 1103 331 131 137 71 97 932 927 171 124 128 30 100 1.21 120 689 978 808 966 799
5269523 0.9191 369 389 166 126 137 73 76 416 434 84 125 128 35 100 .851 80 621 243 291 252 306
5269524 0.6595 360 369 137 129 141 78 70 503 518 108 125 133 68 100 .611 120 828 231 378 228 385
5269525 1.1573 481 511 179 122 133 67 95 486 484 104 121 123 25 100 1.072 120 689 359 365 378 361
5269526 0.9443 483 491 166 136 141 74 92 551 532 143 126 131 56 94 .874 120 720 347 425 350 401
5269527 1.1537 286 297 120 125 136 67 58 272 289 86 128 128 27 92 1.068 120 723 161 144 161 161
5269528 1.1042 2162 2181 487 132 144 83 100 2160 2138 353 134 135 30 100 1.022 80 590 2030 2026 2037 2003
5269529 1.2426 1398 1405 315 137 143 75 100 1279 1229 307 127 133 43 96 1.151 120 744 1261 1152 1262 1096
5269530 1.5512 1428 1437 419 127 136 70 99 1051 1038 211 126 127 28 99 1.436 156 768 1301 925 1301 911
5269531 0.8909 855 889 213 130 136 68 100 1039 1049 144 129 131 28 100 .825 80 612 725 910 753 918
5269532 0.7785 374 396 161 130 157 154 38 420 421 76 52 74 105 100 .721 80 630 244 368 239 347
5269533 0.7843 304 318 121 127 137 67 65 386 394 77 131 139 53 99 .726 120 666 177 255 181 255
5269534 0.8799 302 309 136 133 141 74 54 346 342 72 126 131 37 98 .815 120 684 169 220 168 211
5269535 0.1763 285 296 127 123 138 75 55 1183 1183 170 123 132 73 100 .163 80 622 162 1060 158 1051

Total number of rows: 16512

Table truncated, full table size 1562 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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