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Sample GSM211578 Query DataSets for GSM211578
Status Public on Feb 29, 2008
Title mibm132 72h (AH_WT72hVsm13272h_BRI_TR2_39)
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 1.7955 52720 48920 10150 131 145 107 100 33574 31484 6252 107 112 89 100 1.555 120 813 52589 33467 48775 31372
5269517 1.5562 49543 46841 11225 130 269 1876 98 35291 34761 4994 100 149 850 100 1.348 120 840 49413 35191 46572 34612
5269518 0.6925 580 572 191 124 132 72 95 872 843 194 96 99 36 100 .6 120 778 456 776 440 744
5269519 0.3073 956 984 264 123 152 137 98 3281 3330 567 95 178 517 100 .266 80 612 833 3186 832 3152
5269520 1.2374 710 720 243 121 136 85 95 659 655 171 96 102 46 96 1.072 120 748 589 563 584 553
5269521 0.8496 260 268 110 126 134 75 41 287 291 59 98 101 31 100 .736 120 822 134 189 134 190
5269522 0.9266 817 842 290 119 139 131 98 1021 999 274 98 110 115 95 .802 120 740 698 923 703 889
5269523 0.8991 317 327 128 123 141 81 57 361 356 63 94 98 38 100 .779 80 628 194 267 186 258
5269524 0.6176 334 351 146 121 136 80 62 523 522 119 92 101 81 99 .535 120 823 213 431 215 421
5269525 1.0296 432 443 167 122 135 73 84 446 457 102 97 99 22 100 .892 120 735 310 349 308 358
5269526 0.9211 446 460 178 121 129 70 85 526 523 125 98 99 21 100 .798 120 703 325 428 331 424
5269527 0.9975 279 295 138 130 138 73 50 273 288 82 97 102 31 97 .864 80 620 149 176 157 186
5269528 1.3748 2737 2710 582 130 158 187 100 2281 2273 462 106 140 243 98 1.191 80 590 2607 2175 2552 2133
5269529 1.4207 1680 1689 455 129 278 1917 0 1411 1366 397 98 155 870 6 1.23 120 804 1551 1313 1411 1211
5269530 1.2146 1225 1280 351 123 132 71 100 1181 1194 174 94 97 25 100 1.052 120 741 1102 1087 1148 1097
5269531 0.8426 831 849 205 120 136 83 100 1129 1093 244 94 101 71 100 .73 80 615 711 1035 713 992
5269532 0.9990 314 312 136 126 138 83 55 310 313 71 98 113 96 65 .865 120 715 188 212 174 200
5269533 0.7680 256 268 110 129 139 75 40 285 308 142 99 104 39 100 .665 120 770 127 186 129 204
5269534 1.0421 256 277 122 129 137 75 42 259 262 56 98 107 67 66 .902 80 601 127 161 140 155
5269535 0.1367 250 256 143 117 132 76 42 1316 1268 396 94 97 37 97 .118 120 738 133 1222 124 1171

Total number of rows: 16512

Table truncated, full table size 1543 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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