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Sample GSM211613 Query DataSets for GSM211613
Status Public on Feb 29, 2008
Title mibm132 48h (AH_WT48hVsm13248h_BRII_TR2_167)
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 0.9366 28075 25613 9576 250 251 77 100 31124 36832 19670 139 140 23 100 .691 32 140 27825 30985 25362 36692
5269517 0.8843 30341 30546 3286 237 238 70 100 46015 46575 15211 134 141 50 100 .653 32 193 30104 45881 30308 46434
5269518 0.5209 965 1022 437 227 235 74 94 1880 2199 1131 131 143 86 96 .384 52 195 738 1749 787 2056
5269519 1.1042 24766 24879 6143 222 228 67 100 30978 30397 5405 138 140 28 100 .815 32 154 24544 30840 24651 30257
5269520 1.5032 845 898 281 208 217 64 96 702 757 269 135 137 25 100 1.109 32 154 637 567 681 620
5269521 0.6552 361 377 123 230 232 59 56 407 440 186 136 137 19 100 .484 32 123 131 271 145 303
5269522 1.3431 1489 1468 427 224 224 60 100 1151 1388 569 133 135 19 100 .991 32 176 1265 1018 1244 1253
5269523 0.7773 470 476 169 215 219 65 75 568 592 232 137 138 20 100 .574 32 154 255 431 257 454
5269524 1.0851 1034 1005 251 201 209 63 100 1121 1141 393 137 139 19 100 .801 32 134 833 984 796 1002
5269525 1.0722 693 784 286 219 222 61 100 770 852 270 138 142 46 100 .791 32 192 474 632 562 710
5269526 0.8717 731 729 266 224 223 63 87 884 928 331 143 143 19 100 .643 32 140 507 741 506 785
5269527 0.9937 345 366 114 212 225 72 37 337 348 70 138 138 18 100 .733 32 185 133 199 141 210
5269528 1.0397 1262 1357 571 249 244 64 96 1385 1581 904 137 135 21 100 .767 32 122 1013 1248 1113 1446
5269529 1.0976 684 708 176 239 241 63 96 632 710 226 131 130 16 100 .81 32 113 445 501 467 580
5269530 0.6332 1459 1383 272 241 258 166 100 2648 2580 856 136 236 812 71 .467 32 111 1218 2512 1125 2344
5269531 1.5429 3381 3226 885 221 226 67 100 2883 2771 668 132 133 22 100 1.139 32 131 3160 2751 3000 2638
5269532 0.6909 492 470 112 213 218 55 83 671 641 171 137 142 32 100 .51 12 85 279 534 252 499
5269533 1.1820 430 422 103 258 264 82 58 337 341 86 153 191 77 66 .872 12 54 172 184 158 150
5269534 0.6301 352 368 96 215 224 63 56 425 466 187 137 138 20 100 .465 32 107 137 288 144 328
5269535 1.0824 351 344 91 213 216 61 53 280 302 76 138 140 21 100 .799 32 144 138 142 128 162

Total number of rows: 16512

Table truncated, full table size 1568 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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