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Sample GSM211596 Query DataSets for GSM211596
Status Public on Feb 29, 2008
Title mibm132 48h (AH_WT48hVsm13248h_BRI_TR2_140)
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 0.9725 23796 23380 6464 288 305 190 100 23806 23482 6080 518 534 109 100 1.006 120 734 23508 23288 23075 22948
5269517 0.9375 19047 19080 2951 190 244 525 100 20036 19727 3723 241 342 1182 100 .969 120 794 18857 19795 18836 19385
5269518 0.8975 1172 1213 409 182 191 96 100 1468 1399 367 288 294 65 96 .928 156 894 990 1180 1022 1105
5269519 0.9595 3232 3114 695 222 239 133 100 3225 3232 901 317 331 111 98 .992 120 806 3010 2908 2875 2901
5269520 1.0090 3380 3444 766 170 188 126 100 3470 3406 840 268 282 146 99 1.043 120 704 3210 3202 3256 3124
5269521 0.9408 664 679 238 179 188 96 91 709 742 210 228 240 73 98 .973 120 774 485 481 491 502
5269522 1.1359 1102 1091 280 169 180 104 100 1024 1027 281 242 256 84 95 1.175 120 825 933 782 911 771
5269523 0.9761 673 703 271 157 169 88 92 760 760 220 219 222 48 95 1.009 120 717 516 541 534 538
5269524 0.7499 793 813 301 157 179 107 94 1057 1045 280 199 215 91 99 .775 120 842 636 858 634 830
5269525 1.0102 638 628 262 159 170 98 84 629 638 187 189 194 70 96 1.045 120 734 479 440 458 444
5269526 0.8329 1268 1316 365 193 205 101 100 1534 1538 346 234 239 61 99 .861 120 736 1075 1300 1111 1299
5269527 0.9295 642 666 269 196 205 99 86 690 722 227 233 239 65 96 .961 120 814 446 457 461 483
5269528 0.8583 1571 1608 463 251 260 115 99 2041 2050 462 521 523 100 100 .888 120 692 1320 1520 1348 1527
5269529 1.1197 1146 1167 338 169 185 96 100 1119 1100 232 238 243 61 99 1.158 120 755 977 881 982 857
5269530 1.0330 999 1016 324 185 198 103 97 1083 1067 247 289 304 104 98 1.068 156 929 814 794 818 763
5269531 1.0868 1464 1499 399 219 235 117 100 1469 1460 319 321 334 83 99 1.124 120 720 1245 1148 1264 1126
5269532 1.0835 548 550 190 159 171 89 87 585 599 142 250 258 68 95 1.12 120 690 389 335 379 341
5269533 1.1156 430 429 161 181 194 114 54 432 457 134 242 257 271 0 1.153 156 845 249 190 235 200
5269534 0.9984 521 552 195 169 179 102 85 618 638 188 267 284 93 85 1.032 80 582 352 351 373 354
5269535 1.1202 557 573 204 156 162 85 90 535 568 191 208 210 47 97 1.158 120 680 401 327 411 358

Total number of rows: 16512

Table truncated, full table size 1594 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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