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Sample GSM211614 Query DataSets for GSM211614
Status Public on Feb 29, 2008
Title mibm132 48h (AH_WT48hVsm13248h_BRII_TR3_168)
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 1.1238 23962 25063 5597 235 237 66 100 27338 33167 14179 95 98 18 100 .751 32 177 23727 27243 24826 33069
5269517 0.8895 23116 22792 4130 224 230 74 100 32697 38071 13346 89 100 79 100 .594 32 141 22892 32608 22562 37971
5269518 0.6023 963 990 343 224 271 212 86 1750 1990 930 86 190 368 96 .402 52 209 739 1664 719 1800
5269519 1.2227 24429 22806 6487 214 221 67 100 30038 27751 6222 91 96 26 100 .817 32 134 24215 29947 22585 27655
5269520 1.8447 798 788 271 215 222 69 100 466 549 206 84 84 12 100 1.232 32 158 583 382 566 465
5269521 0.5284 268 264 60 228 237 80 0 197 193 32 91 108 46 68 .353 32 185 40 106 27 85
5269522 1.1308 620 695 243 238 365 531 0 728 696 192 91 169 261 59 .755 32 185 382 637 330 527
5269523 0.8253 432 430 132 215 220 64 75 488 480 210 90 91 11 100 .551 32 148 217 398 210 389
5269524 0.9671 811 767 278 225 241 88 90 918 929 364 90 110 73 100 .646 32 179 586 828 526 819
5269525 0.8572 592 572 168 225 228 71 90 612 694 245 88 100 60 100 .573 32 166 367 524 344 594
5269526 0.8072 657 643 176 217 233 98 87 981 884 306 94 119 144 93 .539 32 179 440 887 410 765
5269527 1.3780 342 355 112 216 219 68 43 203 241 87 90 90 18 100 .921 32 172 126 113 136 151
5269528 1.3833 1491 1551 467 237 245 69 100 1059 1516 979 94 95 18 100 .924 32 146 1254 965 1306 1421
5269529 1.7008 693 724 201 215 237 120 93 513 533 90 85 126 397 0 1.136 32 114 478 428 487 407
5269530 0.7929 1321 1336 366 228 571 1481 0 1837 2178 815 86 961 3415 0 .53 32 138 1093 1751 765 1217
5269531 2.0012 3492 3527 578 217 218 65 100 2618 2563 497 87 90 19 100 1.337 32 114 3275 2531 3309 2473
5269532 0.8500 404 400 103 220 223 56 75 423 400 94 83 84 11 100 .568 12 86 184 340 177 316
5269533 0.6539 400 392 75 233 249 84 46 457 457 135 93 125 89 90 .437 32 150 167 364 143 332
5269534 1.8125 2901 2805 776 237 490 752 87 2361 2213 893 92 217 380 87 1.211 32 111 2664 2269 2315 1996
5269535 1.2725 313 335 87 216 216 62 40 210 233 73 93 92 12 100 .85 32 124 97 117 119 141

Total number of rows: 16512

Table truncated, full table size 1536 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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