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Sample GSM211591 Query DataSets for GSM211591
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR2_82)
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 1.4896 63302 54518 14710 92 215 1618 100 39136 35270 10065 71 101 261 100 1.546 120 806 63210 39065 54303 35169
5269517 1.3853 65535 55195 17989 90 119 456 99 43111 38396 14017 73 82 141 98 1.438 156 943 65445 43038 55076 38314
5269518 0.7246 625 609 239 87 101 77 89 804 763 288 69 80 61 91 .752 208 1108 538 735 508 683
5269519 1.4580 12798 11792 3685 89 96 47 100 8573 7810 2496 77 82 35 99 1.513 120 748 12709 8496 11696 7728
5269520 1.1567 859 860 228 94 99 44 100 728 711 156 73 78 34 100 1.201 120 760 765 655 761 633
5269521 0.9097 342 369 140 98 132 142 42 365 364 117 77 120 182 25 .944 156 953 244 288 237 244
5269522 0.8419 1108 1091 404 100 147 185 93 1253 1212 407 78 142 226 90 .874 120 731 1008 1175 944 1070
5269523 0.8537 501 520 152 92 99 43 100 555 561 143 78 79 27 100 .886 80 637 409 477 421 482
5269524 0.8046 774 789 213 100 144 188 93 867 904 267 79 128 203 97 .835 80 636 674 788 645 776
5269525 0.8184 433 441 153 91 98 45 95 468 486 140 74 77 28 99 .85 120 822 342 394 343 409
5269526 0.7806 803 818 220 92 110 133 98 951 973 312 77 93 138 97 .81 120 767 711 874 708 880
5269527 0.9482 692 717 213 92 99 44 100 727 707 216 72 75 27 100 .984 120 836 600 655 618 632
5269528 1.4619 2286 2215 602 86 185 1558 0 1480 1472 342 69 84 152 98 1.517 156 847 2200 1411 2030 1388
5269529 1.2177 1783 1645 582 89 96 49 97 1430 1302 505 71 75 28 94 1.264 156 843 1694 1359 1549 1227
5269530 1.2388 1343 1278 484 86 113 215 89 1023 1000 391 73 90 126 89 1.286 208 856 1257 950 1165 910
5269531 2.2358 3630 3469 713 90 96 42 100 1593 1529 420 73 77 28 99 2.321 120 679 3540 1520 3373 1452
5269532 0.8041 304 307 105 90 101 57 85 342 334 91 74 81 45 97 .835 80 583 214 268 206 253
5269533 0.9455 425 414 135 97 132 141 57 414 401 157 78 119 170 48 .981 156 814 328 336 282 282
5269534 0.6072 292 309 112 101 120 88 56 418 410 120 80 113 113 83 .63 120 706 191 338 189 297
5269535 0.2012 346 353 112 94 100 42 93 1331 1317 197 77 80 30 100 .209 80 630 252 1254 253 1237

Total number of rows: 16512

Table truncated, full table size 1558 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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