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Sample GSM211588 Query DataSets for GSM211588
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRI_TR1_77)
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 1.5376 23625 22561 3829 143 153 85 100 13592 13747 3271 134 146 73 100 1.647 120 837 23482 13458 22408 13601
5269517 1.2232 18052 16409 6636 151 169 97 99 12733 12555 5787 145 157 79 96 1.31 156 977 17901 12588 16240 12398
5269518 1.1001 1140 1097 438 145 172 147 94 965 961 327 153 172 132 95 1.178 156 1029 995 812 925 789
5269519 1.4151 3876 3851 812 147 159 91 100 2700 2600 709 156 169 80 99 1.516 120 731 3729 2544 3692 2431
5269520 1.1880 2312 2338 541 156 170 90 100 1826 1884 495 169 177 84 100 1.272 120 822 2156 1657 2168 1707
5269521 1.1822 940 947 410 162 204 161 83 743 787 307 167 196 137 87 1.266 156 1031 778 576 743 591
5269522 1.0506 1503 1542 521 167 200 165 99 1388 1398 573 176 206 147 97 1.125 120 732 1336 1212 1342 1192
5269523 0.8040 916 879 364 154 169 95 92 1010 1014 405 172 182 87 93 .861 120 741 762 838 710 832
5269524 0.7710 1522 1539 372 184 278 323 97 1802 1832 489 191 302 360 97 .826 80 646 1338 1611 1261 1530
5269525 0.9275 544 604 275 158 173 99 83 582 630 286 181 192 95 84 .993 120 743 386 401 431 438
5269526 0.7057 1884 1848 578 158 175 98 96 2446 2431 641 195 212 102 99 .756 120 854 1726 2251 1673 2219
5269527 0.8992 1406 1379 389 156 173 95 100 1472 1469 416 199 210 97 100 .963 120 822 1250 1273 1206 1259
5269528 1.3103 1846 1907 727 143 152 84 100 1397 1396 402 139 152 83 100 1.403 120 770 1703 1258 1755 1244
5269529 1.2040 1590 1619 489 149 165 95 99 1271 1284 476 144 156 83 95 1.289 120 772 1441 1127 1454 1128
5269530 1.0854 1258 1302 469 143 164 103 98 1108 1149 501 152 165 91 97 1.162 156 894 1115 956 1138 984
5269531 1.3610 2236 2279 638 148 161 90 100 1637 1621 528 159 168 79 97 1.458 120 692 2088 1478 2118 1453
5269532 1.1009 681 708 259 155 167 87 95 612 632 234 163 172 81 95 1.179 120 693 526 449 541 460
5269533 0.9337 735 787 269 171 219 176 83 804 797 294 181 211 140 88 1 120 721 564 623 568 586
5269534 0.9866 589 611 264 163 189 118 75 597 603 281 179 207 124 71 1.057 120 685 426 418 422 396
5269535 0.7286 788 798 309 162 179 103 95 1002 990 322 175 194 114 97 .78 80 598 626 827 619 796

Total number of rows: 16512

Table truncated, full table size 1622 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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