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Sample GSM211586 Query DataSets for GSM211586
Status Public on Feb 29, 2008
Title mibm132 72h (AH_WT72hVsm13272h_BRII_TR4_56)
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 1.6539 65047 59411 10703 141 150 80 100 37033 35156 5931 126 138 68 100 1.692 120 732 64906 36907 59261 35018
5269517 1.4295 65535 62106 10859 150 180 331 100 43711 42494 5803 128 142 130 100 1.462 120 842 65385 43583 61926 42352
5269518 0.8186 945 954 308 140 154 98 98 1108 1094 361 122 131 65 98 .837 156 959 805 986 800 963
5269519 0.4755 2969 2859 802 142 151 77 99 6006 5703 1384 118 126 59 99 .486 120 748 2827 5888 2708 5577
5269520 1.3404 1270 1291 373 146 159 90 98 979 959 331 124 133 69 95 1.371 120 772 1124 855 1132 826
5269521 1.0029 345 374 157 137 151 81 64 354 361 149 130 135 65 67 1.026 156 961 208 224 223 226
5269522 1.1255 1297 1361 392 144 156 77 100 1198 1184 332 127 136 69 99 1.151 120 720 1153 1071 1205 1048
5269523 0.8527 400 424 146 144 159 85 75 430 448 117 127 137 69 97 .872 80 628 256 303 265 311
5269524 0.7196 539 543 202 144 155 78 86 663 667 218 125 131 65 99 .736 120 735 395 538 388 536
5269525 0.8066 512 532 170 145 155 79 94 567 591 211 122 132 64 95 .825 120 760 367 445 377 459
5269526 0.9380 781 790 242 149 157 78 98 777 795 275 127 138 67 100 .96 120 744 632 650 633 657
5269527 0.9166 428 475 224 144 154 80 81 458 478 215 125 135 64 85 .938 120 750 284 333 321 343
5269528 1.5293 4160 4185 813 144 153 78 100 2745 2715 620 132 141 77 100 1.564 120 708 4016 2613 4032 2574
5269529 1.7652 2125 2135 616 145 154 82 100 1192 1220 347 118 128 65 98 1.806 120 757 1980 1074 1981 1092
5269530 1.3912 1819 1851 469 136 154 103 100 1307 1329 319 124 131 65 100 1.423 120 708 1683 1183 1697 1198
5269531 0.9566 1584 1607 506 140 150 76 100 1671 1620 558 121 127 61 97 .979 120 735 1444 1550 1457 1493
5269532 1.0988 415 438 159 148 162 92 72 372 385 134 127 136 70 76 1.124 80 622 267 245 276 249
5269533 1.0345 330 362 168 144 155 81 55 317 338 136 132 138 67 64 1.058 120 708 186 185 207 200
5269534 0.6997 258 278 122 142 152 78 36 305 313 129 123 137 70 65 .716 120 774 116 182 126 176
5269535 0.1312 333 333 141 145 154 84 54 1547 1523 492 122 133 69 98 .134 120 712 188 1425 179 1390

Total number of rows: 16512

Table truncated, full table size 1584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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