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Sample GSM211597 Query DataSets for GSM211597
Status Public on Feb 29, 2008
Title mibm132 48h (AH_WT48hVsm13248h_BRII_TR1_182)
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 0.7927 13778 13448 4542 156 164 81 100 17053 16498 4831 154 158 42 100 .813 156 993 13622 16899 13284 16340
5269517 0.8214 15184 15175 2530 159 270 1059 100 18781 17970 3886 152 285 1357 99 .843 120 809 15025 18629 14905 17685
5269518 0.8863 898 926 281 154 197 306 73 998 995 247 146 197 348 76 .909 156 1072 744 852 729 798
5269519 1.0490 3496 3471 652 141 149 77 100 3271 3234 470 140 143 36 100 1.076 120 744 3355 3131 3322 3091
5269520 1.0717 1981 1965 403 121 130 66 100 1868 1817 520 140 143 36 97 1.1 120 842 1860 1728 1835 1674
5269521 1.0051 488 496 219 133 151 92 82 481 500 210 148 170 87 76 1.031 156 907 355 333 345 330
5269522 0.9792 1003 1010 325 145 199 198 93 1018 1017 326 156 213 171 95 1.005 120 838 858 862 811 804
5269523 1.0053 588 615 269 123 133 73 89 620 612 216 135 138 33 96 1.031 120 836 465 485 482 474
5269524 0.8448 775 777 286 133 167 133 93 921 886 317 143 179 136 92 .867 120 838 642 778 610 707
5269525 1.0390 565 597 273 129 140 82 88 543 576 217 137 144 60 95 1.066 156 929 436 406 457 432
5269526 0.7909 815 869 285 133 159 133 98 1047 1043 329 136 163 128 98 .811 120 809 682 911 710 880
5269527 0.7786 376 410 183 128 138 72 75 458 492 181 139 140 33 99 .799 120 821 248 319 272 352
5269528 0.9633 1119 1166 359 151 161 79 100 1165 1177 298 150 153 37 100 .988 120 740 968 1015 1005 1024
5269529 1.1414 721 738 206 156 167 86 100 646 648 149 151 152 44 99 1.171 120 770 565 495 571 496
5269530 0.9893 727 762 250 154 213 353 35 745 752 246 153 205 296 50 1.015 156 933 573 592 549 547
5269531 1.2352 1513 1486 473 135 144 77 98 1176 1208 299 142 144 37 100 1.267 120 812 1378 1034 1342 1064
5269532 1.2602 500 504 200 120 130 70 88 428 436 145 139 142 35 98 1.293 120 707 380 289 374 294
5269533 1.0195 300 297 143 138 153 89 43 283 303 129 151 169 79 39 1.046 156 798 162 132 144 134
5269534 0.9203 334 360 178 140 156 92 52 370 388 149 155 182 92 58 .944 120 647 194 215 204 206
5269535 0.9398 420 422 170 125 135 72 77 413 449 175 141 141 35 95 .964 120 722 295 272 287 308

Total number of rows: 16512

Table truncated, full table size 1577 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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