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Sample GSM211582 Query DataSets for GSM211582
Status Public on Feb 29, 2008
Title mibm132 72h (AH_WT72hVsm13272h_BRIII_TR3_62)
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 0.8575 33273 30639 11893 96 102 46 100 35799 32660 11948 130 137 62 100 .939 156 961 33177 35669 30537 32523
5269517 0.9833 50901 47768 11384 100 108 53 100 45895 44409 7510 136 144 75 100 1.077 156 948 50801 45759 47660 44265
5269518 0.6784 938 967 242 89 98 46 100 1309 1310 308 128 136 61 100 .743 156 983 849 1181 869 1174
5269519 1.7624 14545 14382 1530 92 172 722 100 7486 7534 713 129 158 233 100 1.93 120 837 14453 7357 14210 7376
5269520 0.8973 806 826 221 92 118 115 99 883 887 244 140 164 143 98 .983 120 819 714 743 708 723
5269521 1.3276 413 420 152 90 101 78 88 339 350 123 123 138 90 62 1.454 156 988 323 216 319 212
5269522 1.1958 1738 1750 618 91 102 84 99 1435 1397 504 130 146 149 92 1.309 156 948 1647 1305 1648 1251
5269523 0.7736 409 432 131 94 99 44 98 495 528 194 129 140 86 88 .847 120 824 315 366 333 388
5269524 1.1664 822 866 266 92 101 57 100 712 731 274 125 138 82 95 1.277 120 725 730 587 765 593
5269525 0.8370 487 487 151 92 97 44 98 534 559 190 128 133 58 96 .916 156 964 395 406 390 426
5269526 1.0502 885 872 306 90 99 60 98 780 809 299 129 140 93 97 1.15 156 927 795 651 773 669
5269527 1.2201 589 592 243 95 100 45 96 487 503 200 131 138 62 90 1.336 156 974 494 356 492 365
5269528 0.6953 2081 2045 395 99 105 49 100 2687 2687 535 131 137 63 100 .761 120 742 1982 2556 1940 2550
5269529 0.9356 1330 1355 305 97 104 52 100 1350 1361 307 133 147 80 100 1.024 120 741 1233 1217 1251 1214
5269530 0.8263 1491 1506 303 90 114 216 100 1692 1696 342 131 149 209 100 .905 156 847 1401 1561 1392 1547
5269531 1.7322 3476 3476 587 94 184 791 100 1906 1917 465 134 163 245 98 1.897 120 692 3382 1772 3292 1754
5269532 1.3196 401 400 128 98 130 139 58 333 342 137 133 174 180 11 1.445 120 770 303 200 270 168
5269533 1.5044 413 432 154 91 103 81 89 312 333 134 126 142 95 48 1.647 156 863 322 186 329 191
5269534 1.1749 299 309 107 89 102 76 72 291 299 126 128 140 110 30 1.287 120 678 210 163 207 159
5269535 0.1155 324 331 117 90 96 46 93 2018 2033 555 128 138 86 100 .127 120 758 234 1890 235 1895

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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