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Sample GSM211603 Query DataSets for GSM211603
Status Public on Feb 29, 2008
Title mibta52b 48h (AH_WT48hVsta52b48h_BRII_TR1_137)
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 1.2478 62404 55247 16245 76 92 84 100 38191 33921 11557 92 242 1497 93 1.631 156 1039 62328 38099 55155 33679
5269517 1.1410 65535 56353 19044 94 106 70 100 43312 37828 14007 104 113 38 98 1.491 156 943 65441 43208 56247 37715
5269518 0.3030 822 834 177 72 93 109 100 2107 2026 367 102 140 224 100 .396 120 773 750 2005 741 1886
5269519 1.1549 20476 19614 3870 87 105 64 100 14363 13056 4145 120 130 48 98 1.51 120 842 20389 14243 19509 12926
5269520 1.0175 988 979 195 68 72 26 100 800 773 150 88 90 18 100 1.33 120 717 920 712 907 683
5269521 1.3365 206 214 66 76 87 57 60 196 196 39 117 126 47 33 1.747 120 808 130 79 127 70
5269522 0.4863 1082 1049 270 65 95 161 95 1707 1658 307 110 152 234 99 .636 120 692 1017 1597 954 1506
5269523 0.7651 267 275 119 60 63 23 93 317 320 76 105 106 24 97 1 120 758 207 212 212 214
5269524 0.7960 506 502 156 64 126 217 50 572 571 116 150 203 199 58 1.04 120 731 442 422 376 368
5269525 0.9464 691 655 199 60 64 32 96 588 561 162 80 85 36 93 1.237 156 924 631 508 591 476
5269526 0.8836 419 426 85 68 81 90 99 391 393 93 83 95 73 95 1.155 120 777 351 308 345 298
5269527 0.7340 227 234 75 69 73 30 91 258 259 67 87 90 26 96 .959 156 940 158 171 161 169
5269528 1.1286 2588 2623 496 77 90 60 100 1780 1822 327 96 104 33 100 1.475 120 753 2511 1684 2533 1718
5269529 1.1108 1808 1669 572 72 78 59 96 1298 1195 401 95 99 27 96 1.452 156 843 1736 1203 1591 1096
5269530 0.9945 1833 1753 484 75 100 215 96 1503 1393 366 102 121 186 95 1.3 156 828 1758 1401 1653 1272
5269531 2.1099 2068 2148 567 77 82 35 100 866 861 246 110 113 32 98 2.758 120 742 1991 756 2066 748
5269532 0.9081 178 196 64 69 72 27 90 189 196 53 89 90 18 93 1.187 120 665 109 100 124 106
5269533 1.5735 283 292 70 74 84 58 93 220 221 42 115 124 64 28 2.057 120 708 209 105 208 97
5269534 0.8721 276 283 92 63 69 39 95 307 304 76 111 117 65 84 1.14 120 651 213 196 214 187
5269535 0.7018 188 193 64 60 64 24 93 263 272 54 127 131 32 96 .917 80 613 128 136 129 141

Total number of rows: 16512

Table truncated, full table size 1537 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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