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Sample GSM211584 Query DataSets for GSM211584
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR1_81)
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 1.3120 53480 49226 10931 93 102 55 100 39103 35646 8881 82 87 37 100 1.382 120 822 53387 39021 49124 35559
5269517 1.3043 54616 48097 18462 91 101 69 100 40518 35036 14307 82 88 40 100 1.373 156 978 54525 40436 47996 34948
5269518 0.6923 567 565 236 89 98 56 88 770 732 281 79 85 44 91 .729 208 1120 478 691 467 647
5269519 1.4799 10657 10123 2072 92 97 44 100 6994 6516 1811 79 84 31 100 1.558 120 738 10565 6915 10026 6432
5269520 1.0462 642 631 216 89 94 42 95 580 571 170 79 84 31 97 1.102 156 961 553 501 537 487
5269521 0.9338 332 331 126 95 107 61 80 309 326 121 86 96 54 87 .983 156 924 237 223 224 230
5269522 0.8642 806 793 236 95 125 127 97 897 853 267 86 132 167 95 .91 120 744 711 811 668 721
5269523 0.8691 358 391 155 89 95 41 95 386 407 122 77 83 33 100 .915 80 630 269 309 296 324
5269524 1.0596 583 574 207 92 129 167 73 481 516 180 84 133 218 42 1.116 120 792 491 397 445 383
5269525 0.7225 348 354 123 90 95 43 94 443 448 126 101 112 54 99 .761 120 822 258 342 259 336
5269526 0.8311 656 680 187 91 101 55 100 753 759 211 86 95 64 99 .875 120 854 565 667 579 664
5269527 0.8549 558 533 150 91 98 44 100 569 577 186 86 90 34 100 .9 120 717 467 483 435 487
5269528 1.3944 2188 2176 408 91 97 44 100 1494 1503 279 83 87 32 100 1.468 120 756 2097 1411 2079 1416
5269529 1.1068 1538 1551 331 93 102 73 99 1326 1333 313 82 89 44 100 1.165 120 755 1445 1244 1449 1244
5269530 1.1522 1287 1223 295 91 101 73 99 1034 1014 255 81 92 62 99 1.213 156 825 1196 953 1122 922
5269531 2.0646 2574 2499 688 88 95 45 100 1241 1187 284 78 82 30 100 2.174 120 722 2486 1163 2404 1105
5269532 0.9705 273 277 93 91 94 41 85 267 263 73 81 86 32 97 1.022 120 754 182 186 183 177
5269533 0.9943 396 406 137 94 106 59 94 366 384 130 86 97 57 94 1.047 156 847 302 280 300 287
5269534 0.7430 265 280 104 93 108 61 75 317 329 102 90 112 90 70 .782 120 679 172 227 172 217
5269535 0.2930 334 355 223 90 95 40 92 949 939 259 80 84 32 100 .308 80 628 244 869 260 855

Total number of rows: 16512

Table truncated, full table size 1534 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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