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Sample GSM211592 Query DataSets for GSM211592
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR3_91)
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 1.4270 57378 52805 12830 114 128 97 100 40610 38114 9783 86 92 44 100 1.386 120 702 57264 40524 52677 38022
5269517 1.2904 56155 54075 7920 111 152 581 100 43867 43155 7806 85 109 351 100 1.253 120 826 56044 43782 53923 43046
5269518 0.5488 669 677 193 94 103 56 99 1165 1169 242 75 81 37 100 .533 156 1008 575 1090 574 1088
5269519 1.4525 18024 17298 2618 101 110 58 100 12650 12271 2364 78 82 35 100 1.41 120 707 17923 12572 17188 12189
5269520 1.1217 826 847 236 102 113 60 100 766 760 206 76 81 39 100 1.089 120 734 724 690 734 679
5269521 1.1776 358 369 152 98 108 60 82 284 310 126 73 79 39 93 1.143 156 912 260 211 261 231
5269522 0.8064 1026 1080 313 102 118 85 100 1288 1325 336 76 92 92 100 .783 120 822 924 1212 962 1233
5269523 0.8183 340 366 165 103 113 63 79 399 406 151 75 80 41 95 .795 120 720 237 324 253 326
5269524 0.9297 595 619 212 99 112 66 98 621 650 204 74 83 52 100 .903 120 773 496 547 507 567
5269525 0.6594 479 498 209 101 109 57 95 695 695 198 75 79 35 100 .64 120 836 378 620 389 616
5269526 0.8338 516 538 204 100 108 55 95 589 613 200 72 78 36 100 .81 120 822 416 517 430 535
5269527 0.6672 428 446 172 102 109 54 90 592 606 209 75 78 36 100 .648 120 716 326 517 337 528
5269528 1.1675 2398 2420 555 104 113 63 100 2136 2122 488 79 84 37 100 1.134 120 676 2294 2057 2307 2038
5269529 1.1553 1679 1708 336 105 152 627 83 1556 1510 292 81 108 380 98 1.122 120 707 1574 1475 1556 1402
5269530 1.1006 1842 1796 396 99 105 54 100 1688 1665 336 77 82 38 100 1.069 156 838 1743 1611 1691 1583
5269531 2.4843 3855 3712 845 96 106 56 100 1592 1576 389 77 80 34 99 2.412 120 693 3759 1515 3606 1496
5269532 1.1042 279 307 127 99 109 65 68 252 270 111 76 83 47 83 1.072 120 679 180 176 198 187
5269533 1.1804 442 445 151 100 110 61 95 362 375 136 74 82 44 95 1.146 156 838 342 288 335 293
5269534 0.5862 266 290 120 105 118 71 62 409 403 148 78 92 62 92 .569 120 718 161 331 172 311
5269535 0.1294 295 333 141 103 110 61 77 1935 1905 431 74 82 46 100 .126 120 703 192 1861 223 1823

Total number of rows: 16512

Table truncated, full table size 1552 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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