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Sample GSM211594 Query DataSets for GSM211594
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR4_92)
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 1.3602 14931 14471 3715 135 153 185 100 10889 10939 2467 140 156 90 100 1.328 120 758 14796 10749 14318 10783
5269517 1.3207 17488 18159 5444 132 143 84 100 13938 14117 3271 132 147 83 100 1.289 120 798 17356 13806 18016 13970
5269518 1.2192 1146 1140 374 125 137 76 99 970 985 313 132 147 86 98 1.19 120 791 1021 838 1003 838
5269519 1.5533 3408 3391 1012 130 140 73 100 2379 2284 711 133 148 84 98 1.516 120 706 3278 2246 3251 2136
5269520 1.4234 2626 2708 667 142 223 427 100 1947 1980 591 133 206 328 100 1.389 80 629 2484 1814 2485 1774
5269521 1.1403 737 746 235 135 147 79 97 643 680 277 131 150 88 93 1.113 120 707 602 512 599 530
5269522 0.9988 1525 1584 367 153 168 104 100 1534 1609 549 141 163 112 98 .975 80 634 1372 1393 1416 1446
5269523 0.9643 862 898 289 146 161 85 98 871 937 338 138 156 98 97 .941 80 634 716 733 737 781
5269524 1.0834 851 913 319 158 196 188 88 770 856 367 142 187 180 88 1.057 80 626 693 628 717 669
5269525 0.8758 489 517 242 152 160 79 76 502 568 295 141 156 88 80 .855 80 608 337 361 357 412
5269526 1.0325 1299 1327 393 149 159 82 100 1231 1316 479 147 157 89 100 1.008 120 734 1150 1084 1168 1159
5269527 0.8701 759 809 308 150 162 83 96 890 925 419 149 162 91 95 .849 120 748 609 741 647 763
5269528 1.1040 1370 1396 432 131 145 89 100 1302 1311 406 137 148 82 99 1.078 120 718 1239 1165 1251 1163
5269529 1.2948 1347 1371 416 125 138 76 100 1111 1117 428 131 147 85 98 1.264 120 785 1222 980 1233 970
5269530 1.1023 860 876 330 124 136 74 95 825 831 368 132 148 86 92 1.076 156 863 736 693 740 683
5269531 1.3314 1719 1644 640 134 144 75 97 1315 1302 525 140 156 87 96 1.299 120 734 1585 1175 1500 1146
5269532 1.1530 535 570 207 139 156 91 90 518 523 200 140 163 105 78 1.125 80 612 396 378 414 360
5269533 1.0509 635 656 229 137 150 80 97 621 638 276 132 149 88 92 1.026 120 730 498 489 506 489
5269534 0.5866 432 443 145 155 169 92 75 619 646 279 143 164 109 90 .573 80 650 277 476 274 482
5269535 0.8371 843 880 322 148 162 85 100 1005 1039 323 143 162 99 98 .817 80 644 695 862 718 877

Total number of rows: 16512

Table truncated, full table size 1584 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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