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Sample GSM211606 Query DataSets for GSM211606
Status Public on Feb 29, 2008
Title mibta52b 72h (AH_WT72hVsta52b72h_BRI_TR2_125)
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 1.5579 56234 54605 9342 116 137 151 100 34302 33940 3650 114 123 71 100 1.611 120 806 56118 34188 54468 33817
5269517 1.4985 65535 64239 3898 93 127 305 100 42763 41499 8207 99 138 603 99 1.549 120 823 65442 42664 64112 41361
5269518 0.7013 808 800 238 85 144 366 49 1093 1079 236 93 142 259 96 .725 156 942 723 1000 656 937
5269519 1.2710 14564 13692 3009 89 96 44 100 11066 10455 2034 104 108 31 100 1.314 120 758 14475 10962 13596 10347
5269520 1.2036 883 869 271 80 83 37 97 729 725 175 91 91 21 100 1.244 120 734 803 638 786 634
5269521 0.9591 310 326 105 86 122 143 31 331 338 81 96 137 153 18 .992 120 792 224 235 204 201
5269522 0.8321 909 921 194 89 152 193 98 1049 1062 162 95 168 227 100 .86 80 632 820 954 769 894
5269523 0.8188 359 368 135 81 85 38 95 398 426 167 87 87 18 94 .847 120 732 278 311 283 339
5269524 0.7307 695 701 219 86 166 339 37 906 906 255 92 152 245 94 .756 120 782 609 814 535 754
5269525 0.5013 439 450 154 82 88 56 93 800 801 165 91 99 63 100 .518 120 850 357 709 362 702
5269526 0.9700 741 762 206 83 116 194 95 765 767 188 90 121 188 95 1.003 120 823 658 675 646 646
5269527 0.7629 532 548 131 81 87 46 100 667 684 152 92 99 66 100 .789 120 836 451 575 461 585
5269528 1.3630 2407 2423 442 92 117 161 100 1755 1755 348 101 119 152 100 1.409 120 756 2315 1654 2306 1636
5269529 2.0534 2653 2661 492 77 86 47 100 1302 1309 290 92 96 31 100 2.123 120 756 2576 1210 2575 1213
5269530 1.2152 2074 2016 466 86 277 1166 14 1661 1632 325 96 288 1203 0 1.257 156 840 1988 1565 1739 1344
5269531 1.5999 3028 2975 578 85 92 43 100 1963 1848 488 101 104 30 99 1.654 120 720 2943 1862 2883 1744
5269532 0.9764 288 290 107 79 84 37 90 279 301 96 92 94 26 98 1.01 120 693 209 187 206 207
5269533 1.1806 440 440 123 86 124 192 40 388 386 93 96 139 197 12 1.221 120 693 354 292 316 247
5269534 1.2676 446 457 138 90 133 124 85 375 377 72 97 135 93 91 1.311 80 619 356 278 324 242
5269535 0.1153 235 233 99 81 84 36 77 1371 1363 260 88 89 18 100 .119 120 694 154 1283 149 1274

Total number of rows: 16512

Table truncated, full table size 1546 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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