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Sample GSM211581 Query DataSets for GSM211581
Status Public on Feb 29, 2008
Title mibm132 72h (AH_WT72hVsm13272h_BRIII_TR2_60)
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 0.9687 32961 30832 6807 114 124 65 100 33541 31889 6789 115 124 55 100 .967 120 807 32847 33426 30708 31765
5269517 0.9942 37759 37160 5710 116 134 166 100 38650 37455 5437 122 142 247 100 .992 120 824 37643 38528 37026 37313
5269518 0.7093 766 780 224 116 124 61 99 1052 1055 285 117 124 57 100 .708 156 944 650 935 656 931
5269519 2.9698 16895 16367 2945 113 123 59 100 5676 5601 1006 117 127 57 100 2.964 120 749 16782 5559 16244 5474
5269520 0.9803 759 786 243 110 116 60 100 792 805 192 114 121 55 100 .978 120 732 649 678 670 684
5269521 0.9616 310 322 130 108 118 60 72 320 340 128 117 124 54 82 .96 156 924 202 203 204 216
5269522 1.1289 1278 1302 391 110 125 89 100 1171 1176 296 118 135 98 100 1.127 120 795 1168 1053 1177 1041
5269523 0.6939 336 349 149 108 117 56 81 440 458 172 110 121 52 93 .693 120 732 228 330 232 337
5269524 0.9262 641 692 258 118 143 124 91 741 752 211 131 162 134 95 .924 80 546 523 610 549 590
5269525 1.0071 500 508 159 115 123 60 95 490 498 151 107 115 55 97 1.005 120 809 385 383 385 383
5269526 0.9053 667 675 245 113 122 57 97 731 744 213 122 129 57 100 .904 120 824 554 609 553 615
5269527 1.1140 509 509 170 111 123 60 98 465 474 175 116 122 53 97 1.112 120 807 398 349 386 352
5269528 0.9146 2183 2153 665 112 124 68 98 2386 2359 694 123 129 57 98 .913 156 860 2071 2263 2029 2230
5269529 0.9883 1066 1126 297 113 122 61 100 1139 1153 257 126 130 56 100 .986 120 742 953 1013 1004 1023
5269530 0.9674 1407 1376 414 118 126 71 99 1444 1421 349 118 129 79 98 .965 156 901 1289 1326 1250 1292
5269531 1.9461 3235 3072 934 114 123 62 100 1691 1644 452 121 133 69 99 1.942 120 734 3121 1570 2949 1511
5269532 0.9308 293 308 118 112 121 61 71 314 326 121 115 123 57 77 .929 120 694 181 199 187 203
5269533 1.4006 344 363 125 110 117 59 87 277 297 126 116 124 55 69 1.398 156 847 234 161 246 173
5269534 0.7603 234 245 111 116 123 62 45 276 288 103 118 127 60 66 .759 120 692 118 158 122 161
5269535 0.1238 288 290 130 107 117 58 70 1630 1599 420 118 123 52 99 .124 120 710 181 1512 173 1476

Total number of rows: 16512

Table truncated, full table size 1579 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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