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Sample GSM211599 Query DataSets for GSM211599
Status Public on Feb 29, 2008
Title mibta52b 72h (AH_WT72hVsta52b72h_BRI_TR3_134)
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 2.4494 55899 52746 10171 93 106 93 100 22851 22252 3022 91 94 25 100 2.376 120 717 55806 22760 52640 22158
5269517 2.2886 61899 54712 16187 84 164 1121 98 27844 24698 8578 90 107 225 94 2.22 156 977 61815 27754 54548 24591
5269518 0.6821 558 559 156 80 99 119 96 812 818 180 94 109 94 98 .662 156 902 478 718 460 709
5269519 1.4352 13471 13066 2064 88 96 48 100 9756 9435 1670 113 118 36 100 1.392 120 734 13383 9643 12970 9317
5269520 1.3598 788 814 188 78 83 35 100 638 649 126 91 94 27 100 1.319 120 808 710 547 731 555
5269521 0.8111 244 250 84 84 126 200 0 290 305 80 94 137 175 6 .787 120 789 160 196 124 168
5269522 0.7949 605 605 178 83 114 117 94 813 771 203 94 135 144 94 .771 120 818 522 719 491 636
5269523 0.9181 349 367 142 74 80 36 98 411 415 125 86 88 26 100 .891 80 619 275 325 287 327
5269524 0.7982 596 577 202 83 172 275 36 755 729 212 91 175 235 83 .774 120 730 513 664 405 554
5269525 0.6448 430 439 140 80 93 68 96 643 663 173 89 110 99 98 .625 120 794 350 554 346 553
5269526 0.9559 753 759 220 84 132 252 76 841 826 242 98 144 234 85 .927 120 731 669 743 627 682
5269527 0.9060 570 583 181 90 95 41 98 668 666 190 105 108 27 100 .879 120 822 480 563 488 558
5269528 1.9087 2576 2524 440 82 94 89 100 1382 1406 271 87 90 23 100 1.851 120 770 2494 1295 2430 1316
5269529 2.3425 2111 2096 402 76 176 1277 6 958 976 215 87 105 257 97 2.272 120 754 2035 871 1920 871
5269530 1.1532 1445 1414 298 84 101 118 98 1300 1285 300 96 109 84 98 1.119 156 820 1361 1204 1313 1176
5269531 1.7857 2805 2832 447 90 95 50 100 1719 1698 421 115 123 47 99 1.732 120 720 2715 1604 2737 1575
5269532 1.0179 298 315 108 80 85 36 96 320 329 88 91 94 28 99 .987 120 770 218 229 230 235
5269533 1.1722 315 332 107 83 151 293 0 310 311 87 92 156 247 0 1.137 156 840 232 218 181 155
5269534 1.0379 392 387 86 90 120 92 88 390 392 92 97 137 93 88 1.007 80 596 302 293 267 255
5269535 0.1273 217 221 87 76 79 33 80 1295 1261 291 87 87 19 99 .124 120 697 141 1208 142 1174

Total number of rows: 16512

Table truncated, full table size 1535 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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