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Sample GSM211590 Query DataSets for GSM211590
Status Public on Feb 29, 2008
Title mibtfi91 72h (AH_WT72hVstfi9172h_BRI_TR4_80)
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 1.2625 63297 54844 16781 94 101 46 100 46672 42978 12911 84 89 32 100 1.276 156 940 63203 46588 54743 42889
5269517 1.1207 65535 57752 17847 96 110 95 100 57693 50971 17195 85 91 52 100 1.133 156 962 65439 57608 57642 50880
5269518 0.6646 769 770 324 92 122 158 87 1171 1092 383 83 108 137 89 .672 208 1155 677 1088 648 984
5269519 1.3904 16629 16043 2858 95 102 46 100 11850 11430 2057 85 91 40 100 1.406 120 720 16534 11765 15941 11339
5269520 1.0649 953 949 201 92 99 46 100 868 880 180 84 87 30 100 1.077 120 822 861 784 850 793
5269521 0.9833 418 430 161 93 116 97 82 409 425 135 86 113 134 69 .994 156 922 325 323 314 312
5269522 0.8082 1243 1278 394 103 195 312 93 1578 1533 403 95 221 359 96 .817 120 808 1140 1483 1083 1312
5269523 0.8170 443 465 190 90 98 47 95 526 543 171 89 97 79 95 .826 120 755 353 437 367 446
5269524 0.8888 927 924 304 100 195 295 79 1035 1010 311 93 230 428 57 .899 120 744 827 942 729 780
5269525 0.7599 450 460 170 92 105 77 87 581 569 202 90 104 118 89 .768 156 960 358 491 355 465
5269526 0.6562 898 913 226 95 104 57 100 1319 1322 239 89 96 47 100 .663 120 806 803 1230 809 1226
5269527 0.8603 810 800 200 92 98 45 100 911 902 228 88 92 35 100 .87 120 808 718 823 702 810
5269528 1.2337 2734 2716 404 93 100 48 100 2193 2187 331 84 88 32 100 1.247 120 738 2641 2109 2616 2099
5269529 1.2284 2263 2278 503 91 110 106 100 1838 1847 258 86 94 58 100 1.242 120 755 2172 1752 2168 1753
5269530 1.0537 1776 1756 407 91 123 176 98 1650 1645 441 82 110 153 97 1.065 156 804 1685 1568 1633 1535
5269531 1.9957 4305 4201 883 89 95 44 100 2176 2119 603 81 85 32 97 2.018 120 692 4216 2095 4106 2034
5269532 1.0011 418 426 123 92 100 47 98 398 414 115 84 87 31 100 1.012 120 756 326 314 326 327
5269533 1.0848 530 524 162 93 128 152 77 461 481 167 88 136 249 23 1.097 156 908 437 373 396 345
5269534 0.5113 326 343 136 99 122 86 70 559 566 171 94 142 161 84 .517 120 743 227 465 221 424
5269535 0.1986 428 420 133 94 101 51 95 1654 1713 328 89 101 98 100 .201 80 631 334 1565 319 1612

Total number of rows: 16512

Table truncated, full table size 1583 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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