NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM211600 Query DataSets for GSM211600
Status Public on Feb 29, 2008
Title mibta52b 72h (AH_WT72hVsta52b72h_BRII_TR3_129)
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 1.2424 58577 55380 9197 126 137 87 100 42853 40932 6239 132 137 41 100 1.354 120 732 58451 42721 55243 40795
5269517 1.2628 65535 55618 19262 99 114 63 100 47241 40445 15153 109 122 49 100 1.376 156 982 65436 47132 55504 40323
5269518 1.3486 3040 3013 408 79 87 78 100 2189 2090 467 94 103 95 99 1.47 120 792 2961 2095 2926 1987
5269519 1.5133 25871 23099 7904 85 93 51 100 15732 14059 3999 107 116 73 100 1.65 120 774 25786 15625 23006 13943
5269520 1.2004 1086 1091 183 77 82 37 100 868 866 127 91 95 47 100 1.308 80 620 1009 777 1009 771
5269521 0.9550 288 294 82 65 67 25 98 300 302 63 82 83 18 100 1.041 120 810 223 218 227 219
5269522 1.3353 3131 3089 764 66 71 33 100 2295 2160 561 83 85 25 95 1.455 120 717 3065 2212 3018 2075
5269523 1.0925 391 401 175 64 67 24 93 349 364 125 81 82 16 95 1.191 120 746 327 268 334 282
5269524 1.0265 1025 1031 150 71 116 236 100 934 944 171 86 120 183 98 1.119 80 634 954 848 915 824
5269525 1.3324 1012 992 272 64 68 25 99 727 721 121 82 83 16 100 1.452 120 837 948 645 924 638
5269526 1.1177 746 722 196 69 75 53 98 610 623 129 87 90 39 100 1.218 120 824 677 523 647 533
5269527 1.1651 439 452 127 71 74 29 99 386 388 79 88 90 19 100 1.27 120 823 368 298 378 298
5269528 1.1836 3118 3043 650 81 90 49 100 2505 2396 588 100 106 32 99 1.29 120 679 3037 2405 2953 2290
5269529 1.6260 2629 2593 640 78 87 89 100 1511 1511 325 92 96 30 100 1.772 120 738 2551 1419 2506 1415
5269530 1.1634 2275 2243 286 77 82 35 100 1811 1803 196 95 104 76 100 1.268 120 770 2198 1716 2161 1699
5269531 1.2312 2255 2253 244 79 86 48 100 1797 1723 346 103 112 84 100 1.342 80 605 2176 1694 2167 1611
5269532 0.9748 248 260 99 73 77 31 90 266 268 71 92 94 26 98 1.063 120 711 175 174 183 174
5269533 1.0668 305 314 80 64 68 26 100 288 297 64 82 84 18 100 1.163 120 740 241 206 246 213
5269534 1.1024 354 363 102 65 70 29 98 341 333 84 85 88 25 95 1.202 120 693 289 256 293 245
5269535 1.0842 213 219 71 63 66 23 96 208 213 63 81 82 16 95 1.182 120 693 150 127 153 131

Total number of rows: 16512

Table truncated, full table size 1531 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap