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Sample GSM75183 Query DataSets for GSM75183
Status Public on May 23, 2006
Title cow 6877, liver Cy5, day -30 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day -30, labelled with Cy5
Organism Bos taurus
Characteristics Liver, day -30 relative to parturition
Extracted molecule total RNA
Label Cy5
 
Channel 2
Source name reference standard RNA, labelled with Cy3
Organism Bos taurus
Characteristics Mixture of bovine tissues RNA
Extracted molecule total RNA
Label Cy3
 
 
Description Holstein cow fed restricted amounts of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period. Cow consumed ~80% of NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Data processing array centering and Loess normalization
 
Submission date Sep 20, 2005
Last update date May 23, 2006
Contact name Juan J. Loor
E-mail(s) jloor@illinois.edu
Phone 217-244-5957
Organization name University of Illinois
Department Animal Sciences
Lab Mammalian NutriPhysioGenomics
Street address 1207 West Gregory Drive
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Platform ID GPL2864
Series (1)
GSE3331 Plane of nutrition prepartum and bovine hepatic gene expression profiles

Data table header descriptions
ID_REF
VALUE log2 ratio of median defined by CH1/CH2 (not normalized)
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 2 standard deviations over the background
CH2_median CH2 (F635) median fluorescence intensity
CH2_MEAN CH2 (F635) mean fluorescence intensity
CH2_SD CH2 (F635) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F635) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F635) background mean fluorescence intensity
CH2_BKD_SD CH2 (F635) background fluorescence intensity standard deviation
% > CH2_BKD_+2SD % of feature pixels greater than 2 standard deviations over the background
Ratio of Medians (635/532) Unnormalized ratio of medians defined by CH1/CH2
Ratio of Means (635/532) 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 Medians (635/532) Ratio of Means (635/532) AREA BKD_AREA CH1_Median - CH1_BKD CH2_Median - CH2_BKD CH1_Mean - CH1_BKD CH2_Mean - CH2_BKD
1 -2.28 1884 1867 494 224 262 422 94 8233 7846 1995 172 185 105 100 0.206 0.214 52 306 1660 8061 1643 7674
2 -2.347 1907 1933 554 219 237 113 100 8770 7977 2200 181 184 47 100 0.197 0.22 52 420 1688 8589 1714 7796
3 -1.484 990 1004 300 219 235 110 98 2334 2172 643 177 180 50 98 0.357 0.393 80 560 771 2157 785 1995
4 -1.521 939 887 340 218 232 100 88 2239 2174 615 170 178 56 100 0.348 0.334 80 560 721 2069 669 2004
5 -1.978 1892 1826 508 221 251 169 96 6757 6590 1474 174 190 104 100 0.254 0.25 52 340 1671 6583 1605 6416
6 -1.982 1981 1938 533 232 249 140 100 7093 6849 1634 185 192 56 100 0.253 0.256 52 420 1749 6908 1706 6664
7 3.175 49000 47876 9301 234 250 122 100 5582 5299 1923 184 191 59 100 9.034 9.314 52 420 48766 5398 47642 5115
8 3.33 54451 53429 7922 233 247 107 100 5572 5515 1023 181 186 63 100 10.057 9.973 52 420 54218 5391 53196 5334
9 -0.794 508 532 175 237 255 128 57 657 657 126 187 195 79 100 0.577 0.628 52 420 271 470 295 470
10 -1.012 464 503 175 225 236 105 53 660 622 121 178 193 142 84 0.496 0.626 52 420 239 482 278 444
11 -1.764 3649 3407 1021 221 249 185 98 11823 11539 2062 180 186 59 100 0.294 0.28 52 420 3428 11643 3186 11359
12 -1.774 3721 3412 1014 232 249 115 98 12116 12001 1954 184 194 60 100 0.292 0.269 52 420 3489 11932 3180 11817
13 -1.354 1665 1600 552 211 239 153 94 3899 3856 531 182 189 55 100 0.391 0.378 52 420 1454 3717 1389 3674
14 -1.389 1587 1585 442 217 235 110 98 3772 3682 550 184 194 57 100 0.382 0.391 52 420 1370 3588 1368 3498
15 -1.224 662 718 259 236 246 125 80 1177 1172 253 182 189 59 100 0.428 0.487 52 340 426 995 482 990
16 -1.286 676 693 241 223 237 141 76 1291 1264 243 186 196 66 100 0.41 0.436 52 340 453 1105 470 1078
17 -1.39 1761 1709 460 240 254 125 98 4167 3970 943 180 189 55 100 0.381 0.388 52 340 1521 3987 1469 3790
18 -1.442 1621 1538 520 226 249 179 92 3972 3845 985 181 188 52 100 0.368 0.358 52 340 1395 3791 1312 3664
19 -0.853 1837 1864 366 218 229 103 100 3107 2831 913 183 186 52 100 0.554 0.622 52 340 1619 2924 1646 2648
20 -0.753 1748 1773 428 224 241 121 100 2746 2687 454 178 180 48 100 0.593 0.617 52 332 1524 2568 1549 2509

Total number of rows: 16416

Table truncated, full table size 1690 Kbytes.




Supplementary data files not provided
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