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Sample GSM75186 Query DataSets for GSM75186
Status Public on May 23, 2006
Title cow 6886, liver Cy3, day 1 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day 1, labelled with Cy3
Organism Bos taurus
Characteristics Liver, day 1 relative to parturition
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name reference standard RNA, labelled with Cy5
Organism Bos taurus
Characteristics Mixture of bovine tissues RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Holstein cow fed ad libitum amounts of a moderate-energy diet during an entire 65 day dry period. Cow consumed ~120% 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 1.16 1848 1874 542 157 171 97 100 1068 1065 317 311 321 93 98 2.234 2.277 52 332 1691 757 1717 754
2 1.091 1830 1790 488 160 175 94 100 1090 1036 324 306 325 127 88 2.13 2.233 52 340 1670 784 1630 730
3 -0.265 532 568 166 160 179 108 90 770 780 123 323 340 102 100 0.832 0.893 32 236 372 447 408 457
4 -0.176 551 581 173 157 172 92 93 767 777 169 322 330 112 93 0.885 0.932 32 236 394 445 424 455
5 1.005 1703 1676 433 160 186 151 100 1067 1056 284 298 305 82 94 2.007 2 52 340 1543 769 1516 758
6 0.794 1762 1873 473 158 197 220 100 1237 1222 211 312 332 140 100 1.734 1.885 32 236 1604 925 1715 910
7 -1.755 1490 1472 507 155 209 231 92 4797 4469 1152 292 404 548 100 0.296 0.315 52 340 1335 4505 1317 4177
8 -1.908 1497 1558 520 153 170 106 96 5333 5261 935 288 305 200 100 0.266 0.283 52 340 1344 5045 1405 4973
9 -2.422 191 225 101 152 158 65 26 497 497 96 288 295 72 78 0.187 0.349 52 340 39 209 73 209
10 -1.515 227 231 80 149 155 70 25 504 520 115 281 287 72 76 0.35 0.343 52 340 78 223 82 239
11 1.282 3920 3757 833 161 200 264 100 1830 1793 386 284 311 161 100 2.431 2.383 52 340 3759 1546 3596 1509
12 1.237 3838 3795 623 150 159 63 100 1848 1819 306 283 286 68 100 2.357 2.373 52 340 3688 1565 3645 1536
13 0.067 1497 1498 269 154 170 122 100 1579 1532 343 297 311 133 96 1.048 1.088 52 340 1343 1282 1344 1235
14 0.219 1462 1485 250 158 174 128 100 1409 1367 294 289 312 138 94 1.164 1.231 52 340 1304 1120 1327 1078
15 -0.903 324 324 91 154 165 70 55 591 594 117 273 285 69 92 0.535 0.53 52 340 170 318 170 321
16 -0.683 315 325 100 153 160 63 59 548 570 134 288 295 80 80 0.623 0.61 52 340 162 260 172 282
17 -0.189 753 737 205 161 169 64 98 979 957 220 304 311 76 98 0.877 0.882 52 340 592 675 576 653
18 -0.14 816 794 241 148 157 64 98 1021 1012 189 285 289 69 100 0.908 0.889 52 332 668 736 646 727
19 -0.352 696 700 152 157 167 70 100 974 911 216 286 287 65 96 0.783 0.869 52 332 539 688 543 625
20 -0.437 682 735 191 153 161 60 100 1026 1023 219 310 312 75 98 0.739 0.816 52 340 529 716 582 713

Total number of rows: 16416

Table truncated, full table size 1595 Kbytes.




Supplementary data files not provided
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