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Sample GSM75282 Query DataSets for GSM75282
Status Public on May 23, 2006
Title cow 7161, liver Cy5, day -65 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day -65, labelled with Cy5
Organism Bos taurus
Characteristics liver day -65 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
Extracted molecule total RNA
Label Cy3
 
 
Description Holstein cow fed ad libitum amounts of a moderate-energy diet (1.60 Mcal/kg) 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 -1.445 643 648 208 175 190 95 88 1476 1414 315 202 212 68 100 0.367 0.39 52 384 468 1274 473 1212
2 -1.439 634 639 228 179 188 79 92 1427 1372 303 193 193 42 100 0.369 0.39 52 340 455 1234 460 1179
3 -0.83 512 510 159 179 186 77 82 780 799 137 188 189 39 100 0.563 0.542 52 420 333 592 331 611
4 -1.009 346 357 100 178 182 78 53 521 512 86 183 183 38 98 0.497 0.544 52 412 168 338 179 329
5 -1.376 732 744 260 167 178 78 97 1642 1494 467 176 181 41 98 0.385 0.438 80 560 565 1466 577 1318
6 -1.267 813 786 228 168 180 76 96 1734 1709 256 182 185 41 100 0.416 0.405 52 420 645 1552 618 1527
7 3.799 15730 14832 4384 173 181 75 100 1300 1293 425 182 182 40 100 13.915 13.194 80 560 15557 1118 14659 1111
8 3.9 15359 13999 5517 174 183 76 100 1200 1229 451 183 186 55 98 14.931 13.217 80 560 15185 1017 13825 1046
9 -0.506 245 266 109 176 183 73 25 287 288 49 189 188 41 65 0.704 0.909 32 230 69 98 90 99
10 0.068 246 241 98 181 184 71 15 242 249 58 180 185 42 31 1.048 0.87 32 176 65 62 60 69
11 -1.585 1098 1096 365 167 177 72 97 2970 2824 593 177 182 43 100 0.333 0.351 80 560 931 2793 929 2647
12 -1.526 1131 1118 246 170 177 71 100 2940 2762 827 173 177 36 98 0.347 0.366 80 560 961 2767 948 2589
13 -0.662 1410 1310 486 171 176 80 93 2133 2068 450 172 175 40 100 0.632 0.601 80 560 1239 1961 1139 1896
14 -0.612 1396 1296 470 173 182 76 93 2044 1980 535 175 175 37 100 0.654 0.622 80 560 1223 1869 1123 1805
15 -0.762 348 356 115 167 175 75 59 479 471 87 172 175 37 100 0.59 0.632 52 420 181 307 189 299
16 -0.561 355 359 127 172 179 76 63 438 441 81 168 171 45 98 0.678 0.685 80 547 183 270 187 273
17 -0.488 892 877 226 171 179 74 97 1180 1133 284 169 170 39 100 0.713 0.732 80 547 721 1011 706 964
18 -0.532 860 856 291 172 178 72 95 1164 1179 256 169 169 35 100 0.691 0.677 80 560 688 995 684 1010
19 -0.342 737 744 243 165 174 72 96 890 838 259 165 166 34 96 0.789 0.86 80 560 572 725 579 673
20 -0.652 644 662 206 187 193 82 92 921 911 164 203 207 45 100 0.636 0.671 52 412 457 718 475 708

Total number of rows: 16416

Table truncated, full table size 1605 Kbytes.




Supplementary data files not provided
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