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Sample GSM75198 Query DataSets for GSM75198
Status Public on May 23, 2006
Title cow 6952, 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 restricted amounts of a moderate-energy diet (1.60 Mcal/kg) 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 0.616 1145 1145 317 118 123 67 100 795 760 194 125 127 40 100 1.533 1.617 52 320 1027 670 1027 635
2 0.532 1108 1122 302 119 124 58 100 804 807 171 120 124 39 100 1.446 1.46 52 340 989 684 1003 687
3 0.933 520 538 162 119 126 57 98 331 339 113 121 123 38 88 1.91 1.922 80 560 401 210 419 218
4 0.535 463 487 170 121 128 60 95 356 351 113 120 124 45 91 1.449 1.584 80 560 342 236 366 231
5 1.544 1120 1192 336 114 122 59 100 467 461 126 122 124 34 96 2.916 3.18 52 340 1006 345 1078 339
6 1.714 1287 1286 336 122 126 54 100 475 489 114 120 123 38 100 3.282 3.154 52 340 1165 355 1164 369
7 -2.383 1456 1423 411 122 131 61 100 7078 6991 1102 121 124 39 100 0.192 0.189 52 420 1334 6957 1301 6870
8 -2.304 1455 1393 437 116 127 83 98 6734 6759 1000 122 132 91 100 0.203 0.192 52 420 1339 6612 1277 6637
9 -0.387 185 188 75 120 132 71 13 204 207 49 119 123 36 57 0.765 0.773 52 340 65 85 68 88
10 -0.876 184 194 71 117 128 60 26 244 242 61 121 124 36 75 0.545 0.636 52 332 67 123 77 121
11 -0.544 1949 1893 511 127 140 159 98 2775 2793 320 119 137 237 100 0.686 0.66 52 420 1822 2656 1766 2674
12 -0.404 2213 2125 470 121 128 61 100 2888 2719 675 119 123 37 100 0.756 0.771 52 420 2092 2769 2004 2600
13 1.576 1082 1081 256 113 131 164 100 446 432 110 121 174 884 0 2.982 3.113 52 340 969 325 968 311
14 1.678 980 941 261 119 127 59 100 391 386 92 122 124 35 98 3.201 3.114 52 420 861 269 822 264
15 -0.311 252 259 103 119 125 61 53 285 301 92 120 124 39 88 0.806 0.773 52 420 133 165 140 181
16 -0.026 274 274 100 112 122 59 69 285 295 63 120 124 34 94 0.982 0.926 52 420 162 165 162 175
17 0.987 672 707 218 117 123 67 100 403 415 87 123 124 37 100 1.982 2.021 52 420 555 280 590 292
18 0.955 652 636 182 121 127 62 98 396 410 88 122 126 38 100 1.938 1.788 52 420 531 274 515 288
19 1.187 592 615 143 116 121 51 100 336 353 80 127 131 37 98 2.278 2.208 52 332 476 209 499 226
20 1.073 636 667 208 129 135 66 96 361 362 91 120 122 34 98 2.104 2.223 52 420 507 241 538 242

Total number of rows: 16416

Table truncated, full table size 1575 Kbytes.




Supplementary data files not provided
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