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Sample GSM75243 Query DataSets for GSM75243
Status Public on May 23, 2006
Title cow 7105, 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
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 1.059 1842 1831 555 144 187 230 100 1117 1160 359 302 335 160 96 2.083 1.966 32 230 1698 815 1687 858
2 1.019 1938 1887 497 134 184 215 100 1217 1251 310 327 362 187 96 2.027 1.897 32 236 1804 890 1753 924
3 0.483 653 659 185 133 149 77 96 659 673 151 287 291 63 100 1.398 1.363 32 236 520 372 526 386
4 0.42 679 675 208 140 156 84 100 705 709 104 302 307 72 100 1.337 1.314 32 236 539 403 535 407
5 1.26 2644 2516 608 142 158 113 100 1347 1360 209 302 306 84 100 2.394 2.244 32 236 2502 1045 2374 1058
6 1.313 2762 2738 438 129 147 82 100 1336 1359 216 276 286 71 100 2.484 2.409 32 236 2633 1060 2609 1083
7 -1.772 3063 2926 689 133 245 480 100 10298 10080 1560 293 580 1364 100 0.293 0.285 32 236 2930 10005 2793 9787
8 -1.843 3127 3166 674 150 198 260 100 10979 11199 1470 301 474 918 100 0.279 0.277 32 236 2977 10678 3016 10898
9 -0.973 244 285 161 137 155 88 31 497 501 101 287 288 74 68 0.51 0.692 32 176 107 210 148 214
10 -0.532 262 243 106 141 154 79 34 464 471 100 289 293 73 65 0.691 0.56 32 236 121 175 102 182
11 0.393 3695 3512 1197 141 166 175 98 2992 2918 645 285 290 73 100 1.313 1.28 52 340 3554 2707 3371 2633
12 0.484 4015 3733 1020 135 144 76 98 3048 2856 629 273 281 73 98 1.398 1.393 52 340 3880 2775 3598 2583
13 1.174 3556 3481 831 142 169 165 100 1795 1780 269 282 300 108 100 2.256 2.229 52 340 3414 1513 3339 1498
14 1.195 3109 3160 1094 139 158 93 100 1577 1522 444 280 300 106 98 2.29 2.432 52 340 2970 1297 3021 1242
15 0.05 382 391 129 145 151 70 84 505 508 105 276 289 95 63 1.035 1.06 52 340 237 229 246 232
16 0.192 415 429 133 134 142 69 88 519 519 124 273 280 74 80 1.142 1.199 52 340 281 246 295 246
17 0.679 1211 1267 610 129 137 64 98 949 939 235 273 286 91 94 1.601 1.709 52 340 1082 676 1138 666
18 0.599 1139 1160 338 138 148 77 98 942 905 279 281 295 89 90 1.514 1.638 52 340 1001 661 1022 624
19 0.596 1218 1177 418 136 151 111 96 985 974 229 269 280 68 100 1.511 1.477 52 320 1082 716 1041 705
20 0.739 1275 1297 307 132 138 62 100 969 951 153 284 291 65 100 1.669 1.747 52 340 1143 685 1165 667

Total number of rows: 16416

Table truncated, full table size 1612 Kbytes.




Supplementary data files not provided
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