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Sample GSM75180 Query DataSets for GSM75180
Status Public on May 23, 2006
Title cow 6877, liver Cy3, day -14 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day -14, labelled with Cy3
Organism Bos taurus
Characteristics Liver, day -14 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 (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 1.26 5466 5142 1362 209 222 128 100 2374 2437 617 179 202 188 100 2.395 2.185 52 332 5257 2195 4933 2258
2 1.042 6200 6177 1592 201 217 105 100 3086 2938 678 172 173 36 100 2.059 2.161 52 340 5999 2914 5976 2766
3 0.378 1084 1052 325 195 213 109 98 856 836 230 172 178 39 96 1.3 1.291 52 340 889 684 857 664
4 0.292 1165 1227 315 199 228 174 96 967 984 159 178 183 55 100 1.224 1.275 32 236 966 789 1028 806
5 1.476 5093 5252 1026 179 204 113 100 1942 1938 290 176 182 57 100 2.783 2.879 32 236 4914 1766 5073 1762
6 1.611 4910 4725 1484 199 205 92 98 1715 1533 553 173 178 41 94 3.055 3.328 52 340 4711 1542 4526 1360
7 -3.211 3206 3069 796 205 268 324 96 27970 27768 4716 179 439 1708 100 0.108 0.104 32 236 3001 27791 2864 27589
8 -3.195 3337 3274 796 211 316 485 100 28798 28636 4703 179 673 2827 100 0.109 0.108 32 236 3126 28619 3063 28457
9 -0.378 393 410 181 196 205 95 50 439 441 88 183 187 46 96 0.77 0.829 32 236 197 256 214 258
10 -0.33 390 408 158 207 218 105 43 416 419 83 186 201 106 62 0.796 0.863 32 236 183 230 201 233
11 0.531 10257 10161 1282 209 326 793 100 7135 7233 1100 182 377 1006 100 1.445 1.411 32 236 10048 6953 9952 7051
12 0.484 10374 9833 2168 203 213 113 100 7455 7221 1465 181 181 37 100 1.398 1.368 52 340 10171 7274 9630 7040
13 0.265 2254 2227 588 197 209 103 100 1898 1816 458 186 190 49 100 1.202 1.245 52 340 2057 1712 2030 1630
14 0.298 2190 2006 721 190 208 112 98 1813 1700 393 186 194 83 98 1.229 1.199 52 340 2000 1627 1816 1514
15 -0.404 526 537 216 201 213 105 65 602 588 129 172 183 60 96 0.756 0.808 52 340 325 430 336 416
16 -0.275 535 582 233 201 208 99 75 580 564 164 176 182 47 94 0.827 0.982 52 340 334 404 381 388
17 -0.386 1150 1090 416 197 208 102 94 1427 1373 322 182 183 41 100 0.765 0.75 52 340 953 1245 893 1191
18 -0.197 1365 1324 331 203 225 120 100 1520 1522 281 188 220 174 100 0.872 0.84 32 236 1162 1332 1121 1334
19 -0.7 742 775 248 202 216 112 96 1059 1035 270 182 190 45 98 0.616 0.672 52 340 540 877 573 853
20 -0.572 764 768 267 209 217 105 92 1007 996 198 182 189 92 100 0.673 0.687 52 340 555 825 559 814

Total number of rows: 16416

Table truncated, full table size 1656 Kbytes.




Supplementary data files not provided
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