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Sample GSM75231 Query DataSets for GSM75231
Status Public on May 23, 2006
Title cow 7045, liver Cy3, day -65 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day -65, labelled with Cy3
Organism Bos taurus
Characteristics liver day -65 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 1.146 1484 1467 417 167 175 76 100 808 798 178 213 220 71 100 2.213 2.222 52 332 1317 595 1300 585
2 1.13 1460 1496 322 184 229 217 100 807 804 155 224 245 117 100 2.189 2.262 32 236 1276 583 1312 580
3 0.127 628 705 252 166 174 75 100 634 626 140 211 216 53 96 1.092 1.299 52 420 462 423 539 415
4 0.326 720 718 197 161 172 76 98 656 632 148 210 224 86 94 1.253 1.32 52 420 559 446 557 422
5 0.762 1454 1453 448 167 173 68 100 970 1000 220 211 214 50 100 1.696 1.63 52 340 1287 759 1286 789
6 0.698 1504 1505 367 162 187 263 98 1037 1014 247 210 217 62 100 1.623 1.67 52 340 1342 827 1343 804
7 -3.007 1233 1191 365 177 188 84 96 8694 8483 1814 207 215 64 100 0.124 0.123 52 340 1056 8487 1014 8276
8 -3.268 1250 1254 287 175 216 192 100 10573 10013 2324 219 728 2019 96 0.104 0.11 32 236 1075 10354 1079 9794
9 -0.618 257 253 90 171 176 76 26 347 349 70 215 220 58 57 0.652 0.612 52 420 86 132 82 134
10 -0.645 260 258 100 166 180 96 11 360 364 70 213 217 53 76 0.639 0.609 52 340 94 147 92 151
11 1 180 185 77 168 180 89 2 217 228 75 211 219 60 3 2 1 80 552 12 6 17 17
12 1.322 177 207 146 172 194 328 1 220 277 325 218 221 61 5 2.5 0.593 80 560 5 2 35 59
13 0.222 1593 1551 279 167 188 114 98 1448 1434 212 225 229 56 100 1.166 1.145 52 340 1426 1223 1384 1209
14 0.211 1578 1571 342 174 188 86 98 1435 1362 332 222 234 81 100 1.157 1.225 52 340 1404 1213 1397 1140
15 0.106 410 405 134 170 186 102 65 465 477 71 242 249 73 84 1.076 1 32 236 240 223 235 235
16 -0.674 360 425 292 177 211 280 1 517 500 110 225 235 75 90 0.627 0.902 52 340 183 292 248 275
17 0.202 949 1054 336 168 185 99 98 910 917 293 231 241 70 94 1.15 1.292 52 340 781 679 886 686
18 -0.029 725 738 220 177 195 100 100 805 820 130 246 261 89 100 0.98 0.977 32 236 548 559 561 574
19 0.045 698 668 208 181 200 128 82 740 722 162 239 249 71 98 1.032 1.008 52 340 517 501 487 483
20 0.015 828 801 247 165 175 77 94 878 856 154 222 227 75 100 1.011 1.003 52 420 663 656 636 634

Total number of rows: 16416

Table truncated, full table size 1592 Kbytes.




Supplementary data files not provided
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