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Sample GSM75260 Query DataSets for GSM75260
Status Public on May 23, 2006
Title cow 7161, liver Cy5, day 14 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day 14, labelled with Cy5
Organism Bos taurus
Characteristics liver day 14 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 -0.339 1395 1367 397 185 200 93 100 1676 1596 677 145 160 107 92 0.79 0.815 52 332 1210 1531 1182 1451
2 -0.307 1651 1589 503 194 209 100 100 1947 1947 613 145 151 46 100 0.809 0.774 52 340 1457 1802 1395 1802
3 -0.359 543 548 165 207 224 127 62 578 563 78 147 164 91 100 0.78 0.82 32 236 336 431 341 416
4 -0.551 400 407 159 183 199 111 50 460 462 91 142 143 37 100 0.682 0.7 32 236 217 318 224 320
5 -0.961 1215 1187 358 183 196 95 100 2155 2204 233 146 161 129 100 0.514 0.488 32 236 1032 2009 1004 2058
6 -1.061 1256 1280 471 196 208 98 96 2365 2340 351 154 177 153 100 0.479 0.496 32 236 1060 2211 1084 2186
7 2.778 12846 12899 1350 201 381 1104 100 1988 1980 234 145 174 154 100 6.861 6.92 32 236 12645 1843 12698 1835
8 2.735 12687 12709 1197 180 557 1793 100 2026 1999 322 148 171 134 100 6.66 6.769 32 236 12507 1878 12529 1851
9 -0.839 266 275 106 195 204 119 8 272 296 67 145 161 57 75 0.559 0.53 12 104 71 127 80 151
10 0.447 348 348 139 198 198 96 41 266 272 73 156 164 51 50 1.364 1.293 12 104 150 110 150 116
11 -0.036 4009 3765 1331 183 207 168 98 4072 3834 916 148 159 96 100 0.975 0.972 52 340 3826 3924 3582 3686
12 0.059 3804 3491 1144 184 200 142 96 3619 3575 695 145 150 50 100 1.042 0.964 52 340 3620 3474 3307 3430
13 0.174 1775 1754 472 173 190 98 96 1560 1471 362 140 148 55 98 1.128 1.188 52 340 1602 1420 1581 1331
14 0.085 1734 1712 490 190 199 100 100 1601 1531 377 145 147 39 100 1.06 1.098 52 340 1544 1456 1522 1386
15 -0.476 335 355 159 184 193 97 40 354 358 92 144 149 52 92 0.719 0.799 52 420 151 210 171 214
16 -0.169 373 375 141 188 203 105 38 359 374 75 151 155 35 100 0.889 0.839 52 340 185 208 187 223
17 0.178 967 931 292 175 190 97 98 844 795 239 144 146 35 98 1.131 1.161 52 340 792 700 756 651
18 0.152 956 923 265 187 205 122 100 834 851 120 142 151 45 100 1.111 1.038 32 230 769 692 736 709
19 0.252 827 841 201 185 209 128 100 691 702 133 152 170 92 100 1.191 1.193 32 230 642 539 656 550
20 0.324 922 953 278 191 200 98 98 727 714 110 143 150 43 100 1.252 1.335 52 340 731 584 762 571

Total number of rows: 16416

Table truncated, full table size 1603 Kbytes.




Supplementary data files not provided
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