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Sample GSM75248 Query DataSets for GSM75248
Status Public on May 23, 2006
Title cow 7105, liver Cy5, day 28 relative to parturition
Sample type RNA
 
Channel 1
Source name liver, day 28, labelled with Cy5
Organism Bos taurus
Characteristics liver day 28 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 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 -2.563 2052 2062 388 329 346 113 100 10493 10042 2475 308 311 78 100 0.169 0.178 52 420 1723 10185 1733 9734
2 -2.781 1342 1250 500 332 330 97 86 7241 6488 2470 298 306 81 100 0.145 0.148 52 340 1010 6943 918 6190
3 -2.128 981 972 199 314 324 108 98 3210 3258 567 294 305 111 100 0.229 0.222 52 420 667 2916 658 2964
4 -2.029 997 967 366 313 322 105 86 3089 2952 994 298 307 112 96 0.245 0.246 80 560 684 2791 654 2654
5 -2.497 1929 1975 503 319 334 123 100 9387 9354 2337 301 307 90 100 0.177 0.183 52 420 1610 9086 1656 9053
6 -2.433 2123 2007 600 322 393 663 76 10021 9618 2229 294 333 401 100 0.185 0.181 52 340 1801 9727 1685 9324
7 3.356 54329 53314 8974 325 371 435 100 5567 5184 1693 292 337 291 98 10.238 10.832 52 340 54004 5275 52989 4892
8 3.299 57330 56418 7051 339 723 3119 100 6097 6161 928 307 419 646 100 9.843 9.58 32 236 56991 5790 56079 5854
9 -1.56 455 466 125 319 334 142 13 690 684 165 289 307 183 57 0.339 0.372 52 420 136 401 147 395
10 -1.07 455 474 141 325 333 104 21 575 592 148 302 308 76 86 0.476 0.514 52 340 130 273 149 290
11 -2.103 4634 4584 699 330 337 110 100 18799 18358 3695 304 309 78 100 0.233 0.236 52 420 4304 18495 4254 18054
12 -2.111 4874 4621 1235 337 356 188 98 19911 19721 3140 306 318 106 100 0.231 0.221 52 420 4537 19605 4284 19415
13 -1.704 2916 2727 715 340 355 157 96 8698 8678 1223 307 322 120 100 0.307 0.285 52 420 2576 8391 2387 8371
14 -1.657 3007 2967 361 332 340 110 100 8738 8347 1862 304 312 92 100 0.317 0.328 52 340 2675 8434 2635 8043
15 -1.364 854 845 212 332 347 124 86 1651 1622 336 307 313 80 100 0.388 0.39 52 340 522 1344 513 1315
16 -1.268 879 891 214 338 362 197 78 1618 1599 387 315 320 73 100 0.415 0.431 52 340 541 1303 553 1284
17 -1.882 1851 1883 528 336 364 147 96 5905 5881 893 319 379 385 100 0.271 0.278 32 236 1515 5586 1547 5562
18 -1.755 2006 2033 469 361 370 135 100 5883 6039 1074 332 367 261 100 0.296 0.293 32 236 1645 5551 1672 5707
19 -1.375 1640 1536 440 359 377 179 92 3642 3561 1119 319 335 151 98 0.385 0.363 52 340 1281 3323 1177 3242
20 -1.357 1188 1130 276 311 321 104 94 2544 2518 476 297 301 74 100 0.39 0.369 52 332 877 2247 819 2221

Total number of rows: 16416

Table truncated, full table size 1696 Kbytes.




Supplementary data files not provided
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