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| Status |
Public on May 23, 2006 |
| Title |
Plane of nutrition prepartum and bovine hepatic gene expression profiles |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by array
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| Summary |
Cows were selected from two groups of 12 cows enrolled in a large experiment to assess the effects of ad libitum or restricted intake of moderate-energy diets during the entire dry period on pre-partum metabolism and post-partum metabolism and performance. A corn silage-based diet (26% of diet dry matter) providing 1.59 Mcal/kg during the far-off dry period (first 5 wk of an 8-wk dry period) or providing 1.61 Mcal/kg during the close-up dry period (last 3 wk of the dry period) was fed for ad libitum or restricted intake. Four multiparous Holstein cows were randomly selected from the ad libitum and restricted intake groups.
Keywords: time course, ad libitum or restricted feeding prepartum
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| Overall design |
A 7,872-element cDNA microarray spotted in duplicate on amino silane-coated glass slides (Everts et al. 2005, Vet. Immunol. Immunopathol. 105:235-245) was used for transcript profiling. Annotation was based on similarity searches (January, 2005) using sequential BLASTN and TBLASTX against human and mouse UniGene databases and the human genome. The 7,872-element array represents more than 6,300 unique genes. Gene Ontology (GO) terms were parsed from LocusLink to functionally annotate cDNA sequences. RNA (20 ug) from liver tissue and a reference standard derived from a mixture of tissues not including liver were used to make aminoallyl-labeled cDNA followed by incorporation of Cy3-ester and Cy5-ester (Amersham, Piscataway, NJ). Each experimental sample was co-hybridized with the reference standard, which allowed the treatment of fluorescence ratios as measurements of relative expression across all samples and time points. Probes were hybridized to the array for 2 days at 42 C. All samples were hybridized to duplicate slides for a total of 4 spots per cDNA element. A total of 106 microarrays were run to complete the experiment. Slides were scanned for both dye channels with a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
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| Contributor(s) |
Loor JJ, Dann HM, Janovick Guretzky NA, Everts RE, Oliveira R, Green CA, Litherland N, Rodriguez-Zas SL, Lewin HA, Drackley JK |
| Citation(s) |
16757553, 24914544 |
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| Submission date |
Sep 20, 2005 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Juan J. Loor |
| E-mail(s) |
jloor@illinois.edu
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| Phone |
217-244-5957
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| Organization name |
University of Illinois
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| Department |
Animal Sciences
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| Lab |
Mammalian NutriPhysioGenomics
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| Street address |
1207 West Gregory Drive
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| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platforms (1) |
| GPL2864 |
UIUC Cattle 7,872-element cDNA - alternate version |
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| Samples (106)
|
| GSM75159 |
cow 6877, liver Cy3, day 1 relative to parturition |
| GSM75160 |
cow 6877, liver Cy3, day 14 relative to parturition |
| GSM75161 |
cow 6877, liver Cy5, day 1 relative to parturition |
| GSM75162 |
cow 6877, liver Cy5, day 14 relative to parturition |
| GSM75176 |
cow 6877, liver Cy3, day 28 relative to parturition |
| GSM75177 |
cow 6877, liver Cy5, day 28 relative to parturition |
| GSM75178 |
cow 6877, liver Cy3, day 49 relative to parturition |
| GSM75179 |
cow 6877, liver Cy5, day 49 relative to parturition |
| GSM75180 |
cow 6877, liver Cy3, day -14 relative to parturition |
| GSM75181 |
cow 6877, liver Cy5, day -14 relative to parturition |
| GSM75182 |
cow 6877, liver Cy3, day -30 relative to parturition |
| GSM75183 |
cow 6877, liver Cy5, day -30 relative to parturition |
| GSM75184 |
cow 6877, liver Cy3, day -65 relative to parturition |
| GSM75185 |
cow 6877, liver Cy5, day -65 relative to parturition |
| GSM75186 |
cow 6886, liver Cy3, day 1 relative to parturition |
| GSM75187 |
cow 6886, liver Cy5, day 1 relative to parturition |
| GSM75188 |
cow 6886, liver Cy3, day 14 relative to parturition |
| GSM75189 |
cow 6886, liver Cy5, day 14 relative to parturition |
| GSM75190 |
cow 6886, liver Cy3, day 28 relative to parturition |
| GSM75191 |
cow 6886, liver Cy5, day 28 relative to parturition |
| GSM75192 |
cow 6886, liver Cy3, day -14 relative to parturition |
| GSM75193 |
cow 6886, liver Cy3, day -30 relative to parturition |
| GSM75194 |
cow 6886, liver Cy5, day -30 relative to parturition |
| GSM75195 |
cow 6886, liver Cy3, day -65 relative to parturition |
| GSM75196 |
cow 6886, liver Cy5, day -65 relative to parturition |
| GSM75197 |
cow 6886, liver Cy5, day -14 relative to parturition |
| GSM75198 |
cow 6952, liver Cy3, day 1 relative to parturition |
| GSM75200 |
cow 6952, liver Cy5, day 1 relative to parturition |
| GSM75202 |
cow 6952, liver Cy3, day 14 relative to parturition |
| GSM75204 |
cow 6952, liver Cy5, day 14 relative to parturition |
| GSM75206 |
cow 6952, liver Cy3, day 28 relative to parturition |
| GSM75207 |
cow 6952, liver Cy5, day 28 relative to parturition |
| GSM75210 |
cow 6952, liver Cy3, day 49 relative to parturition |
| GSM75212 |
cow 6952, liver Cy5, day 49 relative to parturition |
| GSM75213 |
cow 6952, liver Cy3, day -14 relative to parturition |
| GSM75214 |
cow 6952, liver Cy5, day -14 relative to parturition |
| GSM75215 |
cow 6952, liver Cy3, day -30 relative to parturition |
| GSM75216 |
cow 6952, liver Cy5, day -30 relative to parturition |
| GSM75217 |
cow 6952, liver Cy3, day -65 relative to parturition |
| GSM75218 |
cow 6952, liver Cy5, day -65 relative to parturition |
| GSM75219 |
cow 7045, liver Cy3, day 1 relative to parturition |
| GSM75220 |
cow 7045, liver Cy5, day 1 relative to parturition |
| GSM75221 |
cow 7045, liver Cy3, day 14 relative to parturition |
| GSM75222 |
cow 7045, liver Cy5, day 14 relative to parturition |
| GSM75223 |
cow 7045, liver Cy3, day 28 relative to parturition |
| GSM75224 |
cow 7045, liver Cy5, day 28 relative to parturition |
| GSM75225 |
cow 7045, liver Cy3, day 49 relative to parturition |
| GSM75226 |
cow 7045, liver Cy5, day 49 relative to parturition |
| GSM75227 |
cow 7045, liver Cy3, day -14 relative to parturition |
| GSM75228 |
cow 7045, liver Cy5, day -14 relative to parturition |
| GSM75229 |
cow 7045, liver Cy3, day -30 relative to parturition |
| GSM75230 |
cow 7045, liver Cy5, day -30 relative to parturition |
| GSM75231 |
cow 7045, liver Cy3, day -65 relative to parturition |
| GSM75232 |
cow 7045, liver Cy5, day -65 relative to parturition |
| GSM75233 |
cow 7050, liver Cy3, day 1 relative to parturition |
| GSM75234 |
cow 7050, liver Cy5, day 1 relative to parturition |
| GSM75235 |
cow 7050, liver Cy3, day 14 relative to parturition |
| GSM75236 |
cow 7050, liver Cy5, day 14 relative to parturition |
| GSM75237 |
cow 7050, liver Cy3, day 28 relative to parturition |
| GSM75238 |
cow 7050, liver Cy5, day 28 relative to parturition |
| GSM75239 |
cow 7050, liver Cy3, day -14 relative to parturition |
| GSM75240 |
cow 7050, liver Cy5, day -14 relative to parturition |
| GSM75241 |
cow 7050, liver Cy3, day -30 relative to parturition |
| GSM75242 |
cow 7050, liver Cy5, day -30 relative to parturition |
| GSM75243 |
cow 7105, liver Cy3, day 1 relative to parturition |
| GSM75244 |
cow 7105, liver Cy5, day 1 relative to parturition |
| GSM75245 |
cow 7105, liver Cy3, day 14 relative to parturition |
| GSM75246 |
cow 7105, liver Cy5, day 14 relative to parturition |
| GSM75247 |
cow 7105, liver Cy3, day 28 relative to parturition |
| GSM75248 |
cow 7105, liver Cy5, day 28 relative to parturition |
| GSM75249 |
cow 7105, liver Cy3, day 49 relative to parturition |
| GSM75250 |
cow 7105, liver Cy5, day 49 relative to parturition |
| GSM75251 |
cow 7105, liver Cy3, day -14 relative to parturition |
| GSM75252 |
cow 7105, liver Cy5, day -14 relative to parturition |
| GSM75253 |
cow 7105, liver Cy3, day -30 relative to parturition |
| GSM75254 |
cow 7105, liver Cy5, day -30 relative to parturition |
| GSM75255 |
cow 7105, liver Cy3, day -65 relative to parturition |
| GSM75256 |
cow 7105, liver Cy5, day -65 relative to parturition |
| GSM75257 |
cow 7161, liver Cy3, day 1 relative to parturition |
| GSM75258 |
cow 7161, liver Cy5, day 1 relative to parturition |
| GSM75259 |
cow 7161, liver Cy3, day 14 relative to parturition |
| GSM75260 |
cow 7161, liver Cy5, day 14 relative to parturition |
| GSM75261 |
cow 7161, liver Cy3, day 28 relative to parturition |
| GSM75262 |
cow 7161, liver Cy5, day 28 relative to parturition |
| GSM75263 |
cow 7161, liver Cy3, day 49 relative to parturition |
| GSM75264 |
cow 7161, liver Cy5, day 49 relative to parturition |
| GSM75266 |
cow 7161, liver Cy3, day -14 relative to parturition |
| GSM75278 |
cow 7161, liver Cy5, day -14 relative to parturition |
| GSM75279 |
cow 7161, liver Cy3, day -30 relative to parturition |
| GSM75280 |
cow 7161, liver Cy5, day -30 relative to parturition |
| GSM75281 |
cow 7161, liver Cy3, day -65 relative to parturition |
| GSM75282 |
cow 7161, liver Cy5, day -65 relative to parturition |
| GSM75283 |
cow 7187, liver Cy3, day 1 relative to parturition |
| GSM75284 |
cow 7187, liver Cy5, day 1 relative to parturition |
| GSM75285 |
cow 7187, liver Cy3, day 14 relative to parturition |
| GSM75286 |
cow 7187, liver Cy5, day 14 relative to parturition |
| GSM75287 |
cow 7187, liver Cy3, day 28 relative to parturition |
| GSM75288 |
cow 7187, liver Cy5, day 28 relative to parturition |
| GSM75289 |
cow 7187, liver Cy3, day 49 relative to parturition |
| GSM75290 |
cow 7187, liver Cy5, day 49 relative to parturition |
| GSM75291 |
cow 7187, liver Cy3, day -14 relative to parturition |
| GSM75292 |
cow 7187, liver Cy5, day -14 relative to parturition |
| GSM75293 |
cow 7187, liver Cy3, day -30 relative to parturition |
| GSM75294 |
cow 7187, liver Cy5, day -30 relative to parturition |
| GSM75295 |
cow 7187, liver Cy3, day -65 relative to parturition |
| GSM75296 |
cow 7187, liver Cy5, day -65 relative to parturition |
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| Relations |
| BioProject |
PRJNA93235 |
| Supplementary data files not provided |
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