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| Status |
Public on Oct 08, 2015 |
| Title |
Liver and muscle gene expression and cow fertility at late pregnancy, early lactation and mid lactation |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The transition between pregnancy and lactation is a major physiological change that dairy cows must contend with. Complex systemic and local processes involving gluconeogenesis, energy balance, utilisation of body reserves, insulin resistance and involution of the uterus can have an effect on animal health and farm profitability. Here we used an established Holstein cow model of fertility that displayed genetic and phenotypic divergence in calving interval, a trait used to define reproductive performance using a national breeding index in Ireland. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (‘Fert+’; n = 8) or very poor genetic merit for fertility (‘Fert-‘; n = 8). We investigated three distinct time-points, late pregnancy, early lactation and mid lactation (-18, 1 and 147 days on average with day 0 being birth), using RNA sequencing from both liver and muscle tissue biopsies and conducting a differential expression (DE) analysis. We found 807 and 815 unique genes to be DE in at least one time-point in liver and muscle respectively, of which 79% and 83% were only found in a single time-point; 40 and 41 genes were found DE at every time-point indicating possibly systemic or chronic dysregulation. Functional annotation resulted in evidence for two major physiological processes: immune and inflammation, and metabolic, lipid and carbohydrate-binding. These processes indicate areas of previous interest as well as specific systems that appear differentially regulated, and point towards interesting avenues of further research in a broad and complex field.
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| Overall design |
96 samples total; 8 Fert+ ('high fertility'), 8 Fert- ('low fertility'); no controls; Fert+, Fert- differential gene expression at three timepoints in two tissues
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| Contributor(s) |
Moran B, Butler ST, Creevey CJ |
| Citation(s) |
27514375 |
| Submission date |
Oct 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Moran |
| E-mail(s) |
bruce.moran@gmail.com
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| Organization name |
St. Vincent's University Hospital
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| Department |
Dept. of Pathology
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| Lab |
Molecular Lab
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| Street address |
Nutley Lane, Dublin 4
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| City |
Dublin |
| ZIP/Postal code |
D4 |
| Country |
Ireland |
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| Platforms (1) |
| GPL15749 |
Illumina HiSeq 2000 (Bos taurus) |
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| Samples (96)
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| Relations |
| BioProject |
PRJNA263327 |
| SRA |
SRP048734 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62159_L_1-48.counts.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE62159_M_1-48.counts.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE62159_RAW.tar |
9.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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