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| Status |
Public on Jan 16, 2019 |
| Title |
The effect of breed and diet on the liver transcriptome of beef steers divergent in RFI |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The objective of this work was to investigate differential gene expression of Charolais (n=90) and Holstein Freisian (n=77) steers divergent in RFI. The primary goal was to uncover genes and pathways associated with feed efficiency. Cattle were subjected to three different 70 day dietary phases. Initally animals were offered a high concentrate phase, termed "High Concentrate 1". Following this phase animals were offered sero grazed grass for 70 days followed by another high concentrate phase known as "High Concentrate 2". Prior to each stage beginning a dietary adaption period was allowed. Liver biopsies were taken at the end of each dietary phase for animals deemed as either high or low in RFI. RNA was extracted and liver gene expression was investigated using RNA-Seq.
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| Overall design |
90 samples were analysed in total. 20 samples were from Charolais animals from the high concentrate phase 1 (n=9 low RFI, n=11 high RFI), and an additional 16 samples were from Holstein-Freisian animals from this stage (n=7 low RFI, n=9 high RFI). From the zero-grazed grass phase, 6 biopsies were analysed from Charolais animals (n=3 low RFI, n=3 high RFI) and a further 18 samples were analysed from Holstein-Freisian animals (n=10 low RFI, n=8 high RFI). Finally, 17 Charolais samples were analysed from high concentrate phase 2 (n=9 low RFI, n=8 high RFI) and 13 Holstein-Freisian samples were analysed by RNA-Seq (n=5 low RFI, n=8 high RFI).
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| Contributor(s) |
Higgins M, Morris DW, McKenna C, Blackshields G, Coyle S, Fitzsimmons C, Kenny DA, McGee M, Waters SM |
| Citation(s) |
31242854 |
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| Submission date |
Mar 06, 2018 |
| Last update date |
Jul 16, 2019 |
| Contact name |
Marc Higgins |
| E-mail(s) |
marcghiggins@gmail.com
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| Organization name |
NUI Galway
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| Department |
Discipline of Biochemistry
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| Street address |
University Road
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| City |
Galway |
| ZIP/Postal code |
H91 CF50 |
| Country |
Ireland |
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| Platforms (1) |
| GPL19172 |
Illumina HiSeq 2500 (Bos taurus) |
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| Samples (90)
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| Relations |
| BioProject |
PRJNA437115 |
| SRA |
SRP134019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE111464_genecounts_GEO_MH.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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