The effect of diet and breed on global gene expression profiles of animals divergent for RFI - Dataset

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Additional Info

Field	Value
Title	The effect of diet and breed on global gene expression profiles of animals divergent for RFI
License	Licence Not Specified
Teagasc Department	Animal and Bioscience Research
Teagasc Programme	Animal and Grassland
Description	RNA-seq data from M. longissimus thoracis et lumborum biopsies collected from Charolais (CH) and Holstein-Friesian (HF) beef steers ranked as high-RFI (feed inefficient) or low-RFI (feed efficient) within breed during each of three consecutive 70-day dietary phases: (1) high-concentrate, growing phase (H1); (2) zero-grazed grass, growing phase (ZG); and (3) high-concentrate, finishing phase (H2). The 12 most extreme high-RFI and 12 most extreme low-RFI steers per breed and dietary phase were biopsied. Libraries were sequenced (Illumina HiSeq 2500, 50 bp single-end, ~22 million reads/sample) to identify genes and biological pathways associated with RFI and to test whether these are consistent across breed and diet. No gene was consistently differentially expressed across all six breed x diet comparisons; however, processes related to fatty acid metabolism, immune function, energy production and muscle growth were common across comparisons.
Language	English
Principal Investigator (PI)	Dr David Kenny
Principal Investigator (PI) email	david.kenny@teagasc.ie
Data creator(s)	Kate Keogh Clare McKenna Sinead M.Waters Richard K. Porter Claire Fitzsimons Mark McGee
Citation	Keogh K, McKenna C, Waters SM, Porter RK et al. Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake. Sci Rep 2023 Jun 3;13(1):9034. PMID: 37270611
Landing page	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113135
Related resources	Keogh, K., McKenna, C., Waters, S. M., Porter, R. K., Fitzsimons, C., McGee, M. & Kenny, D. A. (2023). Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake. Scientific Reports 13, 9034. https://doi.org/10.1038/s41598-023-35661-z
Provenance information	Raw read quality was checked with FASTQC; adapters and low-quality reads were removed with Cutadapt. Trimmed reads were aligned to the bovine reference genome ARS-UCD1.2 with STAR (mean 90.62% mapped), and gene-level counts for protein-coding genes were generated using STAR "quantMode GeneCounts" against the Ensembl v87 annotation. Genes with <1 count per million in at least half the samples per comparison were removed; data were TMM-normalised and differential expression between H- and L-RFI steers was tested within each breed x diet comparison using exact tests in edgeR. A separate model evaluated the breed x diet interaction (RFI as class variable, animal as random effect). DEGs were defined as Benjamini-Hochberg FDR < 0.1 and fold change > 1.5 (230 DEGs across six comparisons; 23 interaction genes). DEGs were annotated and analysed for pathway enrichment using Ingenuity Pathway Analysis (Qiagen).