Epigenomic changes in organs from in vitro or in vivo-produced male dairy calves.

Holstein embryos were produced in vitro (IVP, n=4) or in vivo (by ovarian superstimulation followed by AI; MOET, n=4) and transferred to synchronized recipients. Pregnancies were monitored until delivery. Male calves were maintained in similar conditions during the postnatal period until euthanasia at around 100 days of age. The following datasets correspond to the epigenomic modifications in the hypothalamus, pituitary, testicles, adrenals, liver, and muscle from IVP and MOET calves. The WGBS clean reads were aligned to the bovine reference genome (bosTau 9) using the Bismark Bisulfite Read Marker (v 0.22.3). The percent of methylated cytosines was calculated as the number of methylated cytosines/total number of cytosines x 100. Cytosines were annotated with the nearest (no specific cut-off) transcription start site (TSS) and with gene structures (promoter, exon, intron, CpG islands or shores) through Genomation (Bioconductor/R). Promoters and CpG shore were defined as ± 1000 bp and ± 2000 bp of the TSS and CpG islands, respectively.