Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 2]

In this study, we generated six whole-genome bisufite sequencing (WGBS) data that were colloced from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Overall design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. Briefly, DNA from REPC culture was isolated by phenol/chloroform extraction. DNA (100 ng) was bisulfite-converted and subjected to library preparation using the Pico Methyl-Seq™ Library Prep Kit (Zymo) following the instructions of the supplier. High-Sensitivity DNA chips were used to assess libraries for quality on the Agilent Bioanalyzer and quantified with Qubit fluorometer. Libraries were sequenced on an Illumina HiSeq2500 (150-bp paired-end sequencing).