Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 1]

In this study, we generated six RNA-seq data that were collected 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 DNA methylation, 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 hrs.RNA extraction was following the procedure reported previously 54. Total RNA from 6 rumen epithelial cell samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).