Abstract
Discovering the regulatory elements of genomes in livestock is essential for our understanding of livestock's basic biology and genomic improvement programs. Previous studies showed butyrate mediates epigenetic modifications of bovine cells. To explore the bovine functional genomic elements and the vital roles of butyrate on the epigenetic modifications of bovine genomic activities, we generated and deposited the genome-wide datasets of transcript factor binding sites of CTCF (CCCTC-binding factor, insulator binding protein), histone methylation (H3H27me3, H3K4me1, H3K4me3) and histone acetylation (H3K27ac) from bovine rumen epithelial primary cells (REPC) before and after butyrate treatment (doi: 10.1186/s12915-019-0687-8 [1]). In this dataset, we provide detailed information on experiment design, data generation, data quality assessment and guideline for data re-use. Our data will be a valuable resource for systematic annotation of regulatory elements in cattle and the functionally biological role of butyrate in the epigenetic modifications in bovine, as well as for the nutritional regulation and metabolism study of farm animal and human.
Highlights
Data of epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment
We provide detailed information on experiment design, data generation, data quality assessment and guideline for data reuse
Biochemistry, Genetics and Molecular Biology Genetics Table and figures ChIP-seq assay (NextSeq 500) and bioinformatics Raw, filtered and analyzed Bovine rumen epithelial primary cells before and after butyrate treatment Rumen epithelial tissue was collected from a two-week-old Holstein bull calf fed with milk replacer only
Summary
Animal care and tissue isolation work were approved by the Beltsville Area Animal Care and Use Committee Protocol Number 07-025. Rumen epithelial tissue was collected from a two-weekold Holstein bull calf fed with milk replacer only. The tissue was added to 50 ml digestion solution (2% trypsin and 1.15 mmol CaCl2 in phosphate-buffered saline) and was incubated in 37 C incubator for 15 min. Rumen epithelial fragments generally underwent 5e6 cycles of digestion with fresh trypsin solution. After the epithelial tissue had undergone trypsin digestion, the solution was filtered through a 300-mm-nylon mesh. After 24h in culture, the cell media were removed and replaced with fresh DMEM-FBS. Cells removed from the dish by trypsinization, quantified and reseeded for treatment or frozen in liquid nitrogen for further culture. To test the response of the primary rumen epithelial cells to the treatment of butyrate, 5mM of butyrate was added to the culture for 24 h before harvested
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