Data from: Data of epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment
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 (https://doi.org/10.1186/s12915-019-0687-8). This dataset provides 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 cells, as well as for the nutritional regulation and metabolism study of farm animals and humans.
Resources in this dataset:
Resource Title: Table S1 - Length of the merged regions, the bin size and the in-silico extension.
File Name: Web Page, url: https://ars.els-cdn.com/content/image/1-s2.0-S2352340919313381-mmc6.xlsx
Direct download, xlsx.
Funding
USDA-NIFA: 2013-67015-20951
USDA-NIFA: 2016-67015-24886
USDA-NIFA: 2019-67015-29321
United States - Israel Binational Agricultural Research and Development Fund: US-4997-17
USDA-ARS: 8042-31000-001-00-D
USDA-ARS: 8042-31310-078-00-D
History
Data contact name
Li, Cong-junData contact email
congjun.li@usda.govPublisher
Data in BriefIntended use
These 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 animals and humans.Temporal Extent Start Date
2020-02-01Theme
- Not specified
Geographic Coverage
{"type":"FeatureCollection","features":[{"geometry":{"type":"Point","coordinates":[-76.92198157305,39.027438102395]},"type":"Feature","properties":{}}]}Geographic location - description
Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, Maryland, USAISO Topic Category
- biota
- farming
National Agricultural Library Thesaurus terms
histones; binding sites; cattle; rumen; epithelium; butyrates; regulatory sequences; genome; genomics; epigenetics; data collection; binding proteins; methylation; acetylation; experimental design; guidelines; metabolism; humans; Biological SciencesPrimary article PubAg Handle
Pending citation
- No
Public Access Level
- Public