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Data from: Data of epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment

dataset
posted on 2023-12-18, 18:18 authored by Xiaolong Kang, Shuli Liu, Lingzhao Fang, Shudai Lin, Mei Liu, Ransom L. Baldwin, George E. Liu, Cong-jun Li

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:

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-jun

Data contact email

congjun.li@usda.gov

Publisher

Data in Brief

Intended 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

2020-02-01

Theme

  • 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, USA

ISO 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 Sciences

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Kang, Xiaolong; Liu, Shuli; Fang, Lingzhao; Lin, Shudai; Liu, Mei; Baldwin, Ransom L.; Liu, George E.; Li, Cong-jun (2019). Data from: Data of epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment. Data in Brief.

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