Ag Data Commons

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

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

posted on 2024-06-11, 06:03 authored by Animal Genomics and improvement Lab., USDA-ARS
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).


Data contact name

BioProject Curation Staff


National Center for Biotechnology Information

Temporal Extent Start Date



  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

epigenetics; genome; genomics

Pending citation

  • No

Public Access Level

  • Public

Accession Number


Preferred dataset citation

It is recommended to cite the accession numbers that are assigned to data submissions, e.g. the GenBank, WGS or SRA accession numbers. If individual BioProjects need to be referenced, state that "The data have been deposited with links to BioProject accession number PRJNA531215 in the NCBI BioProject database ("

Usage metrics



    Ref. manager