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 7]

posted on 2024-06-11, 06:03 authored by Animal Genomics and improvement Lab., USDA-ARS
In this study, we generated genome-wide data sets for four histone modifications, including H3K9ac, H3K27ac, RNA pol II, H3K9me3, which were collected from MDBK cell line before and after (24h) Butyrate treatment. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated 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: The MDBK cell line was purchased from ATCC (ATCC CCL-22; Manassas, VA, USA) and grown in Eagle’s essential medium with 5% fetal bovine serum. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. ChIP-seq of MDBK cells were performed as reported in our earlier publication. In short, DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt single end reads, using an Illumina HiSeq 2500 platform.


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 PRJNA531210 in the NCBI BioProject database ("

Usage metrics



    Ref. manager