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Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 3]

dataset
posted on 2024-06-11, 06:03 authored by Animal Genomics and improvement Lab., USDA-ARS
In this study, we generated four ATAC-seq 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 methylation 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 hrs. ATAC-seq of rumen primary epithelial cells (RPEC) were performed at Active Motif, Inc. (Carlsbad, CA, USA) according to proprietary methods. The paired-end 42-nt sequencing reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA).

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2019-04-05

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

epigenetics; genome; genomics

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA531214

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 PRJNA531214 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/)."

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