Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell: Part 2—Computational Analysis of Epigenomics Data

Keren Cheng, John R. McCarrey

Research output: Chapter in Book/Report/Conference proceedingChapter


The final data-generation step of genome-wide profiling of any epigenetic parameter typically involves DNA deep sequencing which yields large datasets that must then be computationally analyzed both individually and collectively to comprehensively describe the epigenetic programming that dictates cell fate and function. Here, we describe computational pipelines for analysis of bulk mepigenomic profiling data, including whole-genome bisulfite sequencing (WGBS) to detect DNA methylation patterns, chromatin immunoprecipitation-sequencing (ChIP-seq) to detect genomic patterns of either specific histone modifications or bound transcription factors, the assay for transposase-accessible chromatin-sequencing (ATAC-seq) to detect genomic patterns of chromatin accessibility, and high-throughput chromosome conformation capture-sequencing (Hi-C-seq) to detect 3-dimensional interactions among distant genomic regions. In addition, we describe Chromatin State Discovery and Characterization (ChromHMM) methodology to integrate data from these individual analyses, plus that from RNA-seq analysis of gene expression, to obtain the most comprehensive overall assessment of epigenetic programming associated with gene expression.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press
Number of pages17
StatePublished - 2023
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Assay for transposase-accessible chromatin-sequencing (atac-seq)
  • Chromatin immunoprecipitation-sequencing (chip-seq)
  • Chromatin state discovery and characterization (chromhmm)
  • Epigenomic profiling
  • High-throughput chromosome conformation capture (hi-c)
  • Multiparametric integrative analysis
  • Whole-genome bisulfite sequencing (wgbs)

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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