Computational workflow for integrative analyses of DNA replication timing, epigenomic, and transcriptomic data

Fei Ji, Capucine Van Rechem, Johnathan R. Whetstine, Ruslan I. Sadreyev

Research output: Contribution to journalArticlepeer-review

Abstract

Temporal profiling of DNA replication timing (RT) in combination with chromatin modifications, chromatin accessibility, and gene expression provides new insights into the causal relationships between chromatin and RT during cell cycle. Here, we describe a protocol for in-depth integrative computational analyses of Repli-seq, ATAC-seq, RNA-seq, and ChIP-seq or CUT&RUN data for multiple marks at various time points across cell cycle and changes in their interrelationships upon an experimental perturbation (e.g., knockdown or overexpression of a regulatory protein). For complete details on the use and execution of this protocol, please refer to Van Rechem et al. (2021).

Original languageEnglish
Article number101827
JournalSTAR Protocols
Volume3
Issue number4
DOIs
StatePublished - Dec 16 2022

Keywords

  • Bioinformatics
  • ChIPseq
  • Genomics
  • RNAseq
  • Sequence analysis
  • Sequencing

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