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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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Updated: Jul 12, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

ChromTag: an interactive R-shiny platform for analysis and visualization of CUT&Tag and ChIP-seq peak profiling data.

Siwen Xu1,2, Qingyan Zou1, Rui Shi3

  • 1School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, China.

Frontiers in Bioinformatics
|July 10, 2026
PubMed
Summary

ChromTag is a new web tool that simplifies the analysis of epigenomic data, like CUT&Tag and ChIP-seq. It helps researchers interpret complex chromatin profiling results and understand gene regulation.

Keywords:
Cut&TagR shiny web applicationchromatin profilingepigenomic analysisgene regulationvisualization platform

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Published on: April 16, 2018

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Last Updated: Jul 12, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

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Published on: December 13, 2024

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

Area of Science:

  • Epigenomics
  • Computational Biology
  • Bioinformatics

Background:

  • Chromatin profiling technologies (CUT&Tag, ChIP-seq) map histone modifications and transcription factor binding genome-wide.
  • Interpreting complex epigenomic datasets requires significant technical expertise, limiting accessibility for many researchers.

Purpose of the Study:

  • To develop an accessible, interactive web-based application for the comprehensive exploration and visualization of epigenomic profiling data.
  • To provide a user-friendly solution for downstream analysis of CUT&Tag and ChIP-seq datasets.

Main Methods:

  • Developed ChromTag, an R Shiny application with a modular workflow for epigenomic data analysis.
  • Implemented differential peak detection, gene assignment, Gene Ontology (GO) and KEGG pathway enrichment analysis, and Gene Set Enrichment Analysis (GSEA).
  • Integrated motif enrichment analysis and extensive visualization tools (volcano plots, PCA, heatmaps).

Main Results:

  • ChromTag enables differential peak detection and functional annotation of CUT&Tag and ChIP-seq data.
  • The platform supports pathway analysis (ORA, GSEA) and motif enrichment for identifying regulatory elements.
  • Supports human, mouse, and Drosophila datasets with diverse visualization options.

Conclusions:

  • ChromTag offers a practical and accessible downstream analysis solution for chromatin profiling data.
  • The application bridges preprocessed data with interactive visualization and functional interpretation, empowering researchers.
  • Facilitates deeper understanding of gene regulation, cellular differentiation, and disease mechanisms through accessible epigenomic data analysis.