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Chromatin Immunoprecipitation- ChIP

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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Related Experiment Video

Updated: Nov 17, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.

Rita Jui-Hsien Lu^1,2, Yen-Ting Liu¹, Chih Wei Huang³

¹Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.

Frontiers in Genetics

|February 15, 2021

Summary

ATACgraph is a new bioinformatics tool that simplifies the analysis and visualization of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data. It offers ATAC-seq-specific insights and an intuitive graphical interface for biologists.

Keywords:

ATAC-seq bioinformatics chromatin accessibility epigenomics genomics next-generation sequencing

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Last Updated: Nov 17, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

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Published on: March 22, 2019

Area of Science:

Genomics
Bioinformatics
Epigenetics

Background:

Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is crucial for mapping genome-wide chromatin accessibility.
Existing ATAC-seq tools often adapt ChIP-seq strategies, neglecting ATAC-seq's unique biological properties and quality control needs.

Purpose of the Study:

To develop ATACgraph, a user-friendly bioinformatics software for analyzing and visualizing ATAC-seq data.
To incorporate ATAC-seq-specific quality control and biological insights, including nucleosome-free and occupied regions.
To enable identification of differentially accessible chromatin regions between datasets.

Main Methods:

ATACgraph was developed as a bioinformatics software integrating with the Galaxy platform via a Docker image.
It provides a graphical user interface, eliminating the need for complex local installations.
Users can analyze ATAC-seq data using pre-designed or customized workflows.

Main Results:

ATACgraph effectively profiles accessible chromatin regions and provides ATAC-seq-specific metrics.
The software facilitates the identification of nucleosome-free and nucleosome-occupied regions.
Differential accessibility analysis between two ATAC-seq datasets is supported.

Conclusions:

ATACgraph offers an effective and accessible solution for ATAC-seq data analysis, particularly for biologists with limited bioinformatics expertise.
The tool supports analysis across all genomes and is publicly available for download.
Demonstrated on human genome data, ATACgraph enhances ATAC-seq interpretation.