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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: Dec 23, 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

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data.

Wenbao Yu^1,2, Yasin Uzun^1,2, Qin Zhu³

¹Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

|April 22, 2020

Summary

This summary is machine-generated.

scATAC-pro offers open-source software for processing single-cell chromatin accessibility sequencing data. This tool provides comprehensive quality assessment, analysis, and visualization for diverse experimental protocols.

Keywords:

Bioinformatics Chromatin accessibility Genomics Single cell

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Last Updated: Dec 23, 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

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

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Published on: February 1, 2022

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

Single-cell chromatin accessibility sequencing (scATAC-seq) is vital for studying epigenetic variations in complex biological systems.
Existing software solutions often lack comprehensive support for all scATAC-seq experimental protocols.
A need exists for integrated, open-source tools for scATAC-seq data analysis.

Purpose of the Study:

To introduce scATAC-pro, a novel open-source software package.
To provide comprehensive quality assessment, analysis, and visualization capabilities for scATAC-seq data.
To support a wide range of scATAC-seq experimental protocols.

Main Methods:

Development of an open-source software pipeline named scATAC-pro.
Implementation of flexible quality control metric computation for scATAC-seq data.
Integration of analysis and visualization modules within the software.

Main Results:

scATAC-pro enables robust quality assessment across key experimental steps.
The software offers flexible method choices for quality control metric calculation.
scATAC-pro generates integrated summary reports for quality assessment and downstream analysis.

Conclusions:

scATAC-pro addresses the need for comprehensive, open-source scATAC-seq analysis software.
The tool enhances the ability to analyze epigenetic heterogeneity in complex tissues.
scATAC-pro supports diverse experimental protocols, promoting wider adoption and reproducibility.