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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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Updated: Mar 3, 2026

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

A pipeline for single-cell chromatin accessibility data analysis.

Mengke Zhang^1,2, Changya Chen^1,2

¹State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.

Blood Science (Baltimore, Md.)

|March 2, 2026

Summary

This summary is machine-generated.

This study introduces a streamlined pipeline for single-cell chromatin accessibility analysis, enhancing the understanding of gene regulatory mechanisms and cellular heterogeneity. The workflow integrates multiple tools for comprehensive epigenetic exploration.

Keywords:

Single-cell ATAC sequencing

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Last Updated: Mar 3, 2026

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
Computational Biology

Background:

Single-cell chromatin accessibility analysis offers high-resolution insights into regulatory elements and gene regulation.
Standardized and comprehensive analysis workflows for scATAC-seq data are currently limited.

Purpose of the Study:

To present a streamlined and integrated pipeline for analyzing single-cell chromatin accessibility data.
To enable robust exploration of epigenetic mechanisms and cellular heterogeneity.

Main Methods:

Data preprocessing using scATAC-pro or Cell Ranger ATAC.
Peak calling with MACS2 and differential accessibility analysis.
Transcription factor activity inference with chromVAR, motif enrichment, and footprinting analysis.
Reconstruction of transcriptional regulatory networks using SCENIC+.

Main Results:

The pipeline effectively processes scATAC-seq data from preprocessing to network reconstruction.
It facilitates the detection of open chromatin regions and differential accessibility between cell populations.
The approach allows for in-depth exploration of epigenetic mechanisms at the single-cell level.

Conclusions:

This integrative workflow provides a robust framework for analyzing single-cell chromatin accessibility data.
It aids in decoding the regulatory landscape and understanding cellular heterogeneity in complex biological systems.