Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Monitoring Fetal Somatic Cell Genome Editing <i>In Vivo</i> with Total-Body Positron Emission Tomography: Studies in Rhesus Macaques (<i>Macaca mulatta</i>).

Human gene therapy·2026

Same author

A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells.

Nucleic acids research·2025

Same author

Engineered Silyl Lipids to Modulate Liposome and Lipid Nanoparticle Properties for mRNA Delivery.

ACS applied bio materials·2025

Same author

De-novo DNA Methylation of Bivalent Promoters Induces Gene Activation through PRC2 Displacement.

bioRxiv : the preprint server for biology·2025

Same author

Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons.

Human molecular genetics·2024

Same author

Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters.

Nucleic acids research·2024

Search research articles

Related Experiment Video

Updated: May 29, 2026

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

Using ChIP-seq technology to generate high-resolution profiles of histone modifications.

Henriette O'Geen¹, Lorigail Echipare, Peggy J Farnham

¹Department of Pharmacology and the Genome Center, University of California-Davis, Davis, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|September 14, 2011

Summary

Epigenetic modifications regulate gene transcription by altering DNA packaging. Chromatin immunoprecipitation sequencing (ChIP-seq) provides high-resolution, genome-wide epigenomic profiles from minimal samples.

More Related Videos

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Related Experiment Videos

Last Updated: May 29, 2026

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Area of Science:

Epigenetics and Molecular Biology
Genomics and Bioinformatics

Background:

Dynamic modification of DNA and histones (epigenome) is crucial for transcriptional regulation.
Epigenetic states vary across tissues, developmental stages, and disease, and are influenced by environmental factors.
Genome-wide visualization of epigenomic information is enabled by new technologies.

Purpose of the Study:

To detail the methodology for performing Chromatin Immunoprecipitation (ChIP) assays.
To provide a protocol for preparing libraries for Illumina sequencing.
To focus on characterizing histone modifications in primary cells using ChIP.

Main Methods:

Chromatin Immunoprecipitation (ChIP) assay to characterize DNA-protein interactions in vivo.
ChIP followed by sequencing (ChIP-seq) for genome-wide epigenomic profiling.
Detailed protocols for manual ChIP and automated IP-Star ChIP robot, including library preparation for Illumina sequencing.

Main Results:

ChIP-seq enables high-resolution, genome-wide identification of transcription factor binding, histone modifications, DNA methylation, and nucleosome positioning.
Epigenetic profiles can be generated from as little as 1 μg of chromatin, suitable for primary cells and tissues.
ChIP-seq has surpassed ChIP-chip for epigenomic analyses due to its comprehensive coverage and resolution.

Conclusions:

ChIP-seq is a powerful, high-resolution technology for interrogating the epigenome genome-wide.
The described protocols facilitate the study of epigenetic modifications, particularly histone modifications, in primary cells.
Quality control checkpoints and data analysis methods are essential for extracting meaningful information from ChIP-seq data.