# Protocol for in vivo chromatin immunoprecipitation on purified chromatin isolated from mouse liver nuclei

## TL;DR

This paper provides a detailed protocol for performing chromatin immunoprecipitation on mouse liver samples to study DNA-protein interactions.

## Contribution

A new protocol is introduced for isolating and analyzing chromatin from mouse liver nuclei with high-quality results.

## Key findings

- The protocol includes steps for liver disaggregation, cross-linking, and DNA-protein complex isolation.
- It enables high-quality chromatin shearing and quality control analysis for ChIP.
- Commercial antibodies can be effectively used with this method.

## Abstract

Chromatin immunoprecipitation (ChIP) is used to investigate genome binding by transcription factors, but it can be problematic. We present a protocol to isolate fixed DNA-protein complexes from mouse liver prior to chromatin shearing. We describe steps for liver disaggregation and cross-linking, DNA-protein complex isolation, chromatin shearing, and quality control analysis as well as procedures for ChIP, DNA purification, and ChIP analysis. This protocol yields high-quality samples using commercial antibodies.

For complete details on the use and execution of this protocol, please refer to Akl et al.1

•Steps for conducting ChIP on in vivo mouse liver samples•Protocol for purifying fixed DNA-protein complexes from enriched nuclear fractions•Instructions for chromatin shearing and performing quality control analysis•Detailed procedure for analyzing samples after high-quality ChIP

Steps for conducting ChIP on in vivo mouse liver samples

Protocol for purifying fixed DNA-protein complexes from enriched nuclear fractions

Instructions for chromatin shearing and performing quality control analysis

Detailed procedure for analyzing samples after high-quality ChIP

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Chromatin immunoprecipitation (ChIP) is used to investigate genome binding by transcription factors, but it can be problematic. We present a protocol to isolate fixed DNA-protein complexes from mouse liver prior to chromatin shearing. We describe steps for liver disaggregation and cross-linking, DNA-protein complex isolation, chromatin shearing, and quality control analysis as well as procedures for ChIP, DNA purification, and ChIP analysis. This protocol yields high-quality samples using commercial antibodies.