# Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

## TL;DR

This paper introduces an improved ChIP-exo protocol optimized for mammalian cells and modern sequencing platforms, making it more efficient and robust.

## Contribution

The novel contribution is the development of a mammalian-optimized ChIP-exo protocol (MO-ChIP-exo) that addresses technical limitations of previous methods.

## Key findings

- MO-ChIP-exo was validated as a more robust and efficient method for generating high-quality ChIP-exo libraries.
- The protocol is adaptable to both suspension and adherent mammalian cell lines.
- Systematic optimization improved crosslinking, harvesting, and library construction steps.

## Abstract

By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein–DNA interactions at near basepair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies. We introduce a mammalian-optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it with previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.