ChIP-seq

ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the occupancy sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.

The workflow in a typical ChIP-seq experiment can be divided into sample preparation (A) and data analysis (B). In this course we focus on the data analysis part. Some practical considerations for experiment design and sample preparation are given in Experiment Design for ChIP seq .

Image source: Nakato et al, 2021

These are tutorials for quality control and processing of ChIP-seq data:

• ChIPseq: data processing, QC and narrow peak detection
• ChIPseq: broad peaks detection
• Peak Annotation
• Detection of differential occupancy in ChIP-seq data using DiffBind

Tutorials for processing the results after identification of occupancy regions (i.e. peaks or broad domains) can be found in Downstream Processing .