Measurement and analysis of protein-DNA interactions using chromatin immunprecipitation and next generation sequencing (ChIPSeq) 

Aims: Epigenetics is emerging as an important regulatory mechanism and central to understanding this process is the ability to measure protein-DNA interactions including the effect of histones modifications and transcription factor binding (ChIPseq). This one day course is designed for scientists and clinicians with little or no experience in ChIPseq and is based upon the recommended protocols outlined in the ENCODE project. The course aims to provide the experimental and bioinformatics skills required to prepare samples, quantify the levels of protein-DNA binding (transcription factors and histones) using next generation sequencing and examine the overlap between ChIPseq and RNA expression data (see RNAseq course). We assume that sequencing will be performed by an external provider and will provide advice in this area. The course is computer based and will involve a combination of presentations/exercises to analyse 'actual' next generation sequencing data using publically available programmes. This course is designed to complement the RNAseq.  

Part 1   Sample Preparation, Immunoprecipitation and DNA sequencing

  • Introduction to ChIPSeq analysis and public epigenome databases 
  • Immunoprecipitation and DNA sample preparation
  • Overview of library preparation and next generation sequencing platforms 
Part 2:   Sequencing Data Analysis and Interpretation
  • Overview of file formats (FASTQ, SAM/BAM, BED and GTF)
  • Introduction to Galaxy Bioinformatics Platform
  • Quality control of raw data (FASTQC)
  • Alignment of sequence data to reference genome (Bowtie2)
  • Quality control of aligned data (PICARD)
  • Calling peaks for broad source (histone marks) and point source (transcription factors) data (MACS2)
  • Identification of differentially expressed peaks (MACS2)
  • Visualisation of ChiPseq peaks (IGV)
  • Motif Analysis (MEME-ChiP and RSAT)
  • Peak Annotation and comparison relative to protein coding genes and promoters (Cistome/GREAT/BEDTools)
  • Data presentation (EaSeq and Deeptools)

Dates and Locations:

Friday 19th November 2021 - On-line course (Maximum 8 people)

Cost : £249 

For reservations contact

Course Feedback (Overall 4.4/5.0 from > 150 delegates)

'Course is excellent, gave insight into what's possible'

'Great introduction to ChIPseq analysis and lots of time for questions'

'It was a very good course'



Professor Mark A Lindsay 

Mark Lindsay is Professor of Molecular and Computational Pharmacology at the University of Bath  He obtained a BA in Natural Sciences from Cambridge University and a PhD investigating the mechanism of insulin release from Nottingham in 1991. Following an initial post-doctoral position in renal disease, he moved to the National Heart and Lung Institute, Imperial College London in 1994 where he investigated the mechanisms regulating the inflammatory response in the airways and lung. Between 2001 and 2005 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs and antisense for target discovery and as novel therapeutics.  Since returning to academia in 2005, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon examining the role of the transcriptome in the inflammation associated with multiple diseases. Professor Lindsay has recently undertaken a 12 month secondment as the acting Head of Biology at the MRC Nucleic Acid Therapy Accelerator at the Harwell Science Campus (near Oxford). The nucleic acid therapy accelerator (NATA) is a new UK research initiative with a mission to accelerate the development of nucleic acid therapeutics, building partnerships with industry and academia from around the world.