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:

Tuesday 10th October - IT Rooms, University of Bath

Wednesday 6th December 2017 - Just IT Training Rooms nr Aldgate Tube, London 

Thursday 26th April - Nowgen IT Training Rooms, Manchester

Cost : £349 (2 courses - £649; 3 course - £949)  

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'



 Dr David Sims

David Sims is the Programme Head at the MRC funded Computational Genomics Analysis and Training (CGAT) programme at the University of Oxford. David has a BSc in Biochemistry and an MSc in computer science from Glasgow University. In 2006 he obtained a PhD from UCL working on genome-wide RNA interference screening for cell morphology in Drosophilia. He went on to work in integrative cancer genomics, including shRNA screening, exome sequencing and RNASeq in Alan Ashworths's laboratory at the Institute of Cancer Research in London. He is currently involved in training biologists in computational genomics and works on a wide variety of next generation sequencing projects including RNAseq, ChIPseq, exome sequencing, e4C and methylation sequencing.

Professor Mark A Lindsay 

Mark Lindsay is Professor of Molecular Pharmacology at the University of Bath and Honorary Senior Scientist at the National Heart and Lung Institute, Imperial College London. 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 2004 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs for the validation of novel drug targets and the identification of new approaches for the delivery of biopharmaceutics. Since returning to academia in 2004, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon the role of miRNAs and long non-coding RNAs in the regulation of the innate immune response and the development of respiratory diseases such as asthma, chronic obstructive pulmonary disease and lung cancer.