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Analysis of genome-wide enrichment data
Provider: Faculty of Health and Medical Sciences

Activity no.: 3489-24-00-00There are no available seats 
Enrollment deadline: 17/03/2024
Date and time17.04.2024, at: 09:15 - 29.04.2024, at: 16:55
Regular seats12
Course fee13,920.00 kr.
LecturersMads Lerdrup
ECTS credits5.30
Contact personMads Lerdrup    E-mail address: mlerdrup@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: phdkursus@sund.ku.dk

Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.

Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

Learning objectives

A student who has met the objectives of the course will be able to:

1. Perform the required processing of NGS data from genome-wide enrichment based assays (ChIP-seq, Cut&Run, ATAC-seq, DRIP-seq, Repli-seq etc).

2. Analyse, understand, and test the quality of output data from enrichment based assays.

3. Access, process, and integrate genome-wide data from repositiories in own analyses, and be able to reproduce published conclusions.

4. Understand and critically assess published conclusions relying on this type of data.

5. Know and understand strengths and weaknesses of the assay and analysis types, and identify ways to make studies more robust.


In functional genomics, a wealth of new methods based on high-throughput sequencing of enriched DNA or RNA subpopulations have been developed. These new capabilities have transformed the focus from one or a few genomic loci to more abstract and genome-wide system-level interpretations. ChIP-seq, ChIP-exo, Cut&Run, Cut&Tag, ATAC-seq, Repli-seq, MiDAS-seq, and many similar methods have been applied in thousands of studies of functional properties, such as chromatin accessibility, DNA replication, replication stress, and DNA-repair pathways as well as transcriptional regulation in normal development and many diseases.

This course will enable attendees to perform their own processing, analysis, and interpretation of such data. The emphasis will be on step-wise expansion of capabilities through hands-on excersises, with the end goal being that attendees autonomously can reproduce published figures from deposited raw data.

In addition, the course will provide a theoretical background understanding of data structures, workflows, visualization, and limitations as well as present real-life use cases where these types of analyses have been the core of scientific studies.


Students having a background in cell biology, genetics or disease biology - in particularly students that plan to use high-throughput sequencing based enrichment assays (ChIP-seq, ATAC-seq, DRIP-seq, meRIP-seq etc.) during their PhD project and want to be able to analyse the data. The course will be based on tools with graphical user interfaces, so there are no requirements for knowledge or experience with scripting or command-line interfaces. Students are encouraged to describe whether they have data from their project, and if so the data type, when signing up.

Relevance to graduate programmes

The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:

Cellular and Genetic Medicine

Molecular Mechanisms of Disease

Biostatistics and Bioinformatics




Hands-on exercises, lectures, group work & presentations, and assignments (14 hours).

Course director

Mads Lerdrup, Associate Professor, Center for Chromosomal Stability, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, mlerdrup@sund.ku.dk


Mads Lerdrup, Associate Professor, Center for Chromosomal Stability, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen

Daniel Messerscmidt, Associate Professor, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen

Ali Altintas, Assistant Professor, NNF Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen

Kathleen Stewart-Morgan, Associate Professor, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen

Heike Wollmann, Special Consultant, ReNEW, Faculty of Health Sciences, University of Copenhagen

John Arne Dahl, Group leader, Oslo University Hospital

Aditya Sankar, Scientific Visitor Programme Lead, EMBL Heidelberg

Paul Cloos, Head of BiOrigin Laboratory, BiOrigin


17 - 29 April 2024

Course location

The Panum Building, University of Copenhagen


Please register before 17 March 2024

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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