Graduate School of health and Medical Sciences

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

Activity no.: 3489-26-00-00	There are 8 available seats
	Enrollment deadline: 22/03/2026

Date and time	22.04.2026, at: 09:00 - 04.05.2026, at: 16:00
Regular seats	12
Course fee	14,520.00 kr.
Lecturers	Mads Lerdrup
ECTS credits	5.30

Contact person	Mads Lerdrup E-mail address: mlerdrup@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration SUND E-mail address: phdkursus@sund.ku.dk

Enrolment guidelines 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. Process enrichment-based sequencing data (e.g., ChIP-seq, CUT&RUN/CUT&Tag, ATAC-seq, DRIP-seq, Repli-seq) into outputs you can visualize and analyze. 2. Evaluate and interpret dataset quality by applying appropriate QC metrics and justify whether the data are suitable for downstream analysis. 3. Retrieve, process, and integrate public genome-wide datasets and reproduce key published results and figures. 4. Critically assess how strong published conclusions are by evaluating experimental design, analysis choices, and whether data actually support the claims. 5. Design and justify an new end-to-end analysis workflow (for own data or a chosen paper), and recommend improvements that increase robustness (controls, replication, QC criteria, alternative analyses). Content In functional genomics, a growing set of methods based on high-throughput sequencing of enriched DNA or RNA fractions has enabled genome-wide analyses of regulatory and chromatin-associated processes. These approaches have shifted the focus from single loci to system-level interpretation across the genome. Methods such as ChIP-seq, ChIP-exo, CUT&RUN, CUT&Tag, ATAC-seq, Repli-seq, MiDAS-seq, DRIP-seq, Tracking-seq, DISCOVER-seq, and related assays are widely used to study chromatin accessibility, transcriptional regulation, DNA replication dynamics, replication stress, and DNA repair in development and disease as well as identification of CRISPR and base-editing targets. This course enables participants to process, analyse, and interpret data from enrichment-based sequencing assays. The emphasis is on stepwise development of practical skills through hands-on exercises. By the end of the course, participants will be able to run reproducible analysis workflows and reproduce selected published analyses/figures using their own and deposited datasets. In addition, the course provides the theoretical foundation needed to interpret results responsibly, including data structures and formats, core analysis workflows, visualisation strategies, and key limitations and biases. Real-life case studies from the literature will illustrate how these assays and analyses support (or fail to support) scientific conclusions. Participants The course is intended for PhD students with a interest in cell biology, genetics, genomics or disease biology who plan to use enrichment-based high-throughput sequencing assays (e.g., ChIP-seq, CUT&RUN/CUT&Tag, ATAC-seq, DRIP-seq, Repli-seq, meRIP-seq) and want to be able to analyse and interpret the resulting data. The course uses tools with graphical user interfaces and does not require prior experience with scripting or command-line workflows. Participants are expected to be comfortable with basic biological concepts (DNA/RNA, chromatin, gene regulation) and routine file handling. Participants are encouraged to indicate whether they have project data and the data type when signing up, and where feasible course exercises may be adapted to reflect participant interests. 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 Language English Form 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 Daniel Messerschmidt, Associate Professor, Center for Chromosomal Stability, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, mlerdrup@sund.ku.dk Teachers 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 Mika Zagrobelny, Associate Professor, Center for Chromosomal Stability, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen Erkut Ilaslan, Post doc, Department of Molecular Medicine, Faculty of Health Sciences, University of Copenhagen Mirra Søegaard, Research Assistant, 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 Smaragda Kompocholi, Post doc, CGEN, Department of Molecular Medicine, 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, Biohagen Aps Dates 22 April - 4 May 2026 Duration 22 - 28 April: 9-16 29 April: 9-14 30 April - 4 May: Assignment work with 2-3 hours of daily supervision. Course location The Panum Building, University of Copenhagen Expected frequency Once a year in the spring 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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