Graduate School of health and Medical Sciences

Single-cell and spatial omics
Provider: Faculty of Health and Medical Sciences

Activity no.: 3565-25-00-00	There are 25 available seats
	Enrollment deadline: 01/04/2025

Date and time	11.05.2025, at: 09:00 - 14.05.2025, at: 16:30
Regular seats	25
Course fee	6,720.00 kr.
Lecturers	Konstantin Khodosevich
ECTS credits	3.00

Contact person	MoMed Team E-mail address: momed@bric.ku.dk

Enrolment Handling/Course Organiser	PhD 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. When applying for the above course, all applicants are put on the waiting list until registration deadline. After the deadline, the course secretary will set up a list of participants for the course. Please send letter of motivation for attending this course before registration deadline to: momed@bric.ku.dk. Please include in motivation letter whether you are already using single cell technologies, how important these are for your PhD project and what are your skills in computational analysis of SC data. Learning objectives 1. To understand single-cell transcriptomics, epigenomics, and proteomics technologies 2. To understand spatial transcriptomics and proteomics technologies 3. To understand CRISPR-based perturbation technology at single-cell level 4. Dry lab: To understand how to preprocess single-cell transcriptomics data, annotate, perform differential analyses, gene regulatory networks, and cell-cell interaction 5. Dry lab: To understand how to reprocess spatial transcriptomics data, segment cells, annotate, and integrate with single-cell transcriptomics Content · Introduction to principles, limitations, and challenges in single-cell transcriptomics, epigenomics, and proteomics across different methods · Introduction to principles, limitations, and challenges in spatial transcriptomics and proteomics across different methods · Introduction to the bioinformatic analysis of single-cell and spatial transcriptomics data, in particular processing of single cell data using for example Seurat, Conos, Pagoda, and Baysor (for the data processing part, the participants will be subdivided into beginner and advanced users) Participants 25 PhD students at any year of their studies, some experience in molecular biology (molecular cloning, PCR, work with RNA) is required. There is no prerequisite knowledge necessary of programming or specific data analysis tools that are used for single-cell and spatial omics, and both experienced sequencing data analysis users as well as inexperienced ones can attend the course. However, basic knowledge of R is required. For the data analysis part, the participants will be subdivided into 2 groups and the training will be provided at beginners and advanced levels. 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: Molecular mechanisms of disease All graduate programmes Language English Form Dry-lab course, lectures, group work, exercises and discussions Course director Konstantin Khodosevich, Professor, BRIC, UCPH konstantin.khodosevich@bric.ku.dk Tune Pers, Associate Professor, CBMR, UCPH tune.pers@sund.ku.dk Teachers Konstantin Khodosevich, BRIC, UCPH, Denmark Tune Pers, CBMR, UCPH, Denmark Xin Jin, Scripps Research, USA Marek Bartosovic, Stockholm University, Sweden Paolo Cadinu, Harvard Medical School, USA Other expert researchers from Denmark and abroad Dates 11. 5. 2025 - 14. 5. 2025. Please be aware that the course starts on SUNDAY, 11 May. Time of the course each day is 9:00-16:30 (tentative). Course location UCPH, BRIC/Copenhagen Biocenter, Ole Maaløes vej 5. Registration Please register before 1. 4. 2025. Please send letter of motivation for attending this course before registration deadline to: momed@bric.ku.dk 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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