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. Analyze single cell RNA sequencing data by applying relevant bioinformatic tools
2. Assess the quality of single cell sequence data
3. Assess the results of bioinformatic tools
4. Interpret the implications of a data analysis in broader context than the specific analyzed data
5. Apply the statistical software R for data manipulation and analysis

Content
Rapid progress in the development of high-throughput sequencing (HTS) technologies in recent years has provided new insights into our understanding of biology and reaches deep into human and animal science, for example with respect to diseases and nutrition.
Today it is possible to obtain genome-wide transcriptome data from single cells using HTS (scRNA-seq). The main advantage of scRNA-seq is that the cellular resolution and the genome wide scope makes it possible to address issues that are intractable using other methods, e.g. bulk RNA-seq.
Understanding the opportunities that come with the technological development is crucial for strategy planning and experiment design. This course will introduce you to the bioinformatics analyses of scRNA-seq data starting from the raw reads provided by the sequencing machine. The main focus will be on the data analysis of the RNA-seq count matrix, covering all steps from pre-processing and cluster annotation to more advanced downstream analyses.
Demultiplexing and read mapping will be performed in UCloud (or the web-based platform Galaxy). Statistical computing will be done in the statistical programming language R using primarily Bioconductor packages.

Participants
Students should have a background in genetics or bioinformatics.
The target group are students that are exposed to high-throughput sequencing data in mammals or plants during their PhD study and want to learn how to analyze the data. A basic knowledge of statistics and previous experience with the software R are recommended.
Preferably the students have previously worked with bulk RNA-seq analysis or taken a course such as the complementary PhD course “Bioinformatics analysis of gene expression data from bulk RNA-seq (BAGED-bulk)”.

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:
– Biostatistics and Bioinformatics
– Veterinary Clinical Sciences
– Molecular Mechanisms of Disease

Language
English

Form
The course combines theoretical lectures, tutorials, and student projects. Each participant will define a data analysis project based on their own PhD project and data or relevant publicly available sequencing data. Students with related data and/or scientific questions are encouraged to work together in small groups. Each participant will give an oral presentation of the project work at the last course day and deliver a short report after the course. Students are expected to work on their project during the course hours and six additional hours per week.

Course director
Ernst Stefan Seemann, Assoc. Professor, IVH, sse@sund.ku.dk

Teachers
Anne Wenzel, PhD, reNEW
Dorottya Maria Ralbovszki, MSc, IVH
Jesse James Westfall, MSc, IVH
Stefan E Seemann, Assoc. Prof., IVH
Vanessa Jane Hall, Assoc. Prof., IVH
Viktoria Anita Lavro, Msc, reNEW

Dates
07.10.2024-20.10.2024 (1st week: Monday, Wednesday, Thursday 9-16, 2nd week: Monday 9-16, Thursday 9-15)

Course location
Department of Veterinary and Animal Sciences (IVH), Univ. of Copenhagen

Registration
Please register before 09.09.2024

Expected frequency
annual

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.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.