Overview

In contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expression at a whole population level, single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression profile at a single cell resolution while enabling the discovery of tissue specific subpopulations and markers. For example, contrasting different sample conditions i.e. disease vs. normal using scRNAseq can help identify sub-cellular differential behaviours and thus target specific gene markers. This 3-day course will cover the main technologies as well main aspects to consider while designing a scRNAseq experiment including a hands-on practical data analysis session applied to droplet-based methods.

Audience

This course is intended for life scientists and bioinformaticians familiar with "Next Generation Sequencing" who want to acquire the necessary skills to analyse scRNA-seq gene expression data.

Learning objectives

At the end of the course, participants will be able to:

• distinguish advantages and pitfalls of scRNAseq
• design their own scRNA-seq experiment
• apply a downstream analysis using R

Knowledge / competencies prerequired (Mandatory)

Participants should already have a basic knowledge in Next Generation Sequencing (NGS) techniques, or have already followed the "NGS - Quality control, Alignment, Visualisation". Knowledge in RNA sequencing is a plus. A basic knowledge of the R statistical software is required. Test your R skills with the quiz here, before registering.

Technical requirements

Attendees should have a Wi-Fi enabled computer. An online R and RStudio environment will be provided. However, in case you wish to perform the practical exercises on your own computer, please take a moment to install the following before the course:

• R version > 4.0.
• Latest RStudio version, the free version is perfectly fine.

Program

Program will be communicated in due time. Program of past occurences can be found on GitHub.

Application

The registration fees for academics are 180 CHF and 900 CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications will close once the places will be filled. Deadline for registration and free-of-charge cancellation is set to 30/10/2022. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will ONLY take place in person at the University of Bern

It will start at 9:00 CET and end around 17:00 CET.

Precise information will be provided to the participants in due time.

Additional information

Coordination: Diana Marek

We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.