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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 as the main aspects to consider when designing a scRNAseq experiment, including a hands-on practical data analysis session applied to droplet-based methods.
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.
At the end of the course, participants will be able to:
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.
Attendees should bring a Wi-Fi enabled laptop. An online R and RStudio environment will be provided, but attendees who wish to run the practicals on their own laptop should install R and RStudio, as well as install the R packages Seurat, scran, scater, SingleR and monocle, before the start of the course.
Introduction to scRNAseq:
Normalization and scalability
Dimensionality reduction and cell type clustering
Cell type identification and marker identification
Differential expression analysis
Differential expression analysis - continued
**The course is now full with a long waiting list. **
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 16/02/2021. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.
This course will be streamed.
It will start at 9:00 and end around 17:00.
Precise information will be provided to the participants in due time.
Coordination: Patricia Palagi
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 firstname.lastname@example.org.