Introduction to Sequencing-based Spatial Transcriptomics Data Analysis

Overview

Spatial transcriptomics is a rapidly evolving technology that allows researchers to study gene expression within the spatial context of tissue architecture. This course provides a practical introduction to the analysis of sequencing-based spatially resolved transcriptomics (SRT) data, combining theoretical background with hands-on exercises using mostly the R/Bioconductor ecosystem. Participants will gain an understanding of experimental design, data preprocessing, and downstream analysis workflows. Through lectures and guided practicals, the course aims to equip participants with the skills needed to perform their own spatial transcriptomics analyses and interpret the results in a biological context.

Audience

This course is aimed at PhD students, postdoctoral and other researchers in the life sciences who are seeking to understand and analyze spatial transcriptomics data.

Learning outcomes

At the end of the course, the participants are expected to:

• Explain the principles and describe applications of sequencing-based spatially-resolved transcriptomics (SRT)
• Define the differences between sequencing-based SRT methods and imaging-based SRT methods.
• Identify potential pitfalls and limitations of sequencing-based SRT experiments and analysis workflows.
• Assess and interpret raw sequencing outputs and spatial metadata files, understanding their structure and relevance for downstream analyses.
• Define important aspects of quality control, feature selection, dimensionality reduction and differentail gene expression to SRT data and apply those.
• Clarify various spatial statistics and their application to biological questions.
• Use frequently-used methods to analyze multi-sample SRT experiments.

Prerequisites

Knowledge

You should meet the learning outcomes of:

• Introduction to bulk RNA-Seq: From Quality Control to Pathway Analysis
• Introduction to Sequencing Data Analysis, First Steps with R in Life Sciences
• Single-Cell Transcriptomics with R

In summary, participants must already have a basic knowledge in:
- Next Generation Sequencing (NGS) techniques
- Analyzing gene expression data
- Dimensionality reduction (PCA, UMAP)
- Graph-based clustering
- R (evaluate your R skills here)
- UNIX (self-assess your skills with the e-learning course UNIX Fundamentals, and this quiz)

Technical

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 R (> 4.4) and Rstudio before the course.

Application

The registration fees for academics are CHF 200 and CHF 1000 for for-profit companies. While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

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 close on 02/12/2025 or as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 02/12/2025. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

The course will take at Bern University.

The course will start at 9:15 and end around 17:00.

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

Additional information

Coordination: Geert van Geest

We will recommend 0.5 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.