Introduction to Spatial Transcriptomics Data Analysis

Course Length

3 mandatory days and 1 optional day

Course Description

Discover the exciting field of spatial transcriptomics and learn how to analyze spatially resolved gene expression data in our new introductory course. This class provides a foundational overview of the methods and technologies underlying spatial transcriptomics, a cutting-edge approach that combines gene expression profiling with spatial context. Designed as an introduction, the course focuses on basic data analysis techniques to help participants build a strong understanding of sequencing-based and imaging-based spatial transcriptomics technologies. Hands-on exercises will offer practical experience, making the concepts accessible and easy to grasp. As a special feature, the final day of the course is optional and dedicated to personalized learning. Participants are invited to bring their own datasets and receive expert guidance in applying the fundamental analysis methods covered during the course. Whether you are new to the field or looking to build a foundational understanding, this course will equip you with the basic knowledge and skills needed to begin working with spatial transcriptomics data.

Course Programme

General Overview of Spatial Transcriptomics
• Brief history of spatial transcriptomics
• Overview of different categories of current spatial transcriptomics methods
• Detailed introduction to Spatial Transcriptomics at FGCZ
  -Strengths and limitations of different technologies
• Lab tour for spatial transcriptomics instruments

Introduction to Spatial Transcriptomics Analysis
• Data preprocessing and quality control for Visium HD and Xenium data
• Spatial visualization of gene expression patterns
• Cell type annotation using scRNA-seq reference mapping
• Spatial clustering and region identification
• Differential expression analysis in spatial context
• Analysis of spatial relation between cell types
• Hands-on analysis using Seurat V5 spatial workflows

Optional: Own Data Analysis
• Consultation on participant-provided datasets
• Discussion of experimental design considerations
• Guided analysis of individual research questions
• Troubleshooting common challenges in spatial data
• Implementation of customized analysis workflows
• Integration of spatial data with other omics data types

Didactical approach
The course is conceived highly interactive which includes:
• Theoretical inputs (lectures)
• Interactive discussions on case studies (group discussions)
• Instrument introduction (during lab tour)
• Hands-on activities for data analysis (computer sessions)
• Q&A sessions, feedback and discussions with other participants and instructors

Learning outcomes
At the end of the course, participants will be able to:
• Summarize the principles of current spatial transcriptomics methods and data analysis concepts
• Critically evaluate spatial transcriptomics data and analysis results
• Apply fundamental visualization and interpretation techniques to spatially resolved transcriptomics data
• Discuss how spatial transcriptomics can be integrated into a research experiment
• Make an informed decision, which Spatial Transcriptomics technology to apply to a specific research question

Important facts and how to apply

Language

The course will be taught in English.

Participants

The course is limited to a maximum of 10 participants.

Target audience and prerequisites

The course is aimed at:
Doctoral and post-doctoral scientists who have already generated spatial transcriptomics data or are planning a project soon.

Requirements:
Basic knowledge of R
Experience with bulk RNA-seq data interpretation
Basic knowledge of single-cell RNA-seq is recommended

Costs

PhD Students UZH or ETHZ CHF 300

Postgraduate Member UZH or ETHZ CHF 500

Please note, that these prices can only be applied if the tuition fee is paid through an internal, i.e. University of Zürich or ETHZ, account (valid Kostenstelle/PSP-Element).

Other academics (non-UZH, non-ETHZ) CHF 1200

Industrial delegates CHF 1500

An invoice will be issued. Those participants that register will be sent an email with an ‘Application Form’ to be signed by their correspondent supervisor and e-mailed back to the FGCZ as PDF. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed.

Those participants that register will be sent an email reserving their place together with an ‘Application Form’ to be signed by their correspondent supervisor and emailed back to the FGCZ. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed. An invoice will be issued. Please check our invoicing conditions before registering, see Question 13): FAQ Courses – Functional Genomics Center Zurich.  

Cancellation policy

Please note that due to the high demand for this course any change related to your participation should be informed as soon as possible, but not later than ten (10) working days (for internal participants) prior to the course start date if the invoice has not yet been issued. 20 working days for external participants.The cancellation request must be e-mailed to . If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.

Please do not hesitate to contact us should you need any additional information or encounter any problems.