Spatial gene expression at species agnostic level

Overview

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Course overview

This interactive course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. Objectives The Visium Cytassist Spatial Gene Expression Solution uses probes targeting the whole transcriptome for intact tissue sections in morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Cytassist Spatial Gene Expression slides. Through practical work in the lab and theoretical sessions, the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training in spatial transcriptomics data analysis.

Audience

This is an interdisciplinary course designed for molecular biologists as well as researchers more familiar with morphology analysis by brightfield and fluorescence microscopy who are seeking to introduce the 10x Genomics Visium Cytassist Spatial Gene Expression application into their labs/research.

Modules/resources

• Overview of 10x Genomics Visium Cytassist Spatial Gene Expression technology
• Focusing on fresh-frozen samples with Hematoxylin and Eosin (H&E) staining
• Alternative staining by Immunofluorescence and usage of FFPE samples as starting material
• Pre-recorded application lectures on Spatial Transcriptomics
• Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
• Visium Spatial Gene Expression data analysis using Loupe Browser (license-free)
• 1-on-1 Project Consultation with application specialist (optional service offered at the discretion of the individual participant)

Learning outcomes

After this course you will be able to:

• Appreciate the importance of spatially resolved transcriptomics data
• Realise the significance of properly prepared tissue sections by cryosectioning
• Understand the requirements for brightfield and fluorescent tissue slide imaging
• Analyse and interpret data output using Loupe Browser

What past participants say about the course

“This course provided a week of hands-on practical training on 10X Visium, complemented byscientific talks and discussions. Not only was I introduced to the workflow of the technique,but I also received advice tailored to my specific research question and tissue type. Rounded off with a thorough step-by-step guide on data analysis, I now feel confident to start my experiments soon.” – Lisa Mayrginther, Maastricht University, The Netherlands

“Gene expression at spatial resolution workshop was amazing! Thanks to the organizing team and all the trainers, I could practice each step from sectioning to data analysis. Also, meeting with other participants with varying backgrounds and the expert lecturers was a great opportunity.” – Mustafa Beter, University of Eastern Finland, Finland

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

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