Gene Expression at Spatial Resolution – Virtual

Overview
Speakers, Trainers and Organisers
Programme

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

Course Overview

This interactive virtual course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. The Visium Spatial Gene Expression Solution incorporates unbiased, high-throughput total mRNA analysis for intact tissue sections with morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Spatial Gene Expression slides. Through theoretical and interactive sessions as well as remote demonstrations of some of the practical work in the lab, the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and optimisation of tissue permeabilisation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training of spatial transcriptomics data analysis.

Please note that all participants are expected to engage in all sessions. Each participant will receive a shipment with materials to take part in the practical part of the virtual course.

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 Spatial Gene Expression application into their labs/research.

Modules/Resources

During this course we will cover the following aspects:

Overview of 10x Genomics Visium Spatial Gene Expression technology
Application lectures on Spatial Transcriptomics
Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
Online laboratory demonstration of key steps in the 10x Genomics Visium Tissue Optimization protocol based on real tissue sections
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

Speakers, Trainers and Organisers

Katharina Danielski

10x Genomics,

Germany

Adam Jerauld

10x Genomics,

Sweden

Natalia Anahi Juiz

10x Genomics,

France

Aleksandra Jurek

10x Genomics,

Sweden

Christoph Kuppe

Uniklinik RWTH Aachen,

Germany

Oliver Stegle

EMBL Heidelberg and German Cancer Research Center,

Germany

Scientific Organisers