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This course will introduce participants to a new generation of 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 both theoretical sessions as well as extensive hands-on practical work 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.
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.
During this course we will cover the following aspects:
- Overview of 10x Genomics Visium Spatial Gene Expression technology
- Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
- Laboratory hands-on practice of running the 10x Genomics Visium Tissue Optimization protocol as well as the Visium Spatial Gene Expression assay from real tissue sections
- Visium Spatial Gene Expression data analysis using Loupe Browser
After this course you will be able to:
- Appreciate the importance of spatially resolved transcriptomics data
- Realize the significance of properly prepared tissue sections by cryosectioning
- Understand the requirements for brightfield and fluorescent tissue slide imaging
- Create libraries for downstream sequencing on Illumina platforms
- Analyse and interpret data output using Loupe Browser