Lecture 12

12.0 Lesson learning objectives

By the end of this lesson, we should be able to understand spatial transcriptomics technologies based on spot-based capture and sequencing, how they can work, and begin analyzing some data.

Spatially resolved transcriptomic sequencing with Visium

Visium is a commercial platform that uses glass slides with arrayed oligonucleotides containing positional barcodes to generate cDNA libraries with positional information for RNA sequencing. The technique was introduced in the paper Stahl et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science (2016) and later licensed to 10X Genomics for commercialization.

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Hands-on component 12

Our in-class hands-on component will involve analyzing a spatial transcriptomics dataset.

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Class Lesson Notes 12

Prof. Fan’s notes from class: genomic-data-visualization-Lesson_12.pptx (click to download)

Prof. Fan’s code from class: code-02-20-2023.R (click to download)

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Homework Assignment 12

Analyze the Visium dataset. Perform analyses and create a multi-panel data visualization with a corresponding ‘figure caption’ that describes your data visualization.

See slides for more details on what is expected: genomic-data-visualization-HW_6.pptx (click to download)

Make a pull request to submit your homework (due Thursday midnight).