Single-Cell RNAseq Training Course 2020

What is the course about?

The course will provide an introduction to Single-Cell Genomics for bench-based researchers with no required prior experience of computational data analysis. It covers several aspects such as the experimental design, cell sorting and processing for production of high-quality samples for sequencing, generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level.

Laboratory practicals will produce real sequencing data. Provided the quality is high enough, delegates will have the opportunity to interpret the data that they have produced. All theory lectures and hands-on sessions will include best practices and tips as learned first-hand by EI's own faculty.

The course will consist of a mixture of conceptual lectures, methodological lectures and hands-on sessions for both the laboratory and the computational analyses, as well as ample time for group discussions.

Participants will gain first-hand experience in generating two different libraries for sequencing, will understand how to assess data quality working with the assistance of the faculty, and in small groups troubleshooting small problems, and reviewing the results.

What will I learn?

Lab sessions:

• Introduction to different sequencing platforms and automation at EI
• Experimental design
• Cell handling and preparation
• Cell sorting (FACS and 10x)
• Generating cDNA using Smart-seq2
• Quality control of cDNA
• How to generate libraries for sequencing on the MiSeq (Smart-seq2)

Bioinformatics sessions:

• Understand the different data generated in scRNA-seq experiments and analyses
• Learn how to assess data quality and troubleshoot problematic samples
• Introduction and hands-on experience in available tools and resources for analysing single-cell data and identifying cell types
• Understanding and experience in generating differential expression analyses using Galaxy
• Familiarity with Cell Ranger and Seurat for 10x Genomics data analysis
• Introduction to long read sequencing for identification of splice variants

Target audience and prerequisites

This course is for bench-based researchers, in the experimental planning stages of a project involving single-cell genomics. No prior experience of bioinformatics is expected and the approaches taught will involve the web-based, user friendly interface, Galaxy. You will not be using the command line during the course.

Laboratory session: Delegates are expected to be confident and competent in Good Laboratory Practice and with standard laboratory equipment.

Spaces available

For the hands-on single cell sample preparation sessions, 8 participants will be selected. For the bioinformatics sessions we will select up to 25 participants.