• Event
  • Scientific training

Single-Cell RNAseq Training Course 2020

Providing an introduction to Single-Cell Genomics, this course is for bench-based researchers planning a single-cell project.

Start date:

20 April 2020

End date:

24 April 2020

Time:

09h00 - 17h00

Venue:

Single-Cell Laboratory & Darwin Suite, Earlham Institute

Registration deadline:

02 March 2020

Cost:

£800 - full course, £300 - bioinformatics days only (22 - 24 April)

About the event.

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.

Programme.

Day 1 - 20 April 2020

Time

Topic

10:00 - 10:30

Registration and Coffee

10:30 - 11:00

Welcome and Course Overview

11:00 - 12:30

Cell sorting and QC

12:30 - 13:30

Lunch

13:30 - 15:00

Group A: 10x setup demo
Group B: Smart-seq2 setup

15:00 - 15:30

Coffee

15:30 - 17:00

Group A: Smart-seq2 setup
Group B: 10x setup demo

17:00 - 17:30

PCR set up

Day 2 - 21 April 2020

Time

Topic

08:30 - 09:00

Coffee

09:00 - 10:30

PCR clean-up demo

10:30 - 11:00

Coffee break

11:00 - 12:00

Keynote speaker (TBC)

12:00 - 12:30

Lunch

12:30 - 13:30

cDNA sample QC (Bioanalyser, GX)

13:30 - 15:00

Library prep (mosquito)

15:00 - 15:30

Coffee

15:30 - 17:00

Library pooling and QC/PCR

Day 3 - 22 April 2020

Time

Topic

08:30 - 09:00

Registration and Coffee

09:00 - 10:00

Course overview and flash presentations from participants

10:00 - 10:30

Introduction to bioinformatics

10:30 - 11:00

Coffee

11:00 - 12:00

Lecture: Library mapping and QC

12:00 - 13:00

Lunch

13:00 - 13:45

Introduction to Galaxy

13:45 - 15:00

Galaxy hands-on: Library mapping RNA

15:00 - 15:30

Coffee

15:30 - 16:00

Galaxy hands-on: Data QC (filtering and visualisation)

16:00 - 17:00

Galaxy hands-on: Troubleshooting data sets

18:30 - 20:30

Workshop dinner - Trattoria Rustica

Day 4 - 23 April 2020

Time

Topic

08:30 - 09:00

Coffee

09:00 - 10:30

Galaxy hands-on: QC of sequencing run

10:30 - 11:00

Coffee

11:00 - 12:30

Presentation from 10x and Q&A

12:30 - 13:30

Lunch

13:30 - 14:30

Workshop with 10x

14:30 - 15:00

Demonstration: 10x Genomics data analysis

15:00 - 15:30

Coffee

15:30 - 16:30

Demonstration: 10x Genomics data analysis (continued)

16:30 - 17:00

Case Study on the use of 10x

Day 5 - 24 April 2020

Time

Topic

08:30 - 09:00

Coffee

09:00 - 10:30

Hands-on: Gene Expression Analysis Pt I

10:30 - 11:00

Coffee

11:00 - 12:00

Hands-on: Gene Expression Analysis Pt II

13:00 - 14:45

Lunch

13:00 - 14:45

Future outlook for single-cell analysis and facilitated discussion

14:45 - 15:00

Feedback and depart (coffee available)

Further information.

Options when applying are:

  • Single-Cell RNAseq Course (Mon-Fri: lab and bioinformatics @800)
  • Single-Cell RNAseq Bioinformatics only (Weds-Fri @£300)

Registration includes lunch and refreshments throughout the sessions that you are attending, plus access to training materials. The course dinner will be on Wednesday 24th April and is included for those attending either option.

For more information, please email us on training@earlham.ac.uk

  • Register today.

Registration deadline: 2 Mar 2020 - 00:00

Participation: Open application with selection process