Single cell RNA-seq analysis: From questions to clusters

Date:

 Wednesday 27 Friday 29 November 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday 14 June 2019

Application deadline: 

Monday 29 July 2019

Participation: 

Open application with selection

Contact: 

Marina Pujol

Registration fee: 

£270

Dates additional information: 

Please note accommodation will be provided for the 27th, 28th, and 29th. A bus will be provided on Saturday the 30th at 10:00AM to Cambridge train station.

Overview

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to cell cluster comparisons using data extracted from the Single Cell Expression Atlas. In addition to running a basic pipeline, participants will explore the variety of options within the Galaxy resource and individually analyse case study data. The results will be compared across the cohort to assess reproducibility and demonstrate the effect of analytical choice on research output. Finally, participants will learn about data submission, resources, and standards within the single cell field.

Audience

This course is aimed at researchers who are generating, planning on generating, or working with single cell RNA sequencing data.

Prerequisites

Participants will be using a Galaxy resource in-depth. Please ensure that you complete the free tutorial before you attend the course:

There are other tutorials here, although they are not required: https://galaxyproject.org/learn/

Syllabus, tools and resources

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • EMBL-EBI Single Cell Expression Atlas Service
  • Galaxy scRNA-seq pipelines, including: Seurat, SC3, scanpy, and Scater
  • Case study of single cell data

Outcomes

Learning Objectives

After this course, you should be able to: 

  • Explain the steps in the scRNA-seq pipeline
  • Repeat the course analysis of scRNA-seq data from extraction to cluster maps
  • Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation
  • Apply the pipeline to your own data
  • Employ appropriate data standards for repository submission and contribution to global cell atlases

Programme

 

Day 1 – Wednesday 27th, November 2019
09:45 – 10:30 Arrival, Registration & Light Breakfast  
10:30 – 11:00 Welcome to EMBL-EBI and introduction Wendi Bacon
11:00 – 11:30  Introduction to Single Cell RNA-Seq Wendi Bacon
11:30 – 12:30 Experimental design: Wisdom from your wet lab & computational friends Functional Genomics Team
12:30 – 13:30 Lunch  
13:30 – 15:00 Single Cell Expression Atlas Nancy George & Silvie Fexova
15:00 – 15:30 Break  
15:30 – 16:30 Pipeline Overview Wendi Bacon
16:30 – 18:00 Generating the expression matrix Functional Genomics Team
18:30 Dinner at Hinxton Hall  
Day 2 – Thursday 28th November, 2019
9:00 –  9:15 Questions, Review & Catch-up Wendi Bacon
9:15 – 10:15 Introduction to Galaxy & Uploading data Functional Genomics Team
10:15 – 10:45 Tools: Filtration Functional Genomics Team
10:45 – 11:15  Break  
11:15 – 11:45 Tools: Normalisation Functional Genomics Team
11:45 – 12:45 Tools: Scaling data & cluster mapping Functional Genomics Team
12:45 – 13:45 Lunch  
13:45 – 14:45 Tools: Identifying marker genes & comparing clusters Functional Genomics Team
14:45 – 15:15 Building a pipeline Functional Genomics Team
15:15 – 15:45 Coffee  
15:45 – 16:45 Choosing Methods Functional Genomics Team
16:45 – 17:45 Evaluating Pipelines Functional Genomics Team
17:45 – 18:00 Discussion Functional Genomics Team
18:30 Dinner at Hinxton Hall  
Day 3 – Friday 28th November 2019
9:00 – 9:15 Questions, Review & Catch-Up Wendi Bacon
 9:15 – 10:30 Visualising Data Functional Genomics Team
10:30 – 11:00 Coffee  
11:00 – 12:30 Diagnosing Dodgy Data Functional Genomics Team
12:30 – 13:30 Lunch  
13:30 – 14:30 Keynote Lecture Functional Genomics Team
14:30 – 15:30 Group Project Wendi Bacon
15:30 – 16:00 Coffee  
16:00 – 17:30 Group Project Wendi Bacon
17:30 – 18:00 Biological Reproducibility: Do your results stack up? Wendi Bacon
18:00 – 18:15 Wrap up & Feedback Wendi Bacon
18:45 Dinner at Red Lion Pub