• Event
  • Scientific training

Single-Cell RNAseq Training Course

The course will provide an introduction to Single Cell Genomics. It covers several aspects such as the experimental design, cell sorting and processing for production of quality samples for sequencing, generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level.

Start date:

03 December 2018

End date:

07 December 2018

Time:

09h00 - 17h00

Venue:

Single-Cell Laboratory & Darwin Room, Earlham Institute

Registration deadline:

07 October 2018

Cost:

£800 (full course), £50 (single cell imaging only), £300 (computational analysis only), accommodation optional extra (£380)

About the event.

What is the course about?

The course will provide an introduction to Single Cell Genomics. It covers several aspects such as the experimental design, cell sorting and processing for production of quality samples for sequencing, generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants 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 in both the laboratory and 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?

  • Cell sorting, including introduction to different platforms at EI
  • How to generate libraries for sequencing on the MiSeq (G&T-seq and Smart-seq2)
  • Observe loading samples on the MiSeq
  • Understand 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
  • Hands-on experience in identifying Copy Number Variants at the single cell level

Course Prerequisites

Laboratory session: Delegates are expected to be confident and competent in Good Laboratory Practice and with standard laboratory equipment.
Computational Session: A brief recap of LINUX commands will be given as part of the course, however participants will be expected to have a basic level of prior knowledge and experience. If no previous experience, it is recommended that you follow a tutorial such as the one here prior to attending the course.

Target Audience

Web lab researchers. Early career researchers (PhD and early career PostDocs). Those in the experimental planning stages of a project involving single-cell genomics.

Spaces available

For the hands-on single cell sample preparation sessions, 8-10 participants will be selected. For the imaging sessions, we anticipate around 20 participants. For the bioinformatics sessions we will select up to 25 participants. Please note, priority access to the bioinformatics sessions will be given to those also applying for the whole course, which includes the hands-on single cell laboratory sessions.

Programme.

Day 1 - 03 December 2018

Time

Topic

10:00 - 10:30

Coffee and registration

10:30 - 11:00

Welcome and Course Overview

11:00 - 12:00

Introduction to GP services and delegate Q&A

12:00 - 12:30

Lunch

12:30 - 14:00

Cell Sorting and QC

14:00 - 15:00

Group A: G&T-seq
Group B: Smart-seq

15:00 - 15:15

Coffee

15:15 - 16:00

Group A: Smart-seq2 setup
Group B: GT-seq

16:15 - 18:00

Flash presentations from participants

18:00 - 18:30

PCR set up

Day 2 - 04 December 2018

Time

Topic

09:00 - 10:30

Group A: G&T-seq part 2
Group B: PCR clean-up

10:30 - 12:00

Group A: PCR clean-up
Group B: G&T-seq part 2 (coffee available from 10h30)

12:00 - 12:30

Lunch

12:30 - 14:00

Group A: cDNA sample QC (Bioanalyser, GX)
Group B: cDNA sample QC (low volume qPCR)

14:00 - 14:30

Introduction to smFISH

14:30 - 15:00

Sample preparation demonstration (Lab)

15:00 - 15:15

Coffee

15:15 - 16:15

Sample preparation (continued)

16:15 - 17:15

Optical set up and image analysis

17:15 - 17:15

Course dinner - Trattoria Rustica

Day 3 - 05 December 2018

Time

Topic

09:00 - 10:15

QC Summary
10x demonstration
Collect DNA sample

10:15 - 10:30

Coffee

10:30 - 12:00

Group A & B: Library prep

12:00 - 12:30

Lunch

12:30 - 15:00

Group A: Library pooling and QC (PCR)
Group B: Library pooling and QC (Bioanalyser)

15:00 - 15:15

Coffee

15:15 - 17:00

Loading MiSeq

Day 4 - 06 December 2018

Time

Topic

09:00 - 09:15

Karim Gharbi - Genomics Pipelines Services

09:15 - 10:30

Introduction to Bioinformatics
(Coffee available from 10h00)

10:30 - 12:00

Group A & B: Library mapping - DNA & RNA

12:00 - 12:30

Lunch

12:30 - 15:00

Library QC - DNA & RNA
Index counting

15:00 - 15:15

Coffee

15:15 - 17:00

Hands-on: Gene Expression Analysis

Day 5 - 07 December 2018

Time

Topic

09:00 - 10:15

Hands-on: Copy number variant identification

10:15 - 10:30

Coffee

10:30 - 11:30

Demonstration: 10X Genomics data analysis

11:30 - 12:00

Group activities: Troubleshooting data sets and exploring most appropriate algorithms

12:00 - 12:30

Lunch

12:30 - 14:00

Group activities (continued)

14:00 - 15:00

Discussion of results and final Q&A

15:00 - 15:15

Feedback and depart (coffee available)

Further information.

Registration includes lunch and refreshments, plus access to the training materials and the course dinner on Thursday evening.

Fees and accommodation.

Registration includes lunch and refreshments throughout the sessions that you are attending, plus access to training materials. The course dinner is on the Tuesday 4th December and is included for those attending the whole course. It is also available as an optional extra to those attending the Single-Cell imaging session (cost £40)

Options when applying are:

  • Single-Cell RNAseq Course (Mon-Fri: lab, imaging and bioinformatics @£800)
  • Single-Cell imaging (Tue from 14:00-17:15 @£50)
  • Single-Cell RNAseq Bioinformatics only (Thu-Fri @£300)
  • Register today.

Registration deadline: 07 October 2018

Participation: Open application with selection process

Related reading.