Course at EMBL-EBI

Introduction to RNA-seq and functional interpretation

Gain an introduction to the technology, data analysis, tools, and resources used in RNA sequencing and transcriptomics. The content will provide a broad overview of the subject area, and introduce participants to basic analysis of transcriptomics data using the command line. It will also highlight key public data repositories and methodologies that can be used to start the biological interpretation of expression data. Topics will be delivered using a mixture of lectures, practical exercises, and open discussions. Computational work during the course will use small, example data-sets, and there will be no opportunity to analyse personal data.

In-person course

We plan to deliver this course in-person in our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Who is this course for?

This course is aimed at life science researchers wanting to learn more about processing RNA-seq data and later downstream analysis. It will help those wanting a basic introduction to handling RNA-seq data, guiding them through several common approaches that can be applied to their own datasets. It features taught and practical sessions that cover how to interpret gene expression data and learn more about the biological significance of certain results.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 20 operating system, and the R statistical packages. Some basic tutorials that cover these tools are:

Regardless of your current knowledge, we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area

What will I learn?

Learning outcomes

After the course you should be able to:

  • Describe a variety of applications and workflow approaches for NGS technologies
  • Apply bioinformatics software and tools to undertake analysis of RNA-seq data
  • Evaluate the advantages and limitations of NGS analyses
  • Interpret and annotate data with functional information using public resources
Course content

During this course you will learn about: 

  • RNA-seq file formats and basics of experimental design
  • RNA-seq bioinformatics workflow steps following sequence generation
  • Methods for transcriptomics; QC, mapping, and visualisation tools
  • Data resources to assist in the functional analysis and interpretation of transcriptomic data
  • Introduction to de novo approaches
  • Introduction to single-cell transcriptomics
  • Data resources covered:

Trainers

Simon Andrews
Babraham Institute
Helena Cornu
EMBL-EBI
Nancy George
EMBL-EBI
Vitalii Kleshchevnikov
Sanger Institute

Programme

All times in the programme are listed in GMT.

Time

Topic

Trainer

Day one Monday 20 February 2023

10:00  10:30

Arrival and registration

 

10:30  11:00

Welcome and course introduction

Patricia Carvajal-López

11:00 13:00

Experimental design for RNA-seq lecture and activity

Selene L. Fernández-Valverde

13:00 — 14:30

Lunch break and poster session

14:30 15:30

RNA-seq file formats

Pedro Madrigal

15:30 — 16:00

Coffee break

16:00 17:00

Data reproducibility: Standards and ontologies - lecture and activity

Nancy George

17:00 18:00

Accommodation check-in

 

18:00

Dinner

 

Time

Topic

Trainer

Day two Tuesday 21 February 2022

09:00 10:30

Introduction to RNA-seq

Simon Andrews

10:30 — 11:00

Coffee break

11:00 13:00

RNA-seq practical

Simon Andrews

13:00 — 14:00

Lunch break

14:00 16:30

RNA-seq practical

Simon Andrews

16:30 — 17:00

Coffee break

17:00 18:30

De novo approach to RNA-seq

Selene L. Fernández-Valverde

18:30

Dinner

 

Time

Topic

Trainer

Day three Wednesday 22 February 2022

09:00 10:30

Annotating the genome with RNA-seq data

Leanne Haggerty

10:30 — 11:00

Coffee break

11:00 12:30

Genome annotation practical

Leanne Haggerty

12:30 — 14:00

Lunch break and poster session

14:00 16:30

Next steps in gene prioritisation

TBA

16:30 — 17:00

Coffee break

17:00 18:30

Next steps in gene prioritisation

TBA

18:30

Dinner

 

Time

Topic

Trainer

Day four Thursday 23 February 2022

09:00 10:30

Toward single-cell sequencing

Irene Papatheodorou

10:30 — 11:00

Coffee break

11:00 13:00

Exploring gene expression data

Nancy George

13:00 — 14:00

Lunch break

14:00 15:00

Single cell expression atlas

Nancy George

15:00 15:30

Single cell practical

Nancy George

15:30 — 16:00

Coffee break

16:00 17:00

Human Cell Atlas

TBA

17:00 18:00

Spatial Transcriptomics

Vitalii Kleshchevnikov

18:30

Dinner

 

Time

Topic

Trainer

Day five Friday 24 February 2022

09:00 10:00

Non-coding RNA

Selene L. Fernández-Valverde

10:00 — 10:30

Coffee break

 

10:30 12:00

Galaxy workflows for non-coding RNA

Selene L. Fernández-Valverde

12:00 — 13:30

Lunch break and group photo

13:30 14:30

Exploring biological pathways

TBA

14:30 — 15:00

Coffee break

15:00 16:00

Open Targets Platform  integrating human data for drug discovery

Helena Cornu

16:00 16:30

Course wrap-up

Patricia Carvajal-López

16:30

End of course

17:00 

Coach to Cambridge train station

 

Programme subject to modifications before registration.

Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:

  • Complete the online application form.
  • Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
    • pre-requisite skills and knowledge
    • current work and course expectations
    • data availability
  • Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by midnight on 6 November 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 21 November 2022. If you have any questions regarding the application process please contact Sophie Spencer.

The registration fee, which will be in the region of £825.00 (TBC) includes:

  • Catering as detailed in the course programme
  • Accommodation for four nights (20, 21, 22, and 23 February)
  • Bespoke course handbook with links to all course materials
  • Use of a computer in the EMBL-EBI training suite throughout the course
  • Shuttle bus on the final course day to Cambridge train station

Accommodation 

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Course materials

The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

 

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

Applications close
06 November 2022

20 - 24 February 2023
European Bioinformatics Institute United Kingdom
In the region of £825.00 (TBC)
Contact
Sophie Spencer
Open application with selection
30 places

Organisers

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