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Instructor-led course

Provided by: Bioinformatics

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EMBL-EBI: Transcriptomics Data and Tools (ONLINE LIVE TRAINING)


PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

This workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

This workshop is not going to be a session on how to run your own bioinformatics analysis but to use the tools that have been developed in order to be able to take advantage of others’ work and prepare your work to be reproducible.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • The module is suitable for researchers interested in gene expression analysis and visualisation
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.

Topics covered

Bioinformatics, Database search, Data retrieval, Transcriptomics, Gene expression


After this course you should be able to:

  • browse and retrieve functional genomics data from ArrayExpress with ease
  • search and extract functional genomics data effectively with specific filter
  • describe the caveats and limitations behind the searches made against the ArrayExpress database
  • find information on the abundance and localisation of RNA (and proteins) in different species and biological conditions
  • interpret gene expression analysis results through heatmap visualisation

During this course you will learn about:


Presentations, demonstrations and practicals


Day 1 Topics
Session 1 Welcome and introduction to EMBL-EBI resources and tools
Session 2 Data quality: standards and ontologies
Tea/ Coffee break
Session 3 Discover functional genomics data with ArrayExpress
Session 4 Discover functional genomics data with ArrayExpress: Practical session
Day 2 Topics
Session 1 Explore gene expression data with Expression Atlas
Tea/ Coffee break
Session 2 Explore gene expression data with Expression Atlas: Practical session
Session 3 Single Cell Expression Atlas: a new tool for single cell transcriptomics
Session 4 Q&A Session
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

Two half day sessions


A number of times per year


Related courses
Specialised Research Topics

Events available