EMBL-EBI: Transcriptomics Data and Tools

BeginnersPrerequisites

This workshop will give an introduction to the functional genomics resources provided by EMBL-EBI and hands-on practical experience of searching and accessing appropriate data and information. The session will also cover data submission to ArrayExpress using Annotare.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

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

• This workshop is aimed at researchers who wish to use and submit functional genomics data. This workshop will not however cover the analysis of such data.
• 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 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

Number of sessions: 1

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

After this course you should be able to:

• Explore public datasets within Array Express
• Submit your data using Annotare
• Search for expression information using Expression Atlas

During this course you will learn about:

• Exploring public transcriptomic data: ArrayExpress and Expression Atlas
• Submitting your own data to Array Express

Presentations, demonstrations and practicals

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, 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

0.5 days

A number of times per year

• EMBL-EBI: Introduction to EMBL-EBI resources
• EMBL-EBI: An Introduction to Sequence Searching
• EMBL-EBI: Interactions & Pathways - Reactome
• EMBL-EBI: Interactions & Pathways - IntAct & Complex Portal
• EMBL-EBI: Network Analysis with Cytoscape (Online)
• EMBL-EBI: Introduction to Chemogenomics Resources
• EMBL-EBI: Introduction to Interpro
• EMBL-EBI: Ontologies in life sciences - examples from GO and EFO
• Introduction to RNA-seq and ChIP-seq data analysis
• Analysis of RNA-seq data with Bioconductor
• Analysis of mapped NGS data with SeqMonk (ONLINE LIVE TRAINING)
• CRUK: Analysis of publicly available microarray data