Zebrafish are widely used to study development, toxicity and disease, and functional genomics is used throughout the field to identify new pathways and mechanisms and for comparison to other model systems and humans. In this hands-on course, participants will learn how to design functional genomics experiments, manage and analyse RNA-seq datasets from zebrafish, and compare results to other species. The aim of the course is to equip researchers with tools to carry out functional analysis and data visualisation of RNA-seq data that has already been mapped to the genome and been analysed for differential gene expression. The course will be relevant to researchers working on a wide range of topics and will use real datasets from our lab for hands-on analysis.

Who is this course for?

This course is aimed at researchers currently working with zebrafish and generating genomic and functional data. Graduate students, postdoctoral fellows, research scientists and faculty are encouraged to apply.  Little to no experience with RNA-seq analysis is required, however, applicants who have already generated an RNA-seq dataset from zebrafish samples relevant to their project will gain the most benefit from this course.  Some experience with R is beneficial.

What will I learn?

Learning outcomes

At the end of this course, students will be able to:

• Design and implement RNA-seq experiments using zebrafish
• Know and apply common approaches and tools used in the analysis of zebrafish expression data
• Undertake basic data visualisation
• Query RNA-seq datasets for gene signatures and patterns of gene expression
• Undertake cross-species comparison of gene datasets
• Have working knowledge of web- and R-based approaches for analysing gene expression.

Course content

This course will cover:

• Ensembl
• BioMart
• Reactome
• Gene Ontology
• Zebrafish anatomical term enrichment
• Data and metadata submission
• Expression Atlas
• Basic tools for data visualisation using R

Trainers

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

1. Complete the online application form
2. Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Meredith Willmott (meredith@ebi.ac.uk) by 12:00 GMT on Friday 23 August, 2019.

Incomplete applications will not be considered.

Note that this course focuses only on the analysis of gene lists generated from RNA-seq data that has been mapped and quality controlled, and does not cover in depth methods required for mapping RNA-seq reads and running differential gene expression analysis.

Researchers interested in learning more about the upstream analysis (QC, mapping, counting, differential expression, etc.) are encouraged to enroll in RNA-Sequence Analysis course (April 2020) at EMBL-EBI. To get an idea about what this course may cover, please refer to our previous RNA-Sequence Analysis course (April 2019).