Bioinformatics & Functional Genomics in Zebrafish


 Monday 11 Thursday 14 November 2019


European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 13 May 2019

Application deadline: 

Friday 23 August 2019


Open application with selection


Meredith Willmott

Registration fee: 

£510 - (Including meals and accommodation)

Registration closed

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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.


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.

Syllabus, tools and resources

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


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.

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).



Day 1 – Monday 11 November 2019 
10:30 - 11:00 Arrival and Registration  
11:00 -11:45  Welcome and Introduction Ajay Mishra 
11:45 - 12:30 

Guidelines for Experimental Design: General Considerations & Best Practices 

Ian Sealy
12:30 - 12:45  Group Metadata Exercise   
12:45 - 13:30  Lunch   
13:30 - 15:00  Command Line for Data Filtering  Ian Sealy 
15:00 - 15:15  Break   
15:15 - 16:45  Introductions to R and Data Visualisation with R Richard White
16:45 - 17:00  Break   
17:00 - 18:30  Zebrafish-specific Dataset Practical + Q&A  
18:30  End of Day   
19:00  Dinner  Hinxton Hall Restaurant
Day 2 – Tuesday 12 November 2019 
09:00  Arrival   
09:15 - 10:45  Introduction to Ensembl Ben Moore, Ensembl team
10:45 - 11:00  Break   
11:00 - 12:30  Data visualisation and export with Ensembl Ben Moore, Ensembl team
12:30 - 13:30   Lunch    
13:30 - 15:00  Data visualisation and export with Ensembl (continued) Ben Moore and Michal Szpak
15:00 - 15:15  Break    
15:15 - 16:45  Zebrafish-specific Ensembl Practical and Further Data Visualization Using R + Q&A  
16:45  End of Day   
18:00   Dinner  Hinxton Hall Restaurant
Day 3 – Wednesday 13 November 2019 
09:00  Arrival   
09:15 - 10:45  Gene Ontology  George Georghiou
10:45 - 11:00  


11:00 - 12:00  Reactome  Thawfeek Varusai 
12:00 -13:30  Lunch   
13:30 - 14:15  Cytoscape for Visualisation  Richard White 
14:15 - 15:00  Zebrafish Anatomical Term Enrichment  Ian Sealy 
15:00 - 15:15 Break    
15:15 - 16:45  Practical: Visualisation of GO, ZFA, Reactome With R + Q&A  
16:45  End of Day   
18:30  Dinner at the Red Lion Pub, Hinxton Red Lion Pub, Hinxton
Day 4 – Thursday 14 November 2019 
09:00  Arrival   
09:15 - 10:45  Data and Metadata Submission & Zebrafish Data in Expression Atlas  Nancy George and Silvie Fexova
10:45 - 11:00  


11:00 - 12:30  Guided Practical (making figures for new Zebrafish dataset)  
12:30 -12:45 Feedback and Wrap Up Ajay Mishra
12:45 - 13:30  Lunch   
13:30 - 15:00 Consultations with Instructors (by appointment)   
15:00  End of Course   
15:15  Shuttle from Cambridge Station (Stop 5)