Course at EMBL-EBI
Bioinformatics and functional genomics in zebrafish
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.
Please note that this course will not teach the initial steps of RNA-seq analysis but instead start at the point that you have a list of differentially expressed genes. View other EMBL-EBI's courses cover the initial stages extensively, for instance Introduction to RNA-seq and functional interpretation.
In-person course
We plan to deliver this course in an in-person manner onsite at 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 researchers currently working with zebrafish and generating genomic and functional data. Graduate students, postdoctoral fellows, research scientists, and faculty are encouraged to apply.
The course starts at the point where the participant will have a list of differentially expressed genes, therefore 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.
- If you want to get familiar with the initial steps of RNA-seq analysis you can view the materials from other courses that cover them extensively, such as the EMBL-EBI’s Introduction to RNA-seq and functional interpretation course. The Bioinformatics and functional genomics in zebrafish course does not cover these stages.
Some experience with R is beneficial. During the course some of the practicals will make use of a Linux-based command line interface, and R statistical packages. We recommend completing some basic tutorials on this topic in preparation for the upcoming course. There are many tutorials available online and here are some that may be of help:
- To complete the following suggested tutorials you may want to install Ubuntu for Windows Users if you are using a computer with a Windows Operating System.
- Learn Enough Command Line to Be Dangerous - tutorial
- Learn Enough Command Line to Be Dangerous - manipulating files
- Introduction to R tutorials - Programming basics (if you are completing the R tutorials make sure you complete this one first)
- Introduction to R tutorials - Data Visualization Basics
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 this course you should 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
During this course you will learn about:
- Ensembl
- BioMart
- Reactome
- Gene Ontology
- Zebrafish anatomical term enrichment
- Data and metadata submission
- Expression Atlas
- Basic tools for data visualisation using R
Trainers
Elisabeth Busch-Nentwich
Queen Mary University of London Nancy George
EMBL-EBI Louisse Paola Mirabueno
EMBL-EBI Aleena Mushtaq
EMBL-EBI Gun Antonia Nilsson Lock
EMBL-EBI Eliot Ragueneau
EMBL-EBI Ian Sealy
Queen Mary University of London Krishna Kumar Tiwari
EMBL-EBI Richard White
Queen Mary University of London
Queen Mary University of London
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
EMBL-EBI
Queen Mary University of London
EMBL-EBI
Queen Mary University of London
Programme
Time | Subject | Trainer |
Day one – Tuesday 27 September 2022 | ||
10:30 – 11:00 | Arrival and registration | Patricia Carvajal-Lopez and Meredith Willmott |
11:00 – 11:15 | Welcome and introduction | Patricia Carvajal-Lopez |
11:15 – 12:15 | Guidelines for experimental design: General considerations and best Practices | Ian Sealy |
12:15 – 12:30 | Group metadata exercise | Busch-Nentwich Group |
12:30 – 13:30 | Lunch break | |
13:30 – 15:00 | Command line for data filtering | Ian Sealy |
15:00 – 15:15 | Break (with coffee) | |
15:15 – 16:45 | Introduction to Tidy Data and data visualisation with R | Richard White |
16:45 – 17:00 | Break (with coffee) | |
17:00 – 18:00 | Zebrafish-specific dataset practical & Q&A | Busch-Nentwich Group |
18:00 – 18:15 | Break | |
18:15 – 19:00 | Zebrafish-specific dataset practical & Q&A | Busch-Nentwich Group |
19:00 | End of day | |
Day two – Wednesday 28 September 2022 | ||
09:00 | Arrival | |
9:15 – 10:45 | Introduction to Ensembl | Aleena Mushtaq, and Louisse Mirabueno |
10:45 – 11:00 | Break | |
11:00 – 12:30 | Data visualisation and export with Ensembl | Aleena Mushtaq, and Louisse Mirabueno |
12:30 – 13:30 | Lunch break | |
13:30 – 15:00 | Data visualisation and export with Ensembl (continued) | Aleena Mushtaq, and Louisse Mirabueno |
15:00 – 15:30 | Break (with coffee) | |
15:30 – 17:00 | Zebrafish-specific Ensembl practical and further data visualization using R & Q&A | Busch-Nentwich Group |
17:00 – 17:30 | Break (with coffee) | |
17:30 – 19:00 | Zebrafish-specific dataset practical & Q&A | Busch-Nentwich Group |
19:00 | End of day | |
Day three – Thursday 29 September 2022 | ||
09:00 | Arrival | |
9:15 – 10:45 | Gene Ontology | Antonia Lock |
10:45 – 11:00 | Break | |
11:00 – 12:00 | Reactome | Eliot Ragueneau and Krishna Tiwari |
12:00 – 13:30 | Lunch Break | |
13:30 – 14:15 | Cytoscape for visualisation | Richard White |
14:15 – 15:00 | Zebrafish anatomical term enrichment | Ian Sealy |
15:00 – 15:15 | Break (with coffee) | |
15:10 – 16:45 | Practical: Visualisation of GO, ZFA, Reactome & Q&A | Busch-Nentwich Group |
16:45 – 17:15 | Break (with coffee) | |
17:15 – 19:00 | Practical: Visualisation of GO, ZFA, Reactome & Q&A | Busch-Nentwich Group |
19:00 | End of day | |
Day four – Friday 30 September 2022 | ||
09:00 | Arrival | |
9:15 – 10:45 | Data and metadata Submission and zebrafish data in Expression Atlas | Nancy George |
10:45 – 11:00 | Break | |
11:00 – 12:30 | Guided practical (making figures for new zebrafish dataset) | Busch-Nentwich Group |
12:30 – 12:45 | Feedback and wrap up | Patricia Carvajal-López |
12:45 – 13:30 | Lunch break | |
13:30 – 14:30 | Consultation with instructors (by appointment) | |
14:30 | End of course | |
14:40 | Coach to Cambridge train station |
There are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are 6+ weeks. For more information please visit the UK Gov website: https://www.gov.uk/guidance/visa-decision-waiting-times-applications-outside-the-uk#when-you-might-wait-longer
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:
- 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 a 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 Friday 08 July 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 Friday 22 July 2022. If you have any questions regarding the application process please contact Meredith Willmott.
The registration fee of £660.00 includes:
- All meals on the course days (breakfast, lunch, dinner, and refreshment breaks)
- Accommodation for three nights
- Course materials
- Use of a computer in the EMBL-EBI training suite throughout the course
Accommodation
Accommodation will be provided offsite at the Holiday Inn Express. Please contact them directly if you wish to arrange to stay additional nights around the course dates.