3rd Programmable nucleases (CRISPR/Cas9) – Transgenesis Course: Ensembl sessions


 Monday 16 Tuesday 17 April 2018


Czech Centre for Phenogenomics, Institute of Molecular Genetics - Prumyslova 595, 252 50,  Prague-Vestec, Czech Republic

Application opens: 

Friday 15 December 2017

Application deadline: 

Wednesday 31 January 2018


Open application with selection

Registration fee: 

EUR 950

Registration closed

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Course Overview

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. These sessions offer participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provide them with the necessary background information. The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users. 

Feedback from previous courses: "There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become" Browser workshop, CRUK, April 2016

"Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert." Browser workshop, Cardiff, March 2014

If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.

Session 1 - Exploring mouse genomes and CRISPR target genes with Ensembl

Ensembl provides access to a comprehensively annotated mouse reference assembly of the C57BL/6J strain. This assembly has been generated by the Genome Reference Consortium, annotated by the Ensembl automatic pipeline and manual curated by the HAVANA group.

In addition, Ensembl imports assemblies and strain-specific gene annotation for 16 laboratory and wild-derived strains generated by the Mouse Genomes Project (http://www.sanger.ac.uk/science/data/mouse-genomes-project), an ongoing effort to sequence genomes of key mouse strains and identify inter-strain variation. Ensembl performs additional analyses, e.g. ab initio gene predictions, annotation of protein domains and comparative genomics analyses, namely Murinae-specific gene trees, orthologue predictions and alignments.

Session 2 - Combining data available in Ensembl for CRISPR design

Ensembl allows to visualise CRISPR/Cas9 sites from the WTSI Genome Editing resource (http://www.sanger.ac.uk/htgt/wge) in any region of the C57BL/6J genome. It includes data for over 84 million short (from dbSNP) and structural variants (from DGVa) and 141,000 phenotypes (from the International Mouse Phenotyping Consortium and the Mouse Genome Informatics resource) for C57BL/6J.

Furthermore, Ensembl provides strain-specific short and structural variants from the Mouse Genomes Project (http://www.sanger.ac.uk/science/data/mouse-genomes-project) and summarises further information such as consequences of variants and genotypes.

This session consists of a presentation giving background to the CRISPR/Cas9 and variant sources used in Ensembl, which are explored in a subsequent demonstration. A set of linked exercises shows how genome, CRISPR/Cas9, variation and comparative genomics data can be combined to design CRISPR experiments for any mouse strain in Ensembl.


Wet-lab researchers and bioinformaticians

Learning outcomes

Participants should be able to:

  • Find mouse genomes in Ensembl and more information about them

  • Understand the different gene annotation processes and additional analyses

  • Explore potential CRISPR target genes and their sequences

  • View nearby genomic regions and manipulate the view to add features they are interested in

  • Understand and find CRISPR/Cas9 and variation data in Ensembl

  • Explore mouse genomic variants and associated phenotypes

  • Combine data types and tools available in Ensembl to design CRISPR experiments for the strain they are interested in.


Monday 16th pm: Session 1 - Exploring mouse genomes and CRISPR target genes with Ensembl
Presentation: Mouse genomics resources in Ensembl, gene annotation and additional analyses
Demonstration: Finding and visualising mouse genomes, genes and genomic regions
Exercises: Exploring genomes of different mouse strains and potential CRISPR target genes

Tuesday 17th am: Session 2 - Combining data available in Ensembl for CRISPR design
Presentation: CRISPR/Cas9, variation and phenotype data in Ensembl
Demonstration: Exploring CRISPR/Cas9, variation and phenotype data
Exercises: Combining genome, CRISPR/Cas9, variation and comparative genomics data for CRISPR design