Work Package 2: Phenotyping

We will conduct phenotyping in a three-tiered approach in order to create a comprehensive and data-rich annotation of the mutants and utilise the specialist expertise of the European zebrafish research community:

  • Initial phenotyping for morphology and behaviour at day 5 will be carried out by the laboratories that generate the mutants (mainly by GRL, UK).
  • Second-level phenotyping will be carried out for a subset of mutants with first-level phenotypes, as well as on selected mutants from earlier screens, as well as morphants or pharmacologically-treated animals. It will include behavioural phenotyping (by CNRS, France, KIT-G, Germany, and UZH, Switzerland), 3D / 4D imaging (CNRS and KIT-G) and transcript Amounting (mainly by GRL).
  • Third-level phenotyping will include shelf screens for additional phenotypes in which all project partners as well as external researchers will be invited to participate, contributing their assays; as well as in-depth phenotyping and analysis of disease-relevant pathways in the home labs of the participants.

(Work Package Leader: CNRS)

Dissemination of results

All results from initial and second-level phenotyping and shelf screens will be made publicly available as follows:

  • Initial phenotyping, behavioural phenotyping, and shelf screen results will be recorded in a standardised manner using Phenote software and the PATO ontology. Within 6 months of the phenotyping they will submitted to ZFIN, the central model organism database for zebrafish. This will ensure that the phenotyping efforts will contribute to the publicly available annotation of the mutants.
  • Digital reconstructions from 3D / 4D imaging will be made publicly available through a web interface that provides a zoomable “virtual embryo” accessible to the general public, while at the same time encouraging specialists to contribute to the analysis of the phenotype.
  • Transcript Amounting results will be made publicly available through a custom interface to be developed based on the experience of ArrayExpress.

Standardised protocols for all assays used to generate these results will be deposited in a public database which will be modelled on the EmPreSS database of mouse assays, and which will be accessible through the project website.

Results from in-depth analysis of phenotypes and pathways will be released through scientific publications.