The Fish Research Facility (FRF) offers several services. We can offer our technical expertise to support the zebrafish community at UCL with all aspects of zebrafish research from experimental design through to data analysis. In addition to providing bespoke services and advice we also manage outreach activities for ZebrafishUCL, introducing the next generation of scientists to a thriving research environment. We are the hub for local safety inductions, risk assesments and training. We coordinate and promote our sustainability efforts on the fish floor through our ZF Green Lab pages. We also coordinate purchasing for ZebrafishUCL and maintain communal equipment (listed below). Please read more about the services FRF offers below.

The latest addition to the FRF is the Capital Equipment Funded VAST Bioimager.  This remarkable piece of equipment can automate imaging analysis of intact embryos to facilitate genetic screens and other experimental approaches.  We are currently optimising protocols for automated handling and imaging embryos and for analysing data and will have the machine up and running soon.

FRF Services

  • Next-generation sequencing (NGS) library preparation and sequencing using the Illumina NextSeq 550 and MiSeq. MiSeq analysis is cost effective to sequence a large number of short amplicons with high data quality, for example to assess the efficacy of a CRISPR/Cas9 guide.

  • Multiplex whole-mount RNA fluorescence in situ hybridization. We can help you visualise your favourite genes with this powerful technology. HCR probes can even be multiplexed allowing 3D spatial gene expression in the same brain. Stage matched samples can be registered to a single reference brain to make an atlas of gene expression in both mutant and wt zebrafish. This protocol is also compatible with our VAST imager for high-throughput imaging.

  • The VAST Bioimager can automate imaging analysis of intact embryos to facilitate genetic screens and other experimental approaches.  

  • headloop pcr is a simple sequencing-free tool to validate guide RNAs. Headloop PCR works by suppressing amplification of a known wildtype haplotype using a target sequence-specific tagged primer to form a stable hairpin. This doesn’t affect mutant haplotypes, rendering the PCR allele-specific without a priori knowledge of the lesion. This can be used to quantify the efficiency of CRISPR/Cas9 RNPs, and to identify and sequence stably inherited alleles in F1 embryos.

  • We provide help and support to analyse your sequencing data. With our experienced team we can help you with every stage of your research from experimental design to data analysis.

  • Our CRISPR design and targeted Knock Out platform uses innovative headloop PCR. This can be used to quantify the efficiency of CRISPR/Cas9 RNPs, and to identify and sequence stably inherited alleles in F1 embryos.

  • We offer expert support for your whole transcriptome analysis. From experimental design to tissue collection, library creation through to data analysis.

  • We offer expert technical support for your single cell analysis. We use a BD Rhapsody™ HT Xpress single cell partitioning system that collects the cDNA libraries using magnetic bead technology. DNA sequencing libraries are then sent off for sequencing. Support for bioinformatics analysis of sequencing results is also available.

  • We use the CRISPR/Cas9 system to create targeted knock-in transgenic lines. We can support you to design your guides and advise on suitable fluorescent tags to fit your research question.

ZFG Available Equipment

  • Microinjectors and needle puller

  • A wide variety of dissecting and fluorescent microscopes with associated cameras.

  • PCR machines and gel rigs and imager.

  • VAST bioimager

  • Incubators with a variety of temperatures and with specific light cycles for behaviour experiments.

  • cryostat

  • microtome for plastic sections

  • RO water purifier

  • -80 freezers


Our ZGF Facility Manager is Dr Gareth Powell. His decades of research experience at the highest level, with a particular focus on proteomics and genomics mean he is an invaluable resource for the ZebrafishUCL community. Please contact Gareth (g.powell@ucl.ac.uk) for more information about any of our services or for bespoke help with your experimental design and data analysis.