How CGaP are using protocols.io to communicate their research

image credited to Wellcome Sanger Institute

Authors: Alexandra Neaverson and James Haldane

The Wellcome Sanger Institute is a non-profit research organisation based in Cambridge, UK, that works to tackle some of the most difficult scientific challenges in genomic research; a task that demands science at scale. Where other research groups delve into the finer details of, for example, the role of a single gene in a single process, the Wellcome Sanger Institute advances that research and scales it up to gain as much data as possible. Historically, this included the Human Genome Project, completed in 2004 with the Institute providing the largest single contribution to the human genome. Current examples include the Tree of Life project, the UK-wide initiative to read the genomes of all 60,000 complex species in the British Isles, and the Human Cell Atlas project, which aims to chart the types and properties of all human cells, across all tissues and organs, to build a reference map of the human body.

Who are CGaP?

The Cellular Generation and Phenotyping (CGaP) core facility provides central cell biology support to the Sanger Institute, functioning as a contract research group in partnership with faculty groups to carry out multiple, distinct cell biology-based projects. Our department practices cell biology at scale; carrying out practical work for academic researchers and various large scale projects; from creating a central resource of derived induced pluripotent stem cells from hundreds of donors (HipSci), to contributions to the Human Cell Atlas project. Notable works include the differentiation of hundreds of pooled iPSC lines into dopaminergic neurons for single-cell RNA-Seq profiling, in order to explore how their differentiation efficiency and response to oxidative stress is affected by genetic background (Jerber et al, 2020). CGaP also contributes to the Deciphering Developmental Disorders project (aiming to improve understanding of rare developmental conditions), derives organoid model systems from normal human tissue and tumours, and carries out whole genome knockout CRISPR library screens to help identify new drug targets using cancer cell lines, iPSCs and organoid models. As of recently, CGaP also plays an instrumental role in the Institute’s contribution to the COVID-19 Genomics UK Consortium, involving large-scale, nation-wide virus sample and metadata collection, preparation, sequencing, analysis and data visualisation.

image credited to Wellcome Sanger Institute

Why are we using protocols.io?

All the protocols published by CGaP can be found here.

Our expertise in large-scale research means that our protocols have been rigorously tested to ensure they are robust and effective, and therefore highly replicable. There is great value in sharing such protocols amongst the scientific community, both for others to discover, and for labs to easily compare the specifics of their methodologies to other groups practicing similar work.

However, whilst most groups publish their methods alongside their work, many scientific journal publications do not provide an in-depth set of instructions for lab protocols. This can sometimes make it difficult for other labs to reproduce the same conditions or test adjustments to their own processes.

image credited to Wellcome Sanger Institute

Whilst we and many others are actively publishing our protocols and methods in journals, protocols.io does a great job of bridging the gap between protocols used in the lab and those published in a journal; allowing us to quickly and effectively share our established in-house methods with others. In addition, many of our internal protocols are frequently updated and adjusted, in accordance with our ongoing research and development. Having the opportunity to update these protocols with new versions on a timely basis, and share them on a public platform, is a strong benefit over traditional publications.

On top of this, we also appreciate the opportunity to discover detailed protocols by other groups in areas where we have less expertise, as well as being able to contrast other methods against our own; allowing us to better understand the more subtle differences in approaches that similar institutions employ. Additionally, whilst many journals do not provide open access articles, we appreciate that protocols.io provides a free platform that anyone can access, widening the audience and increasing accessibility.

Communication is an integral aspect of advancing scientific research, and we are hopeful that services provided by sites like protocols.io become more widespread, allowing for greater transparency, as well as providing a central resource for accessing and reviewing methodology.

Get in touch:

Visit www.jobs.sanger.ac.uk for our latest vacancies, or www.sanger.ac.uk/group/cellular-generation-and-phenotyping/ to find out more about CGaP or get in touch.

References:

J Jerber, DD Seaton, ASE Cuomo, N Kumasaka, J Haldane, J Steer, M Patel, D Pearce, M Andersson, MJ Bonder, E Mountjoy, M Ghoussaini, MA Lancaster, HipSci Consortium, JC Marioni, FT Merkle, O Stegle, DJ Gaffney. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. bioRxiv 2020.05.21.103820; doi: https://doi.org/10.1101/2020.05.21.103820

All images credited to the Wellcome Sanger Institute.

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A secure platform for developing and sharing reproducible methods.