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Addgene AAV Data Hub: a platform for sharing AAV experimental data

Nature Methods volume 20, pages 1271–1272 (2023)Cite this article

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Data sharing increases transparency and reproducibility of experimental work, and there are rapidly growing requirements for data sharing by journals and bodies that govern and fund scientific research1. While there is support in the field for increased data sharing, particularly in accessing it for one’s own experiments, the time and effort it takes for those generating the data to make it accessible to others remain a barrier to widespread adoption of both data sharing and best data sharing practices2. It is therefore important that data sharing platforms, or data repositories, focus on creating an excellent user experience for contributing scientists through creation of a process that minimizes time and effort needed to submit data while simultaneously maximizing the utility of the data. In this article, we discuss the creation of the AAV Data Hub (https://datahub.addgene.org), designed to meet the needs of the scientific community.

Addgene, a nonprofit repository for DNA-based biological materials, is an established hub for the creation of community resources, such as our 125,000-plus plasmid collection, complete with sequence data for each plasmid. Our repository includes adeno-associated viruses (AAVs), versatile vehicles for gene delivery used clinically for gene therapy and in basic science for a variety of disciplines, particularly in the study of neuroscience. Despite their widespread use, there is a lack of accessible data allowing users to understand which AAV serotypes, promoters and/or dosages work best in a given system. Subtle differences in AAV production such as buffer, cell line and batch-to-batch variation can lead to profound differences in AAV expression profiles3,4,5. While publications often share the AAV serotype and promoters used, they do not require standardized reporting of experimental methods and details and thus do not have sufficient details to replicate AAV experimental conditions or to robustly compare experimental results. Importantly, manuscripts often exclude negative data6,7.

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Fig. 1: AAV Data Hub examples.

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Acknowledgements

The authors would like to acknowledge J. Snair for his contributions to the visual design and overall user experience of the website; L. Haery and N. Waxmonsky for their contributions to the beta Data Hub project; and J. Dwyer for her help in preparing the manuscript. The AAV Data Hub is supported by a grant (2021-236375, J.S.N and D.B.W) from the Chan Zuckerberg Initiative. The content of this article is solely the responsibility of the authors and does not necessarily represent the views of the Chan Zuckerberg Initiative.

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Authors and Affiliations

  1. Addgene, Watertown, MA, USA

    Jason S. Nasse, Rachel Leeson, Heather Zirkle, Daniela Bourges-Waldegg, Brook Pyhtila & Melina Fan

Authors
  1. Jason S. Nasse
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  2. Rachel Leeson
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  3. Heather Zirkle
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  4. Daniela Bourges-Waldegg
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  5. Brook Pyhtila
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  6. Melina Fan
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Contributions

M.F. and D.B.W. conceived the Data Hub. J.S.N., B.P., H.Z. and D.B.W. led the design and implementation of the Data Hub website, form submission and database. J.S.N. collected user feedback and acquired reports. R.L. drafted the manuscript. All authors commented on the manuscript.

Corresponding author

Correspondence to Melina Fan.

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All authors are employees of Addgene.

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Nasse, J.S., Leeson, R., Zirkle, H. et al. Addgene AAV Data Hub: a platform for sharing AAV experimental data. Nat Methods 20, 1271–1272 (2023). https://doi.org/10.1038/s41592-023-01963-3

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