spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content

Copyright and License

© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Acknowledgement

J.D.J. received scholarship support from the BBSRC, T.S.K. was supported by EU H2020 Marie Skłodowska-Curie Individual Fellowship (MSCA-IF 750772), A.L.E. was supported by the Cambridge Trusts and the EU H2020 Marie Curie ITN MMBio and T.N.K. by an AstraZeneca studentship. M.T. was supported by the International Centre for Translational Eye Research (MAB/2019/12) project, which was carried out within the International Research Agendas programme of the Foundation for Polish Science, co-financed by the European Union under the European Regional Development Fund. This work was supported by the EU Horizon 2020 programme (ERC Advanced Investigator Awards to F.H., 69566 and M.Z.G., 669198), the Wellcome Trust (WT108438/C/15/Z to F.H. and 207415/Z/17/Z to M.Z.G.) and the NIH (Pioneer Award to M.Z.G., DP1 HD104575-01). The authors would like to thank the members of the Hollfelder laboratory for their feedback. We thank Dr. Anna Alemany for help and suggestions for the data analysis.

Contributions

These authors contributed equally: Joachim De Jonghe, Tomasz S. Kaminski.

J.D.J., T.S.K. and F.H. conceptualised the study. T.S.K. and J.D.J. developed and optimised the droplet microfluidic workflow. J.D.J. developed and optimised the molecular workflow. J.D.J., A.L.E. and T.N.K. retrieved the cultured cells. G.A., C.H. and J.D.J. retrieved and processed the mouse embryos. J.D.J., T.S.K. and D.B.M. performed the encapsulations. J.D.J. performed library preparation and sequencing. J.D.J. and M.T. performed downstream analysis of sequencing results. J.D.J., T.S.K. and F.H. wrote the manuscript, with input from all authors. F.H., G.M.F., S.T. and M.Z.G. supervised the work.

Data Availability

The sequencing data are available at the following accession number GSE208156. The 1:1 3T3 and HEK293T mixture 10x Chromium v2 dataset used for benchmarking HEK293T cells is available on their website in the'Datasets' category (1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells [https://www.10xgenomics.com/resources/datasets/1-k-1-1-mixture-of-fresh-frozen-human-hek-293-t-and-mouse-nih-3-t-3-cells-2-standard-2-1-0]). The mouse PBMC dataset generated using the 10x Single Cell Immune Profiling (v2) kit is available on their website in the 'Datasets' category (Integrated GEX and VDJ analysis of Connect generated library from mouse PBMCs [https://www.10xgenomics.com/resources/datasets/integrated-gex-and-vdj-analysis-of-connect-generated-library-from-mouse-pbm-cs-2-standard-6-0-1]). The sci-RNA-seq3 E8.5 mouse dataset was obtained from the TOME dataset [https://shendure-web.gs.washington.edu/content/members/cxqiu/public/nobackup/tome_summary_data/mm/seurat_object_E8.5b.rds]; similarly to the E10.5 mouse dataset [https://shendure-web.gs.washington.edu/content/members/cxqiu/public/nobackup/tome_summary_data/mm/seurat_object_E10.5.rds]. The 10x v1 mouse brain dataset was downloaded from SRA with accession number PRJNA637987. The inDrop mouse organogenesis dataset at E8.5 is available on GEO with accession number GSE189425. The designs in Supplementary Fig. 1A and B can be found in our repository DropBase [https://openwetware.org/wiki/DropBase:Devices]. Source data are provided with this paper.

Code Availability

Code for sorting and bioinformatic computation is available at https://github.com/droplet-lab/spinDrop78.

Conflict of Interest

J.D.J., T.S.K. and F.H. are inventors on a patent application (PCT/GB2021/052111) related to the methods presented in this publication and submitted on behalf of the University of Cambridge via its technology transfer office, Cambridge Enterprise. S.A.T. is a Scientific Advisory Board member of Foresite Labs, Qiagen and Element Biosciensces, and a co-founder and equity holder of TransitionBio and EnsoCell. The remaining authors declare no competing interests.