The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data

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Fig. 1: EPIC bio-informatics toolkit.
Fig. 2: Exploration of EPIC data and user-generated data.
Fig. 3: EPIC data analytics using an elderly cohort and user uploaded data.

Data availability

The EPIC web portal and its associated database and analytic tools will be made available for investigation as described in the manuscript to researchers who do not belong to a for-profit entity.

Code availability

The web applications Sci-Atlas Miner and Discovery Tool can be freely accessed on all modern web browsers at https://www.epicimmuneatlas.org. The source code of the R Shiny applications and R scripts for the creation of Immune Atlas data files are available on request for academic use.

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Acknowledgements

This research is supported by the National Research Foundation Singapore under its NMRC Centre Grant Programme (NMRC/CG/M003/2017) and administered by the Singapore Ministry of Health’s National Medical Research Council. Other grant support from NMRC (NMRC/TA/0059/2017, NMRC/STaR/020/2013, NMRC/MOHIAFCAT2/2/08, MOHIAFCAT2/0001/2014, NMRC MOHIAFCAT1-6003, TCR15Jun006, NMRC/CIRG/ 1460/2016, MH 095:003\016-0002), Duke-NUS, A*STAR-BMRC (IAF311020) and BMRC (SPF2014/005) is gratefully acknowledged. The pediatric patients were recruited with the strong support of Yew Nam Siow and the Department of Anaesthesia, KK Women’s and Children’s Hospital. Testing of EPIC and feedback by Antonio La Cava, Femke van Wijk, Eveline Delemarre, Antonio Bertoletti, Michelle Hong Li Wen, Matthew Kirkey and Rosa Bacchetta are greatly appreciated. We also acknowledge Loshinidevi Thana Bathi for processing the large number of samples used in EPIC.

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Contributions

S.A. conceived and oversaw the study. E.S.C.L., K.T.Y., A.Y.J.T., S.Y.L., A.L., T.A., M.S.Z.N., T.P.N., S.C., M.G., A.M., S.P.T., S.K.N. and C.F.Y. oversaw the ethics approval, patients screening and recruitment. J.G.Y., S.L.P., F.A., L.L., A.J.M.L. and K.N.Y. performed the experiments. S.L.P. oversaw and coordinated all the mass cytometry staining. P.L. and J.G.Y. performed the initial bioinformatics analysis with input from J.C., F.G., C.-A.D., B.S.P. and J.L. M.W. developed the R-Shiny-based Sci-Atlas Miner tool and P.K. developed the Discovery tool. P.K. and C.J.H.C. constructed the web-based interface and server system. S.A., J.G.Y., M.W. and P.K. wrote the manuscript with input from all other authors.

Corresponding author

Correspondence to Salvatore Albani.

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The authors declare no competing interests.

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Yeo, J.G., Wasser, M., Kumar, P. et al. The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0532-1

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