Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with severity in hospitalized COVID-19 patients

Code and data for the manuscript "Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with severity in hospitalized COVID-19 patients".

Contains all code located at https://github.com/lasalletj/COVID_Neutrophils as well as additional data files needed to run the code.

Three additional publicly available data objects are required to run the code from start to finish. The first, covid.combined_final.Robj, from the Sinha et al. Nature Medicine 2022 paper (https://doi.org/10.1038/s41591-021-01576-3), is downloadable from the following link: https://figshare.com/ndownloader/files/31562957. The other two required objects, seurat_COVID19_Neutrophils_cohort2_rhapsody_jonas_FG_2020-08-18.rds and seurat_COVID19_freshWB-PBMC_cohort2_rhapsody_jonas_FG_2020-08-18.rds, are from the Schulte-Schrepping et al. Cell 2020 paper (https://doi.org/10.1016/j.cell.2020.08.001), and can be downloaded from https://beta.fastgenomics.org/datasets/detail-dataset-ee4b1a0f339140ad82f861aea35076f1#Files and https://beta.fastgenomics.org/datasets/detail-dataset-1ad2967be372494a9fdba621610ad3f3#Files, respectively.

Any additional information required to reanalyze the data reported in this work paper is available from the Lead Contact, Moshe Sade-Feldman (msade-feldman@mgh.harvard.edu) upon request.