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

<p>Code and data for the manuscript &quot;Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with severity in hospitalized COVID-19 patients&quot;.</p> <p>Contains all code located at&nbsp;<a href="https://github.com/lasalletj/COVID_Neutrophils">https://github.com/lasalletj/COVID_Neutrophils</a> as well as additional data files needed to run the code.</p> <p>Three additional publicly available data objects are required to run the code from start to finish. The first,&nbsp;covid.combined_final.Robj, from the Sinha et al. Nature Medicine 2022 paper (<a href="https://doi.org/10.1038/s41591-021-01576-3">https://doi.org/10.1038/s41591-021-01576-3</a>), is downloadable from the following link:&nbsp;<a href="https://figshare.com/ndownloader/files/31562957">https://figshare.com/ndownloader/files/31562957</a>. The other two required objects,&nbsp;seurat_COVID19_Neutrophils_cohort2_rhapsody_jonas_FG_2020-08-18.rds and&nbsp;seurat_COVID19_freshWB-PBMC_cohort2_rhapsody_jonas_FG_2020-08-18.rds, are from the Schulte-Schrepping et al. Cell 2020 paper (<a href="https://doi.org/10.1016/j.cell.2020.08.001">https://doi.org/10.1016/j.cell.2020.08.001</a>), and can be downloaded from&nbsp;<a href="https://beta.fastgenomics.org/datasets/detail-dataset-ee4b1a0f339140ad82f861aea35076f1#Files">https://beta.fastgenomics.org/datasets/detail-dataset-ee4b1a0f339140ad82f861aea35076f1#Files</a> and&nbsp;<a href="https://beta.fastgenomics.org/datasets/detail-dataset-1ad2967be372494a9fdba621610ad3f3#Files">https://beta.fastgenomics.org/datasets/detail-dataset-1ad2967be372494a9fdba621610ad3f3#Files</a>, respectively.</p> <p>Any additional information required to reanalyze the data reported in this work paper is available from the Lead Contact, Moshe Sade-Feldman&nbsp;(msade-feldman@mgh.harvard.edu)&nbsp;upon request.</p>