Single-cell characterization of acute inflammation in patients with COVID-19

Work Group

Project Lead(s)

Project Status

Ongoing

Project Deliverable

Single-cell RNA-seq analysis of bronchoalveolar lavage samples from 80 patients with COVID-19

Collaborator Name

Jonathan Kagan, PhD

HMS Department

Virology

Project Description

Dr. Kagan is working on COVID as part of a collaboration between HMS and AbbVie. As part of a deeper molecular characterization of inflammation processes in acute COVID-19, the Kagan Lab aims to profile 80 bronchoalveolar lavage (BAL) samples from 71 patients via 10x Genomics single-cell RNA-sequencing (scRNA-seq). In an initial pilot phase of the project, Dr. Kagan and his team have obtained scRNA-seq data for 10 of the patients including 6 confirmed COVID cases, 2 cases of non-covid respiratory failure, and 2 healthy controls. Before proceeding with scRNA-seq of the full cohort of patients, Dr. Kagan would like to get a basic impression of the quality and informativeness of the data for the first 10 patients with regard to the biomedical question at hand, including cell type composition of the samples and whether a meaningful differential expression signal is observed in the data.