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

Work Group

Project Lead(s)

Project Status


Project Deliverables

An assessment of the quality of the scRNA-seq data obtained for the first 10 samples; 2) a characterization of the cell type composition of the first 10 samples; and 3) a statistical analysis of differential cell type abundance and investigation of T-cell receptor sequencing data and cytokine measurements between samples for defined contrasts.


HMS Department


Project Description

CCB works with the Kagan lab on a single-cell study of 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.