Analysis of transcriptomic phenotypes of lung macrophages in severe COVID-19 and SARS-CoV-2 stimulated primary monocytes.

This repository contains the code used to analyze the phenotype of macrophages from bronchoalveolar lavage (BAL) fluid as well as primary monocytes stimulated with, among others, SARS-CoV-2 as shown in

Wendisch, D., Dietrich, O., Mari, T., von Stillfried, S., SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis, Cell (2021), doi: https://doi.org/10.1016/j.cell.2021.11.033.

Data accessibility

Count matrices (matrix.mtx, features.tsv, barcodes.tsv) as well as Seurat objects are stored on the DESY cloud service

https://syncandshare.desy.de/index.php/s/c4kdBJaBjRSGLR7

Count matrices are downloaded directly via R as part of the analysis workflow, manual download is not necessary.

Structure

• *-counts.h5 - Count matrix in HDF5 format
• *-counts - Directory containing
  • matrix.mtx
  • features.tsv
  • barcodes.tsv
• monocyte-clusters-*.tsv - Souporcell clusters to demultiplex samples (Numbers on file match barcodes)
• *.Rds - Seurat object with analysis intermediates (normalized data, embeddings, annotations)

Analysis workflow

To run the analyses please run the following steps:

1. Clone the git repository

   git clone https://github.com/saliba-lab/covid19-profibrotic-macrophages.git
   cd covid19-profibrotic-macrophages
   

2. Install packages via conda

   conda env create -f envs/default.yml
   conda activate covid19-profibrotic-macrophages
   

3. Run analyses

   Rscript R/BAL-macrophages.R
   Rscript R/Monocytes.R
   

License: MIT