Data and code availability
scRNA-seq data generated during this study are deposited at the European Genome-phenome Archive (EGA) under the accession numbers EGAS00001004928 and EGAS00001005634, which is hosted by the EBI and the CRG. snRNA-seq data generated previously (Gassen et al., 2021) are accessible under the accession number EGAS00001004689. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier: PXD022709.
R code used for the analysis of scRNA-seq data has been deposited on GitHub: https://github.com/OliverDietrich/SARS-CoV-2-infection-triggers-profibrotic-macrophage-responses-and-lung-fibrosis
Count matrices and Seurat objects have been deposited via Nubes: https://nubes.helmholtz-berlin.de/s/XrM8igTzFTFSoio.
Python code used for scRNA-seq data integration has been deposited on GitHub: https://github.com/theislab/covid_macrophages_integration