Processing and analyzing single-cell RNA-seq (scRNA-seq) from lung cells are challenging due to the complexity of cell subtypes and biological variations within sample groups. Here, we present a protocol for performing an in-depth assessment on lung lymphocyte populations derived from healthy and Mycobacterium tuberculosis-infected mice. We describe steps for downloading processed scRNA-seq data, integrating samples across different conditions, and performing cluster analysis. We then detail procedures for identifying lymphoid cell subtypes, differential analysis, and pathway enrichment analysis.
For complete details on the use and execution of this protocol, please refer to Akter et al. (2022).
Details
Title
A protocol to analyze single-cell RNA-seq data from Mycobacterium tuberculosis-infected mice lung
Data availability statement
The accession number of the raw and processed data for single-cell RNA sequencing has been deposited in GEO. DOIs are listed in the key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.
Funding Information
University of Chicago National Institutes of Health, HL105427 National Institutes of Health, AI111914 National Institutes of Health, AI134236 National Institutes of Health, AI155024 National Institutes of Health, AI123780