Overview of the single-cell and spatial data generated from TB-diseased and control lungs. (A) Schematic showing the experimental flow for the isolation of cells from human lung tissues, generation of single-cell libraries using Seq-Well S3. Four TB-negative and nine TB-positive lung samples were processed through scRNA-seq. Shown adjacent to the process flow is a low-dimensional embedding (UMAP) of the 19,632 cells passing quality control annotated with high-level cell types (middle) or detailed cell subtype (right). (B) 10x Visium platform workflow for spatial transcriptomics profiling on FFPE samples from TB-diseased lung resections. 21 of these samples come from current TB patients with detectable M.tb; 9 came from post-TB patient, where bacteria are no longer detected in BAL TB culture after infection. Samples contain either granulomas, iBALTs, or lung LNs, representing different pathological states.