Single cell spatial transcriptome and RNA-seq analysis in human lung tissues with mycobacterial infection: Single cell spatial transcriptome

Tuberculosis and non-tuberculous mycobacterial (NTM) diseases are infections caused by Mycobacterium tuberculosis and non-tuberculous mycobacteria, leading to the formation of granulomatous lesions with caseous necrosis in the lungs. We applied spatial transcriptomics at single-cell resolution (CosMx Spatial Molecular Imaging) to human lung samples from patients with mycobacterial infections. RNA-seq was also performed on the samples. CosMx technology [CosMx Human Universal Cell Characterization RNA Panel (1000-plex) genes; Nanostring, USA] was applied to 7 FFPE samples: 3 Mycobacterium tuberculosis (MTB) and 4 non-tuberculous mycobacterial (NTM) patients with a mean of 30.9 fields of view (FoVs) per sample. The mean area explored was 4.6 mm2 per sample. The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 antibodies and DAPI.