Deep tissue profiling and spatial transcriptomics of the human lung and airways shows micro-anatomical tissue compartments and a survival niche for IgA plasma cells in the airway submucosal glands. NBThighlight
. H&E images generated during the Visium protocol were captured at ×20 magnification on a Hamamatsu Nanozoomer S60.
Dual-indexed libraries were prepared as in the 10X Genomics protocol, pooled at 2.25 nM and sequenced with read lengths 28 bp R1, 10 bp i7 index, 10 bp i5 index, 90 bp R2 for fresh frozen samples or 50 bp R2 for FFPE.). Tissue blocks for smFISH in situ hybridization were chosen based on H&E staining. Ten micron-thick cryosections cut onto superfrost plus slides were processed using the RNAScope 2.5 LS multiplex fluorescent assay on the Leica BOND RX system .
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