title: Spatial transcriptomics of mouse lung: Mouse D Section 1 at 10 days post influenza infection
design: Sections obtained from four distinct mice were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomics kit (10x Genomics). Lungs were inflated with 300ul of 50% OCT and 50% PBS v/v and immediately snap-frozen in OCT using isopentane that was cooled in a liquid nitrogen bath. For each lung, the same left lobe was harvested and stored at -80C until cryosectioning. For cryosectioning, samples were equilibrated to -22C. Exploratory sections were stained with a fluorescent lectin and dapi to determine areas of immune infiltration and remodeling, and then blocks were trimmed to 5x5mm to encompass normal and remodeled areas prior to sectioning directly onto the spatial transcriptomics kit slide. Tissue permeabilization was optimized at 12 minutes on independent lung sections. Libraries were sequenced on the Illumina NovaSeq platform at 28x120 basepairs.