Spatial transcriptomics of post-mortem lung tissue from COVID-19 donors

Visualization of gene expression in lung tissue was performed using Visium spatial gene expression kits (10x Genomics) following the manufacturer`s protocol. The four capture areas in a 10x Genomics Visium Gene Expression slide consist of 5000 spots with DNA oligos for mRNA capture that have a unique spatial barcode and a unique Molecular Identifier (UMI). Each spot has 55 µm diameter and can therefore capture mRNA from 1 to 10 cells. We report the spatially resolved transcriptome of 3 control lung samples from non-COVID-19-related pneumonia donors and 9 COVID-19 lung samples analyzed with the 10x Visium platform. Control (n=3) and COVID-19 lung samples (n=9) from donors categorized based on disease durations (acute n=3, chronic n=3, prolonged n=3) were cut into 10μm sections using a MH560, cryotome (ThermoFisher, Waltham, Massachusetts, USA), and mounted on 10X Visium slides, which were pre-cooled to −20°C. The sections were fixed in pre-chilled methanol for 30 min, stained with CD45-AF647, CD31-AF594 and DAPI for 30min and imaged using an LSM 880 confocal microscope (Zeiss). The sections were then permeabilized for 10 minutes and spatially tagged cDNA libraries were constructed using the 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit. Tissue sections from the same fresh frozen human lung samples used for MELC and snRNA-seq were analyzed by ST.