Multi-Section Xenium In Situ Protocol for FFPE Human Lung Tissue v1

We adapted the 10x Genomics Xenium In Situ workflow to place six 5 × 6 mm FFPE human lung sections within the 10.45×22.45 mm fiducial-framed capture area of one slide. With two slides per run, each slide one reaction, a single run profiles 12 lung tissue sections. FFPE human lung blocks are scored to one region of interest, sectioned at 5 µm, and processed with multimodal cell segmentation staining, followed by post-run H&E on the same tissue sections. Samples include lung tissue from older donors and upper and lower lobe tissue from explanted lungs of patients with idiopathic pulmonary fibrosis (IPF). Gene expression was assessed using the CH7CY9 panel, a custom 480-gene standalone panel designed from in-house single-cell RNA sequencing data.