Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients

To understand the cellular composition and transcriptional phenotype of fibrotic lung tissue we performed single-cell RNA-seq on stromal, immune, epithelial, and endothelial cell populations from human lung explants. Tissue was collected from normal control lungs, patients with idiopathic pulmonary fibrosis (IPF), and patients with systemic sclerosis associated interstitial lung disease (SSc-ILD). Using the 10X Genomics Chromium platform, we generated transcriptional profiles of approximately 200,500 cells across 4 IPF, 3 SSc-ILD and 3 normal control lungs. Overall design: Fresh lung explant tissue from 4 IPF patients, 3 SSc-ILD patients, or 3 transplant rejection controls were stored in complete media on wet ice overnight. Tissue was washed, minced, digest and sorted via FACS into separate preparations of EPCAM+, CD31+, CD45+, and triple negative (EPCAM- CD31-, CD45-) cells. For a limited number of samples, unsorted, CD90+, EPCAM+SAbGAL+/- or EPCAM+HT2-280+/- preparations were also made. Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3' Library and Gel bead kit v2, followed by sequencing on the Illumina HiSeq 4000 platform.