library_construction_protocol: PBMCs were isolated from whole blood by density gradient centrifugation using Histopaque 1077 (Sigma Aldrich) and immediately cryopreserved in 70% DMEM, 20% FBS and 10% DMSO. PBMCs were later thawed and DMSO was removed by 5 serial dilutions in cold growth medium added at 1:1 ratio, followed by cetrifugation and removal of suprenatant. Then, cell pellets were resuspended in PBS + 0.04% BSA, filtered using a 40 micron strainer, counted and loaded to the 10x chromium platform. To minimize batch effects, samples were processed in five randomized and balanced batches of 8, each containing 2-3 samples of each of the 3 patient categories: stable IPF, progressive IPF, and controls. The division into batches can be found in Table E1 in the online manuscript. Cells from each sample were loaded onto the 10x Chromium Chip A, according to the manufacturer's user guide (Chromium Single Cell V(D)J Reagent Kits User Guide, document number CG000086, revision J, November 2018), aiming for recovery of 10,000 cells per lane. The loaded Chip A was placed in 10x Chromium Controller to create Gel Beads-in-emulsion (GEMs). The next steps were carried out according to the manufacturer's user guide, including GEM-RT incubation, post GEM-RT Dynabead cleanup, cDNA amplification and cleanup, fragmentation, end-repair and A-tailing, adaptor ligation, sample Index PCR and double-sided size selection using SPRIselect (Beckman Coulter).