library_construction_protocol: Lung tissue was digested in 1mg/ml Collagenase D and 10ug/ml DNase1 in RPMI for 45min. After digestion, cells were FC-blocked stained and sorted. 60,000 cells (per sample) were sorted directly into FBS, then stained with TotalSeq hashing antibodies, pooled and stained with CITESeq antibodies for 30min further processing. Approximately 20,000 cells per sample pool were loaded onto the 10X Genomics Chromium Controller (Chip K). Gene expression and feature barcoding sequence libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B). The final libraries were diluted to ~10nM for storage. The 10nM library was denatured and further diluted prior to loading on the NovaSeq6000 sequencing platform (Illumina, v1.5 chemistry, 28bp/98bp paired end sequencing).