Tumor Cell Isolation for Single-Cell RNA-Seq

Micro-dissected lung tumors were dissociated with collagenase IV, dispase, and trypsin at 37°C for 30 minutes as previously described^{118 (link)}. The digestion buffer was then neutralized with cold L-15 media (Thermo Fisher Scientific: 21083027) containing 5% FBS (Gemini Bio) and DNaseI (Sigma-Aldrich: DN25). Dissociated cells were treated with ACK Lysis Buffer (Thermo Fisher Scientific: A1049201) and resuspended in PBS containing 2 mM EDTA (Promega: V4233), 2% FBS, and DNase I. For the isolation of neoplastic cells, dissociated cells were stained with DAPI and antibodies against CD45 (BioLegend: 103112; 1:800 dilution), CD31 (BioLegend: 102402; 1:800 dilution), F4/80 (BioLegend: 123116; 1:800 dilution), and Ter119 (BioLegend: 116212; 1:800 dilution) to exclude hematopoietic and endothelial cells. FACSAria™ sorters (BD Biosciences) were used for cell sorting. For sorting of total cells within tumors for single-cell RNA-seq, dissociated cells were stained with DAPI only to exclude dead cells. Representative gating scheme included in Supplementary Fig. 20a.