mRNA from single cells sorted from human and mouse lungs and human blood into lysis plates was reverse transcribed to complementary DNA (cDNA) and amplified as previously described2 (link). Illumina sequencing libraries for cDNA from single cells were prepared as previously described2 (link). Briefly, cDNA libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131–1096). Nextera tagmentation DNA buffer (Illumina) and Tn5 enzyme (Illumina) were added, and the sample was incubated at 55°C for 10 minutes. The reaction was neutralized by adding “Neutralize Tagment Buffer” (Illumina) and centrifuging at room temperature at 3,220 x g for 5 minutes. Mouse samples were then indexed via PCR by adding i5 indexing primer, i7 indexing primer, and Nextera NPM mix (Illumina). Human samples were similarly indexed via PCR using custom, dual-unique indexing primers (IDT)2 (link).
Following library preparation, wells of each library plate were pooled using a Mosquito liquid handler (TTP Labtech), then purified twice using 0.7x AMPure beads (Fisher A63881). Library pool quality was assessed by capillary electrophoresis on a Tapestation system (Agilent) with either a high sensitivity or normal D5000 ScreenTape assay kit (Agilent) or Fragment analyzer (AATI), and library cDNA concentrations were quantified by qPCR (Kapa Biosystems KK4923) on a CFX96 Touch Real-Time PCR Detection System (Biorad). Plate pools were normalized and combined equally to make each sequencing sample pool. A PhiX control library was spiked in at 1% before sequencing. Human libraries were sequenced on a NovaSeq 6000 (Illumina) and mouse libraries on a NextSeq 500 (Illumina).
Cells isolated from each compartment (“immune and endothelial enriched”, “epithelial enriched”, “stromal”) and subject blood were captured in droplet emulsions using a Chromium Single-Cell instrument (10x Genomics) and libraries were prepared using the 10x Genomics 3’ Single Cell V2 protocol as previously described2 (link). All 10x libraries were pooled and sequenced on a NovaSeq 6000 (Illumina).
Following library preparation, wells of each library plate were pooled using a Mosquito liquid handler (TTP Labtech), then purified twice using 0.7x AMPure beads (Fisher A63881). Library pool quality was assessed by capillary electrophoresis on a Tapestation system (Agilent) with either a high sensitivity or normal D5000 ScreenTape assay kit (Agilent) or Fragment analyzer (AATI), and library cDNA concentrations were quantified by qPCR (Kapa Biosystems KK4923) on a CFX96 Touch Real-Time PCR Detection System (Biorad). Plate pools were normalized and combined equally to make each sequencing sample pool. A PhiX control library was spiked in at 1% before sequencing. Human libraries were sequenced on a NovaSeq 6000 (Illumina) and mouse libraries on a NextSeq 500 (Illumina).
Cells isolated from each compartment (“immune and endothelial enriched”, “epithelial enriched”, “stromal”) and subject blood were captured in droplet emulsions using a Chromium Single-Cell instrument (10x Genomics) and libraries were prepared using the 10x Genomics 3’ Single Cell V2 protocol as previously described2 (link). All 10x libraries were pooled and sequenced on a NovaSeq 6000 (Illumina).
