GSM8409612: BAL_Rep_1; Macaca nemestrina; RNA-Seq
For single-cell sequencing of bronchoalveolar lavage (BAL) cells, we collected samples before SARS-CoV-2 inoculation and on days 2, 7, 21, and 28 post-challenge. BAL samples were centrifuged at room temperature for 5 min at 1800 rpm, and the resulting cell pellets were resuspended in DMEM supplemented with 10% FBS and 1% Anti-Anti. We used the Parse Biosciences cell fixation kit, following the manufacturer's instructions for PBMCs, to fix the cells (Parse Biosciences, Seattle, WA, USA). Specifically, we fixed 1 million cells per animal/timepoint in a 15 mL falcon tube. The fixed cells were stored at −20 °C until all samples were collected. To enable multiplexing of samples, the Parse Single-Cell whole transcriptome kit, which utilizes a combinatorial barcoding approach (Evercode WT, Parse Biosciences, USA), was employed following the ParseBiosciences Evercode WT v2 User Manual v2.3 . This allowed us to barcode and multiplex 10 samples collected from the coinfected animals across five timepoints.