GSM8067649
Single cell suspensions were generated in 2 % v/v FCS in PBS by mashing fresly isolated lymph nodes, incubated with fluorochrome labelled antibodies for 30 minutes on ice and sorted with a BD FACSAria sorter. After the sorting, cells from the infected and uninfected samples labelled with different hashtag (HTO) antibodies (Uninfected steady state with TotalSeq-A301, infected with TotalSeq-A306, BioLegend). Library construction was performed according to manufacturer's instructions (Single Cell 3' v3, 10x Genomics). Briefly, single cells were encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer's specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Next GEM Single Cell 3' Reagent Kit (10x Genomics) following the detailed protocol provided by the manufacturer.