scRNA-seq of 4 uninfected MISTRG-6-15: pooled male and female HSPCs (mCD45hCD45+CD34+) from bone marrow
Bone marrow cells harvested from 2 female and 2 male uninfected MISTRG-6-15 mice at the age of 11 weeks and pooled. HSPCs were sorted (mCD45hCD45+CD34+) using the BD FACSAria III Cell Sorter in PBS with 1% BSA. The cellular suspension was loaded onto a 10 Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3 v3.1 Reagent Kit with dual indexes according to the manufacturers protocol. Library quantification and quality assessment were conducted using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High Sensitivity chip, Agilent Technologies). The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturers protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library. Basecalling and demultiplexing were performed using Illuminas DRAGEN and BCL converts version 4.2.4 software.