Single-cell RNA transcriptomics of thymic iNKT cells from C57BL/6 and Hivep3-/- mice

Single-cell RNA-seq analysis of murine thymic iNKT cells from two independent C57BL/6 mice and two independent Hivep3-deficient mice Processed thymocytes were enriched for PBS57-CD1d reactive cells by incubating thymocyte cell suspensions with PE or APC conjugated PBS57-CD1d tetramers for 45 minutes at 4C, then incubated with anti-PE or anti-APC magnetic microbeads (Miltenyi Biotec) for 15 minutes at 4C, followed by separation by using an autoMACS Pro Separator (Miltenyi Biotec) according to manufacturer’s instructions. A 50:50 mix of CD44low and CD44high PBS57-CD1d tetramer+ cells were sorted using a BD Facs Aria. Single-cell RNA-seq was performed using 10X Genomics Chromium isingle-cell controller and 5' gene expression kit.