“…To define transcriptional differences among naïve CD4 + T cells with single cell resolution, we first performed scRNA-seq using CEL-Seq2 (Hashimshony et al, 2016) on a population of 1152 naïve CD4 + T cells (sorted from the spleen), of which 697 cells passed quality control tests (Table S1). During the cell sorts, we included measures of CD5 protein level expression for each individual T cell given prior studies implicating CD5 as a key read-out of diversity among naïve T cells (Bartleson et al, 2020;Fulton et al, 2015;Henderson et al, 2015;Mandl et al, 2013;Matson et al, 2020;Persaud et al, 2014;Vrisekoop et al, 2017). We verified that among cells in which Cd5 was detected, transcript counts correlated with measured CD5 protein levels, and drop-outs were more frequent in cells with lower CD5 mean fluorescent intensity (Figure S1), consistent with prior evidence for regulation of CD5 at the transcriptional level (Arman et al, 2004;Tung et al, 2001).…”