Extended Data Fig. 8: Single-cell RNA-seq data quality and inclusion criteria.

a, Histograms of total read counts (left) or features (right) for each single cell. Red represents Flare25 thymic tuft cells and blue represents Flare25;Aire^−/− thymic tuft cells. Cells with fewer than 100,000 reads or 750 detected features were discarded from further analysis. b, Scatter plot of total features versus mitochondrial read percentage. Red represents Flare25 thymic tuft cells and blue represents Flare25;Aire^−/− thymic tuft cells. Triangles and circles denote cells from two separate sorts. Cells with more than 10% of their reads mapping to mitochondrial genes were discarded from further analysis as indicated by the black line.