Supplementary Figure 4: Quality control information for the dscATAC-seq mouse brain dataset and comparison with existing data.

(a) Distribution of number of beads per cell identified across the two mice (bead input concentration = 5,000 beads/μL) for high-quality cells that pass quality controls. The corresponding bead merging curves are shown to the right for the twelve libraries. (b) Mouse brain cells in the t-SNE from Fig. 2a colored by number of bead barcodes detected per cell. The same coordinates are shown for (c) mouse donor, and (d) experimental well. (e) De novo embedding using latent semantic indexing (LSI). Colors match annotations from Fig. 2a. All plots show the same (n = 46,653) cells shown in Fig. 2a. (f) t-SNE of previously published sciATAC-seq data for mouse brain (Cusanovich et al., Cell 174(5), 1309–1324.e18, 2018) using the same 7-mer method (Louvain, t-SNE; compare to Fig. 2a; n = 5,744 cells). (g) Comparison of the percentage of reads mapping to the nuclear genome (separated into TSS-proximal or distal chromatin accessibility peaks) between whole mouse brain data generated using dscATAC-seq or a recently optimized sciATAC-seq method (Cusanovich et al., Cell 174(5), 1309–1324.e18, 2018). Center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range. (h) Raw total number of reads mapping to distal chromatin accessibility peaks (see blue from panel (g) between dscATAC-seq and the sciATAC-seq method described in (g)). Boxplots summarize thousands of cells for each comparison. Center line, median; box limits, first and third quartiles; whiskers, 1.5x interquartile range.