assumptions were not met. We repeated this analysis after separately depleting three additional cell populations (B cells, CD8+ T, CD14+ monocytes), and observed similar results (Supplementary Fig. 4a). Moreover, we found that substantially reducing bridge data quality by discarding UMI (86% downsampling to 750 RNA UMI/cell, or 70% downsampling to 2,500 ATAC fragments/cell) did not adversely affect integration, though we did observe performance reductions after further downsampling (Supplementary Fig. 4b,c).
