Extended Data Fig. 3: Quality control steps of experiment 2.

(A) QC violins from Seurat for RNA-seq and ATAC-seq, dashed red lines indicate thresholds used for filtering, as described in the methods. Outliers with high y-axis values have been removed from selected plots: Percentage of Mitochondrial Genes, 27 outliers; Total ATAC Counts, 16 outliers; TSS Enrichment, 30 outliers. (B-D) QC plots of nCountRNA (B), nCountATAC (C) and nFeatureRNA (D) versus nFeatureRNA (B) or nFeatureATAC (C,D), colored by percent mitochondrial reads, with lines indicating cutoff thresholds shown in violin plots in (A). (E-G) UMAPs showing cells from the MitoPerturb-Seq dataset in Experiment 2, clustered based on overall RNA expression patterns (E), chromatin accessibility profiles (F) and a combined Weighted Nearest Neighbor (WNN) analysis (G), following regression of cell cycle heterogeneity from the RNA-seq dataset. Each point represents an individual cell. Cells are colored by cell cycle phase. (H,I) Percentage of ATAC-seq reads (H) and distribution of mtDNA coverage (I) in the replicate MitoPerturb-Seq dataset aligning to the mtDNA using the standard mm10 reference (light green), a NUMT-masked version of the mm10 genome (dark green), and following addition of enriched mtDNA reads following hybridization capture (purple). Mean coverage values for each group are indicated in (I).