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. Author manuscript; available in PMC: 2024 Jun 21.
Published in final edited form as: Nat Genet. 2023 Jul 27;55(8):1288–1300. doi: 10.1038/s41588-023-01445-4

Extended Data Fig. 1 |. Quality control of single cell RNA and ATAC datasets. Related to Figure 1.

Extended Data Fig. 1 |

(A) Scatter plots of the number of unique fragments by the transcription start site (TSS) enrichment for each of the scATAC-seq samples. Gray dots indicate cells that did not pass quality control filters (Methods). Colorbar indicates the density of points.

(B) Violin plots of the number of unique reads (UMIs, top) and the percent of reads from mitochondrial genes (bottom) for each of the scRNA-seq samples.The inset box plot represent the median, 25th percentile and 75th percentile of the data, and whiskers represent the highest and lowest values within 1.5 times the interquartile range of the boxplot.

(C) Violin plots of the TSS enrichment (top) and number of unique fragments (bottom) for each of the scATAC-seq samples. Box plot as in (B).

(D) UMAP projection of full scRNA-seq dataset, colored by patient sample.

(E) UMAP projection of full scATAC-seq dataset, colored by patient sample.

(F) Differential scATAC-seq peaks between samples processed immediately after collection or after cryopreservation for each of the major cell groupings. Differential peaks (FDR < 0.1) are indicated by colored dots.

(G) Differential scRNA-seq genes between samples processed immediately after collection or after cryopreservation for each of the major cell groupings. Differential genes (FDR < 0.1) are indicated by colored dots.