Extended Data Fig. 9: Analysis of sequencing depth.
(a–c) Effects of sequencing depth on (a) the number of detected genes and transcript counts per single cell, (b) the number of detected PLA products and their UMI counts, and (c) the number of detected proteins and protein UMI counts in 10x-based Prox-seq. (d) Effects of sequencing depth on automated cell type annotation based on mRNA data with singleR package. The cell type annotation at the maximum sequencing depth is used as the ground truth annotation. (e) Effects of sequencing depth on the number of detected protein complexes. Clusters were identified using mRNA data (see Extended Data Fig. 7). Clusters 0 and 3 were chosen as examples because they had the most number of cells per cluster. In (a–e), the sequencing results of the mRNA and PLA product libraries from the 10x PBMC experiment were downsampled to 10%, 20%, 40%, 60%, and 80% to simulate different sequencing depths. (f, g) Effects of sequencing depth on (f) the number of detected PLA products and their UMI counts, and (g) the number of detected proteins and protein UMI counts in plate-based Prox-seq. In (f, g), the sequencing results of the mRNA and PLA product libraries from the plate-based PBMC experiment were downsampled to 0.5%, 1%, 5%, 10%, 25%, 50%, and 75% to simulate different sequencing depths. The red dashed lines in (e, f) indicate 10,000 mean reads per cell.
