Fig. 6

Contamination levels for different scRNA-seq protocols, and contamination levels between different tissues and 10X platforms. a Distributions of DecontX-estimated contamination for psudo-cells generated by mixing RNA extracted from three cell lines in ratios of 68%, 16%, and 16% (red), or aliquoting 100% of RNA from one cell line (gray) which were sequenced in either CEL-seq2 or SORT-seq. b Distributions of DecontX-estimated contamination for three cell lines that were mixed and sequenced with the 10X Chromium, Drop-seq, or CEL-seq2 protocols. Additionally, five cell lines were mixed and sequenced using CEL-seq2 protocol in three distinct replicates. c The three-cell-line (left two columns) mixture dataset and the five-cell-line (right two columns) mixture dataset sequenced with 10X Chromium are shown on two dimensions using PCA with normalized counts with and without decontamination. Decontamination decreased within cluster variability while maintaining the overall relationships between clusters. d Distributions of DecontX-estimated contamination for cell types from three different tissues (mouse brain, mouse heart, and PBMC from a healthy donor) profiled using two chemistries (V2 and V3) using 10X Chromium