Supplementary Figure 7: Comparison of Gene and Transcript Capture and Percent Contamination Among Massively-Parallel scRNA-Seq Methods Using Mouse and Human Cell Lines

Histograms of the percent cross-species contamination in (a) Seq-Well, (b) Drop-Seq (Ref. 12), and (c) Yuan and Sims (Ref. 15). In each plot, cells with greater than 90% of human transcripts are displayed in blue and cells with less than 10% human transcripts are displayed in red. (d) Transcript capture in human (blue) and mouse (red) cell lines across three massively-parallel, bead-based single-cell sequencing platforms (Seq-Well, Drop-Seq, and 10X Genomics, with downsampling to an average read-depth of 80,000 reads per cell, consistent with 10X genomics data (Center-line: Median; Limits: 1^st and 3^rd Quartile; Whiskers: +/- 1.5 IQR; Points: Values > 1.5 IQR). We detect an average of 32,841 human transcripts and 29,806 mouse transcripts using Seq-Well compared to an average of 39,400 human transcripts and 24,384 mouse transcripts using Drop-Seq, an average of 24,751 human transcripts and 22,971 mouse transcripts using 10X Genomics (available from http://support.10xgenomics.com/single-cell/datasets/hgmm). (e) Gene detection across human and mouse cell lines across the same three single-cell sequencing platforms with down-sampling to the average read-depth of 80,000 reads per cell, consistent with 10X genomics (Center-line: Median; Limits: 1^st and 3^rd Quartile; Whiskers: +/- 1.5 IQR; Points: Values > 1.5 IQR). We detect an average of 6,174 human genes and 5,528 mouse genes using Seq-Well, an average of 5,561 human genes and 4,903 mouse genes using Drop-Seq and an average of 4,655 human genes and 3,950 mouse genes using 10X Genomics. (f) Downsampling to an average of 42,000 reads per cell consistent with data published in Yuan and Sims 2016, results in average detection of 23,061 mouse transcripts using Seq-Well compared to an average of 24,761 mouse transcripts using the Yuan and Sims platform (Center-line: Median; Limits: 1^st and 3^rd Quartile; Whiskers: +/- 1.5 IQR; Points: Values > 1.5 IQR). (g) Downsampling to an average of 42,000 reads per cell results in average detection of 4,827 mouse genes using Seq-Well compared to an average of 4,569 mouse genes using the Yuan and Sims platform (Center-line: Median; Limits: 1^st and 3^rd Quartile; Whiskers: +/- 1.5 IQR; Points: Values > 1.5 IQR).