Figure 2: Demonstration of technical performance of GemCode single-cell technology with cell lines and ERCC.

(a) Scatter plot of human and mouse UMI counts detected in a mixture of 293T and 3T3 cells. Cell barcodes containing primarily mouse reads are colored in cyan and termed ‘Mouse only’; cell barcodes with primarily human reads are colored in red and termed ‘Human only’; and cell barcodes with significant mouse and human reads are coloured in grey and termed ‘Human:Mouse’. A multiplet rate of 1.6% was inferred. Median number of genes (b) and UMI counts (c) detected per cell in a mixture of 293T (red) and 3T3 (cyan) cells at different raw reads per cell. Data from three independent experiments were included, mean±s.e.m. (d) Mean observed UMI counts for each ERCC molecule is compared with expected number of ERCC molecules per GEM. A straight line was fitted to summarize the relationship. (e) Principal component analysis was performed on normalized scRNA-seq data of Jurkat and 293T cells mixed at four different ratios (100% 293T, 100% Jurkat, 50:50 293T:Jurkat and 1:99 293T and Jurkat). PC1 and PC3 are plotted, and each cell is colored by the normalized expression of CD3D. (f) SNV analysis was performed, and 293T- and Jurkat-enriched SNVs were plotted for each sample. A 3.1% multiplet rate was inferred from the 50:50 293T: Jurkat sample.