Fig. 1

a Schematic overview of the mESC scRNA-seq experiment and sequencing. Three sets of 96 mESCs are profiled using SMARTer and Smart-seq2 protocols on C1-system. For each single-cell, we prepared two sets of libraries for Illumina and BGISEQ-500 platform resulting in 576 matched libraries. b Single-cell detection limit (Sensitivity) of mESC cells, downsampled across two orders of magnitude. The single-cell sensitivities are largely similar between different library preparations across scRNA-seq protocols. c Single-cell accuracy of mESC cells also downsampled across two orders of magnitude. The grey dotted lines in b and c indicate downsampled single cells at different depths, while red line indicates limit for sequencing saturation. d PCA for matched single-cells performed using SMARTer and two replicates of Smart-seq2 and sequenced across both sequencing platforms. Each single cell is represented with a red and green colored circle to indicate HiSeq200 and BGISEQ-500 sequencing platforms respectively. The dotted lines represent distance, i.e., measure of similarity across sequencing platforms. e Single-cell correlations of sensitivity (i.e., lower detection limit computed from spike-in concentrations) for each scRNA-seq protocol and across sequencing platforms. The correlations (R = 0.52~0.70) are comparable between sequencing platforms