Supplementary Figure 1: Single-cell transcriptomic workflow and quality control.
Experimental approach for analysis of gene expression in single MDPs, CDPs and pre-DCs using the Fluidgim C1 autoprep system (a). Box plot of log2 r.p.k.m. values of the 264 most commonly expressed genes in single MDPs, CDPs and pre-DCs. Single MDPs, CDPs and pre-DCs were ranked according to their median values of the gene expression of these 264 genes from high to low. The dashed horizontal line in red indicates the threshold used to predict the outlier cells. Red boxes indicate outlier cells that had median log2 r.p.k.m. values below the threshold due to poor sequencing efficiency (b). Principal component Analysis (PCA) plot of cells using the 264 most commonly expressed genes. Red boxes indicate outlier cells that were identified in Supplementary Fig. 1b (c). Bar plot of total number of reads, number of mapped reads and mapping rate in each individual MDP, CDP and pre-DC (d). Correlation of ERCC spike-in RNA and detected r.p.k.m values detected across all mRNA sequenced cells (R2: Pearson’s correlation coefficient, (e)). Assessment of capture batch effect on CDP single cell mRNA sequencing data. CDP color coded for different capture batches analyzed using hierarchical clustering (f). Assessment of capture batch effect on pre-DC single cell mRNA sequencing data. pre-DC color coded for different capture batches analyzed using hierarchical clustering (g). MDP was captured using 1 Fluidigm C1 IFC, CDP was captured using 5 Fluidigm C1 IFCs, pre-DC was captured using 3 Fluidigm C1 IFCs.
