Fig. 2

scRNA-seq of low RNA-content samples with SHERRY2. A Proportions of genome regions covered by reads from SHERRY2 without DNase treatment, SHERRY2 with AG DNase I addition, SHERRY2 with AG DNase I and DNA carrier addition, and SmartSeq2. B Gene number (FPKM > 1) detected by SHERRY2 with AG DNase I addition, SHERRY2 with AG DNase I and DNA carrier addition, and SmartSeq2 when subsampling to 20, 50, 100, 200, 400, and 600 thousand reads. Only samples with an intergenic rate lower than 25% were counted. Samples in A and B were single lymphocyte cells from murine eyeball blood. C Library quality of SHERRY2 tested with different DNases, including gene number (FPKM > 1) at 0.25 million reads, coverage uniformity across gene body, and percentage of reads that were mapped to intergenic regions. The labels below the figure indicate the amounts and names of the DNases, as well as the EDTA concentration that was added during DNase inactivation. SmartSeq2 was also performed as a reference. D Components of reads covering different genome regions detected by SHERRY2 without DNase treatment, SHERRY2 with optimized AG DNase I, and SmartSeq2. E Gene body coverage detected by SHERRY2 (with AG DNase I) and SmartSeq2. The gray region shows the standard deviation of the normalized depth among replicates. F Gene number (FPKM > 1) detected by SHERRY2 (with AG DNase I and DNA carrier) and SmartSeq2 when subsampling to 20, 50, 100, 200, 400, and 600 thousand reads. G Gene Ontology analysis of genes that were only detected by SHERRY2 (left) or SmartSeq2 (right). The top 20 most commonly occurred GO terms were shown. Samples in C–G were single B cells isolated from murine GC light zones. The p-values in B and F were calculated by the Mann-Whitney U test. The error bars in A and D show the standard deviation