Fig. 4

Sensitivity and accuracy of SHERRY2. A Gene number (RPM > 1) of single HEK293T nuclei detected by SHERRY2 and SmartSeq2 when subsampling reads to 0.1, 0.2, 0.4, 0.6, 0.8, and 1 million reads. B Gene expression correlation between single HEK293T nuclei and 200-ng RNA extracted from the HEK293T nuclei. Single-nucleus data were acquired by SHERRY2 and SmartSeq2. Bulk RNA results were acquired by the standard NEBNext protocol. The correlation R-value was calculated by a linear fitting model with normalized gene counts. C Clustering of HEK293T cellular and nuclear RNA-seq data from SHERRY2, SmartSeq2, and NEBNext using principal component analysis. The analysis utilized differentially expressed genes (adjusted p-value < 1e−4 and fold change > 2) between cells and nuclei detected by NEBNext. D Gene number (RPM > 1) of single neuron nuclei detected by SHERRY2 and SmartSeq2 when subsampling reads to 0.1, 0.2, 0.4, 0.6, 0.8, and 1 million reads. The nuclei were isolated from the mouse hippocampi that were freshly prepared or previously frozen at − 80 °C. E Clustering of the single hippocampal neuron nuclei visualized by UMAP plot. The snRNA-seq library was prepared by SHERRY2. The analysis utilized genes expressed (counts > 0) in more than 4 nuclei. F Marker gene expression of different cell types on UMAP plot from E. The gradient colors correspond to the normalized counts of a specific gene ranging from 0 to 1. The p-values in A, B, and D were calculated by the Mann-Whitney U test