Fig. 3: Validation of snCED-seq quality control data. | Nature Communications

Fig. 3: Validation of snCED-seq quality control data.

From: snCED-seq: high-fidelity cryogenic enzymatic dissociation of nuclei for single-nucleus RNA-seq of FFPE tissues

Fig. 3

a–c Number of nuclei (a), UMIs per nucleus (b) and genes (c) per nucleus detected in fresh frozen, PFA-fixed and FFPE samples. d Gene detection per nucleus comparison of our data (> 10,000 nuclei) with mouse tissues (5795 (kidney), 4287 (liver), 6732 (heart) and 3774 (testis) nuelci) by snRandom-seq10, mouse brain (7031) by snFFPE-seq9 and breast (5721) by snPATHO-seq8. Data in the box plot correspond to the first (lower hinges) quartiles, third quartiles (upper hinges), and median (center). The upper whisker extends from the hinge to the maxima no further than 1.5 * IQR from the hinge. The lower whisker extends from the hinge to the minima at most 1.5 * IQR of the hinge. e, f Percentage of mitochondrial (e) and ribosomal (f) genes. g Saturation analysis of snCED-seq based on the different samples. h Percentage of reads mapped to different genomic regions under different conditions. i Counts of different RNA biotypes detected in FFPE brains. j The Pearson’s correlation coefficient (R) of the normalized gene expressions between technical replication samples and post-fixed/fresh samples (All p values = 0). n = 3 biological duplication, and bars show mean ± SD (a–c, e, f and i). a–c, ns p > 0.05, *p < 0.05, **p < 0.01, ***p < 0.001 (Tukey’s multiple comparisons test), and the specific p values are in the source data. Source data are provided as a Source Data file (a–j).

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