Fig. 2

FixNCut protocol tested in mouse lung samples. a Mapping analysis of sequencing reads within a genomic region. b Comparative analysis of the number of detected genes (top) and UMIs (bottom) across various sequencing depths. c Cumulative gene counts analyzed using randomly sampled cells. d Principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) representation of gene expression profile variances of fresh and fixed samples. e Linear regression model comparing average gene expression levels of expressed genes between protocols. The coefficient of determination (R²) computed with Pearson correlation is indicated. f Hierarchical clustering of coefficient of determination (R²) obtained for all pair comparisons between protocols for biological hallmarks, including apoptosis, hypoxia, reactive oxygen species (ROS), cell cycle G2/M checkpoint, unfolded protein response (UPR), and inflammatory response genes. g UMAP visualization of 19,606 fresh and fixed mouse lung cells, colored by 20 cell populations. h Comparison of cell population proportions between fresh (n = 10,289) and fixed cells (n = 9317). The top figure shows the difference in cell population proportions between fresh and fixed samples, and the bottom figure shows the results of the compositional cell analysis using the Bayesian model scCODA. Asterisks (*) indicate credible changes, upregulated for the fresh sample. i Differential gene expression analysis between fresh and fixed samples. The top differentially expressed genes (DEGs) with significant adjusted p-values (FDR) < 0.05, upregulated (red), and downregulated (blue) with Log2FC > |1| are indicated