Fig. 3
From: FixNCut: single-cell genomics through reversible tissue fixation and dissociation
FixNCut protocol tested in mouse colon 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), uniform manifold approximation and Projection (UMAP) prior data integration, and harmony integrated UMAP representation of gene expression profile variances of fresh and fixed samples. e, f Linear regression model comparing average gene expression levels of expressed genes (e) and biological hallmarks, including apoptosis, hypoxia, reactive oxygen species (ROS), cell cycle G2/M checkpoint, unfolded protein response (UPR), and inflammatory response genes (f). The coefficient of determination (R2) computed with Pearson correlation and the corresponding p-values are indicated. g UMAP visualization of 14,387 fresh and fixed mouse colon cells, colored by 16 cell populations. h Comparison of cell population proportions between fresh (n = 6009) and fixed (n = 8378) mouse colon samples with the Bayesian model scCODA. Asterisks (*) indicate credible changes, upregulated for the fixed 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