Journal: bioRxiv

Article Title: Comparative Analysis of Single-Nucleus and Single-Cell RNA Sequencing in Human Bone Marrow Mononuclear Cells: Methodological Insights and Trade-offs

doi: 10.1101/2025.09.08.675012

Figure Lengend Snippet: A–C) Split violin plots display the distribution of key sequencing and cell quality metrics, with red representing snRNA-seq and blue representing scRNA-seq. Each pair of samples is connected by a line. Samples are coloured by the laboratory to indicate batch origin (A, B, C, F, H, I, L). Median number of genes detected per cell for each sample (A), Library size per sample after removing MT genes (B) and Sequencing saturation (C). D–E) Scatter plots showing an example of the correlation between library size and number of genes per cell in scRNA-seq (D) and snRNA-seq (E), coloured by cell type. Scatter plots for all samples are shown in Figure S7. F) Split violin plots showing proportion of reads mapped to intronic regions per sample. G) Distribution of total UMI counts per gene length bin across 50 gene length bins across all 22 samples. H–I) Split violin plots comparing the percentage of MT gene content (H) and ambient RNA (I). J) Correlation between the percentage of detected doublets and the total number of cells recovered per sample. K) Boxplots showing Jaccard scores representing similarity of HVGs identified within each method, based on the variance-stabilising transformation method. L) Comparison of the average number of clusters detected in three comparable resolutions in each sample.

Article Snippet: Among the most widely adopted of these are singlecell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq), commercialised by 10x Genomics ( ).

Techniques: Sequencing, Transformation Assay, Comparison