Fig. 2

Elevated noise levels of nuclear versus whole-cell transcriptomes in human PBMCs. a Clustering and UMAP representation of single-nucleus RNA-seq data, consisting of human peripheral blood mononuclear cells (PBMCs) profiled with the Single Cell Multiome kit from 10x Genomics (See Additional file 1: Table S1). b As a, but showing single-cell RNA-seq data. c Quantification of cellular noise (average \(\varepsilon\) across all genes per cell) across clusters shown in a. The horizontal line indicates the median of CD4 naïve T cell estimates (cluster 3), exhibiting reduced noise levels. d As c, but for cellular noise estimates for the single-cell dataset (see b). The horizontal line indicates the median of CD4 naïve T cell estimates (cluster 3). e Comparison of cellular noise levels between both datasets. The scatter plot shows the average cellular noise per cluster and their corresponding standard deviation (error bars). The x-axis corresponds to the estimates of the nucleus data and the y-axis to the cell data estimates. Similar cell populations between both datasets were identified by dataset integration, see Additional file 1: Figure S2d. f Gene-wise average noise in CD8 naïve T cells, comparing nucleus and cell datasets. Only genes without change in gene expression were selected and grouped into ten equally populated bins based on mean expression as shown in Additional file 1: Figure S2f. g Quantification of PDCD4 (elevated nuclear noise) and PPP1R2 (no changes in noise) expression by smFISH in human CD8 naïve T cells (see also Additional file 1: Figure S2h). Representative images of maximum intensity projections are shown. DAPI in blue, scale bar is 5 μm. h Noise ratio between nuclear and cellular compartments, estimated with VarID2 and smFISH. Error bars indicate standard error (“Methods”). DC, dendritic cells; NK, natural killer cells; TEM, effector memory T cells; Mono, monocytes. Boxplots in c, d, and f: boxes indicate inter-quartile range (IQR), and whiskers correspond to ±1.5*IQR of the box limits. Outliers beyond the whisker limits are depicted