Fig. 1

The impact of sampling time on single-cell transcriptional and open chromatin profiles. a, b scRNA-seq-based tSNE or UMAP embeddings of 7378 PBMC (a, male donor) and 22,443 CLL cells (b, 3 donors) color-coded by sampling time. c Distribution of the first principal component (PC1) across processing times computed for each PBMC subtype independently. d scATAC-seq-based UMAP embedding color-coded by sampling time and highlighting major PBMC cell types. Unlabeled cluster corresponds to cells of unknown type. e Violin plot showing changes in RNA expression for the 50 genes associated with the top 50 distal (enhancer) peaks changing in accessibility (down: closing sites; up: opening sites); p value in Z score scale, Wilcoxon test *p < 0.05, **p < 0.01, ***p < 0.001. f Dot plot representing the time-dependent expression changes of the top up- and downregulated genes with a minimum log (expression) of 0.5, a minimum absolute log fold-change of 0.2 and an adjusted p value < 0.001. The arrows highlight the cold-inducible response binding protein (CIRBP) and the RNA Binding Motif Protein 3 (RBM3) genes. g M (log ratio)-A (mean average) plot showing the log₂ fold-change between biased (> 2 h) and unbiased (≤ 2 h) PBMC as a function of the log average expression (Scran normalized expression values). Significant genes are colored in green (adjusted p value < 0.001), and a locally estimated scatterplot smoothing (LOESS) line is drawn in blue. h Motif enrichment analysis performed over the DNA sequences of the top 50 distal peaks with a change in accessibility (same peaks as e). i Time score distribution across processing times (female donor) calculated with the sampling time signature defined in the male PBMC donor. j Receiver operating characteristic (ROC) curve displaying the performance of a logistic regression model in classifying “biased” and “unbiased” PBMC