Extended Data Fig. 2: Quality control and comparison of genomic datasets.
(a-b) Scatter plot of the RNA UMIs, ATAC fragments, Nucleosome signal and TSS enrichment per cell, colored by experimental condition. The cells within the square box were retained for further analysis. (c) Aggregated scATAC-seq (multiome) fragment size distribution, colored by cell condition. (d) Aggregated fragment enrichment at all TSSs from the scATAC-seq (multiome), colored by experimental condition. (e) Dot plot showing gene activity estimated by gene body accessibility at the indicated set of markers genes. (f) UMAP projection of RNA expression and gene activity for Sox9 and Rnd2 respectively. (g) Correlation heatmaps comparing this study with in vivo single-cell dynamics in the E14.5 developing mouse cortex19 (h) Correlation heatmaps showing the similarity between gene expression or ATAC using single cell (10x multiome) and bulk RNA/ATAC. (i) Genome track depicting the chromatin accessibility measured by single cell and bulk ATAC-seq and the transcriptional output measured by bulk RNA-seq at the Rnd2 gene locus. Full rectangle demarcates the gene body of Rnd2 while the dashed rectangles denote the putative distal regulatory regions of Rnd2.
