Fig. 5: Transcription, gene accessibility, and active enhancer utilization are highly correlated and dynamic during neuron lineage commitment in the mouse forebrain.

a, b Line charts of “early expressed” (a) and “late expressed” (b) DEG clusters detected by degPatterns using embryonic integrated snATAC-Seq/scRNA-Seq data. Y-axis is Z-score for RNA, GAS, or enhancers counts per gene. The X-axis is binned pseudotime periods. RNA, GAS, or enhancers for individual genes in these clusters are plotted (156 “early” and 90 “late” genes). c–r Line chart and UMAP visualizations of RNA, GAS, and enhancer read counts for representative “early” genes Hes1 and Lmo1 (c-j) and “late” genes Myt1l and Lhx6 (k–r). For line charts, Y-axis is Z-score for RNA, GAS, or enhancers counts per gene. The X-axis is binned pseudotime periods. Gray dots in the background of UMAP plots represent cells/nuclei from other assays. In panels c, g, k, o, the shaded gray region represents a 95% confidence interval. s–u Heatmaps of RNA (s), GAS (t), and enhancers (u) counts for 210 variable genes. Heatmap columns were ordered by hierarchical clustering of 210 variable genes with correlation distance and average linkage. Rows were ordered by pseudotime (assigned by Moncole3). Color bars in s indicate genes grouped together based on “early”, “transition” and “late” profiles (as assigned by degPatterns and manually refined).