Fig. 2: Dynamic changes in accessible regions accompany gene expression changes.

a Principal component analysis on ATAC-seq data at all timepoints. Circles of the same color represent biological replicates. b The percent of top 100k genomic regions that lose accessibility or become newly accessible between consecutive timepoints. c The percent of total peaks or differential peaks that are proximal (within 2 kb) or distal (>2 kb away) from transcription start sites. Error bars represent SEM and p value is from two-tailed t-tests, n = 7 (all peaks), 12 (differential peaks). d, e The distribution of differentially accessible regions near genes that are upregulated during maturation between E10.5 and E13.5, and E13.5 and P21. The gene expression heatmaps show the expression values of top 500 upregulated genes. The box plots show the number of peaks around each of the 500 upregulated genes that become newly accessible (red) or lose accessibility (blue) between E10.5 and E13.5, and E13.5 and P21. Center line of box plots is the median, the interquartile range is 25th–75th percentile, and outliers are eliminated; p values are from two-tailed t-tests; n = 500 genes. f ATAC-seq reads around upregulated genes. Source data are provided as a Source Data file.