Fig. 5

Normalized accessibility from root and leaf ATAC-seq correlates with gene expression. a and b Aggregate plots of per base TN5 insertion counts for the 1 kb region upstream of transcription start sites for high confidence genes in root (a) and leaf protoplast (b) ATAC-seq. Genes were stratified in 11 quantiles by expression level using previously published RNA-seq for root and leaf [30]. For each of the 11 stratified sets of genes, fold accessibility above genomic average was calculated for each of the 1000 bases upstream of transcription start sites, as indicated in the figure and described in the methods. A LOESS curve (Local Polynomial Regression) was added for dots corresponding to each gene set. Gray bars indicate a 150-bp region centered 225 bp upstream of the TSSs that was used to calculate average accessibility for each gene. c and d Heatmaps for accessibility 1 kb up- and down-stream of each gene for fresh root (c) and leaf protoplast (d) data. Genes are order from the highest expression on the top to the lowest expression in the bottom. The scale is log10 counts in 150 bp windows with 20 bp slide