Extended Data Fig. 1: Pipeline of cell identity annotation and quality control of rice ACRs.

a, A pipeline of cell identity annotation corresponding to nine strategies shown in Supplementary Fig. 1. b and c, A comparison between ACRs (n = 120,048) and control regions (n = 120,048) in terms of SNP density (b) and conservation scores (c). For panel b, the center line indicates the median; the box limits indicate the upper and lower quartiles; the whiskers indicate 1.5 times the IQR; the dots represent the outliers. The SNP data were downloaded from Rice SNP-Seek Database¹⁴⁹. The SNP density is the number of SNPs per 1,000 bp within the ACRs or control regions. The ACRs exhibited lower SNP density and higher conservation scores compared to a control composed of non-ACR DNA. The control set was created to match each ACR by excluding exons, ACRs, and unmappable regions, and they possess a similar GC content (< 5% average difference) compared to the positive set. d, Row-normalized chromatin accessibility z-scores for ACRs across cell types. e, Two-tailed spearman correlation is shown between the total number of Tn5 insertions and number of cell-type-specific ACRs across all cell types. f, A two-dimensional density plot illustrates the median chromatin accessibility across 126 cell types for 120,048 ACRs, along with the range of chromatin accessibility (calculated as the difference between the maximum and minimum values). g, Categories of distal cell-type-specific leaf ACRs showing potential interaction with genes based on examining chromatin loops derived from rice leaf Hi-C data.