Extended Data Fig. 7: Cell-type and developmental classification of PADREs.

Cell-type specificity assignment and developmental dynamics of PADREs a, An example genomic region shows cell-type assignment of PADREs derived from single-cell ATAC-seq data (bottom track) and the gene model (top track). The name of PADREs contains their cell-type assignment. PADREs in this track are color-coded by their cell-type assignment as well, each colour representing a different cell-type. The state number in the name corresponds to those defined in McGarvey et al.³⁰. b, Overlap of matches between the cell-type assignment and activity tissue determined by transgenic assay. Of 155 transgenically validated enhancers active at the Prim-5 stage, 117 have a cell-type specificity assignment. For details of anatomical terms and statistics see Supplementary Table 11. In 72 (62%) assigned transgenic enhancers the scATAC-seq derived anatomical annotation matches at least one of the activity domains of the transgenic reporter (left-hand side of the bar chart). Partial overlap indicates transgene activity in a related tissue, but without no identifiable direct overlap with that of the cell type assignment. Not assigned elements were not registered for cell type specificity by McGarvey et al.³⁰. Undetermined elements were not possible to directly compare due to ambiguity of anatomical terms. The functional annotation of transgenically validated PADREs (right column) shows that most transgenic elements have an enhancer relevant ChromHMM registration at the Prim-5 stage. Waterfall plot between the left and right columns indicate overlap between cell type assignment and cis regulatory element category. c, Openness of distal (non-promoter) cPADREs throughout development at stages indicated on the x-axis in the defined SOM classes. Numbers in brackets indicate the number of elements in each class.