Fig. 1: Isolation and characterization of tissue-specific endothelial signatures throughout development.
a, Workflow for genetic affinity tag labeling of ECs using Cdh5-PAC-CreERT2 and R26Sun1-sfGFP mice for INTACT. Far left: representative schematic of a blood vessel with GFP-tagged nuclei. Nuclear isolation was followed by RNA-seq profiling of nuclear transcripts and ATAC-seq mapping of accessible chromatin and aligning reads to the mouse genome (far right). b, Far left: various tissues and timepoints used to map endothelial cell diversity in the developing (E12.5), postnatal (P6) and adult (2 months of age) mouse. Far right: representative genome browser tracks from ATAC-seq highlight accessible chromatin regions unique to organ-specific genes such as Map2 in neurons, Rnf207 in cardiomyocytes, Gckr in hepatocytes, Ager in alveolar cells of the lung and Magi-2 in proximal tubule cells of the kidney, and ECs including Cdh5, Pecam1 and Erg. c, Volcano plots show differentially expressed genes (DESEQ2 Wald test two-tailed P values in which differential genes were counted if log2(FC) > 0.5 and alpha < 0.1.) between input nuclei (blue) and endothelium (red). Note that all developmental timepoints (E12.5–adult) are combined and treated as a single sample for these analyses.
