Fig. 4: Trans-acting and cis-acting regulatory networks inferred for specific limb cell types.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, STRING networks of skeletal muscle lineage for cell-type differential TFs from 10x data (see Methods); edges are coloured by types of STRING evidence (cyan for database and magenta for experimental); nodes coloured according to 10x RNA-seq levels; arrows indicate lineage transitions (see text). b, Schematic for discovering cell-type enhancer and promoter elements using scRNA-seq and IDEAS chromatin state elements defined in whole tissue chromatin assays (see text, Methods and Extended Data Fig. 11a). c, Candidate upstream limb skeletal enhancers (CA1–CA3) for Sox5 with in vivo enhancer data from VISTA for a CA3-containing segment at right (https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&experiment_id=895&organism_id=1). Computed IDEAS limb cell-type elements (purple track); IDEAS epigenomic segmentation tracks below with poised and active enhancer type (orange) and promoter type (red) states below. d, Summary of IDEAS and scRNA-seq cell-type elements in the VISTA resource. Top, IDEAS limb elements in VISTA, n = 235/371 (63%). Bottom, VISTA-positive IDEAS elements by cell-type (n = 66 cell-type-specific elements).
