Extended Data Fig. 13: Analysis of CREs using ENCODE chromatin data and single-cell RNA-seq data I.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, A flowchart of the analysis. b, Computationally predicted regulatory elements at the Myog locus. From the top to the bottom are the tracks for limb IDEAS active DHS (black bars), cell-type affiliated ones among the former (purple bars), IDEAS scores of limb and liver samples from early to late time points, bulk DNase-seq raw data, bulk RNA-seq raw data, and aggregated C1 single-cell RNA-seq data per cell type. Validation of the Mu3 element in mouse embryo by enhancer assay is also included at the bottom right. (Modified, with permission, from Yee and Rigby 1993, © Cold Spring Harbour Laboratory Press64.) Bottom, examples of limb-positive enhancer results from the VISTA database that are not cell-type-specific.
