Figure 1.

Differentiating myoblasts follow similar single cell chromatin accessibility and gene expression trajectories. A) Single cell chromatin accessibility profiles for human skeletal muscle myoblasts (HSMM) were constructed with sci-ATAC-seq. Contaminating interstitial fibroblasts (common in HSMM cultures) were removed informatically prior to further analysis. B) Aggregated read coverage from sci-ATAC-seq experiments in the region surrounding TNNT1 and TNNI3 in myoblasts (0 hours) and myotubes (72 hours). Bulk ATAC-seq prepared from the same wells as experiment 2 are shown alongside DNase-seq from ENCODE for comparison (ENCODE experiments ENCSR000EOO and ENCSR000EOP (The ENCODE Project Consortium, 2012)). C) The single cell trajectory inferred from 2,725 myoblast sci-ATAC-seq profiles from experiment 1 by Monocle (see Methods). In subsequent panels and throughout the paper, we exclude cells on the branch to outcome F₂ unless otherwise indicated. Inset shows the sc-RNA-seq trajectory reported for HSMMs (reproduced from Figure 2 of (Qiu et al., 2017a), cells were from the same lot and were cultured under identical conditions to those for sci-ATAC-seq). D) Distribution of cells in chromatin accessibility pseudotime from the root to trajectory outcome F₁. E) Percent of differentiating cells whose promoters for selected genes are accessible across pseudotime. Black line indicates the pseudotime-dependent average from a smoothed binomial regression. F) Percent of cells whose promoters for selected genes in E are accessible in fibroblasts collected in growth medium (GM) or differentiation medium (DM), as well as myoblasts localized to the branch to F₂. See also Figure S1.