Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons

We profiled chromatin accessibility and gene expression changes along the differentiation of human pluripotent stem cells to dopaminergic neurons. We integrated the epigenomic and transcriptomic profiles to infer the activity of transcription factors (TFs) and DNA regulatory regions such as enhancers and long non-coding RNAs. Overall design: Time series gene expression profiles and chromatin accessibility genome-wide maps were obtained through ATAC-sequencing and RNA-sequencing of samples obtained during dopaminergic neural induction of human pluripotent stem cells. We used 3 induction time points: day 0, day 14, and day 28. H9 cells expressing GFP (WA09-GFP) were used as pluripotent stem cells. For RNA-seq we obtained 3, 4, and 2 replicates from induction time points D0, D14, and D28 respectively. For ATAC-seq we used one replicate for each time point.