Allele-specific open chromatin in human neurons elucidates functional noncoding disease variants

ASoC variants are prevalent and cell type-specific ASoC variants were over-represented in intergenic regions and active enhancers. The collection includes ATAC-Seq and RNA-Seq data that were taken from human iPS cells and their derived neuronal cells (neural progenitor cells, cortical glutamatergic neurons, GABAergic neurons, and dopaminergic neurons). Overall design: In order to detect the changes in chromatin accessibility as well as associated changes at the transcriptional level during neuronal differentiation, we applied human induced pluripotent stem cells (hiPSCs) and hiPSC-derived neurons as a neurodevelopmental model. Generally, 8 iPSC lines from RUCDR were induced to differentiate into neural progenitor cells (NPC), 15-day cortical glutamatergic neurons (CN, Glut d15), GABAergic neurons, and dopaminergic neurons. Their open chromatin landscape, as well as transcriptional activities, were measured using ATAC-Seq and bulk RNA-Seq, respectively. An additional 12 lines were used to generate NPC cells and Glut-d15 neurons for ATAC-Seq, with the aim in gaining extended statistic power for ASoC analysis.