ATAC-seq of human lung cell types

We report the application of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) for the profiling of open chromatin human primary lung cell types implicated in lung disease pathology, such as chronic obstructive pulmonary disease. We generated chromatin accessibility profiles for human primary bronchial epithelial cells, small airway epithelial cells, alveolar type II pneumocytes, and lung fibroblasts using Omni-ATAC-seq. We further profiled open chromatin in a commonly used bronchial epithelial cell line (16HBE14o-) to evaluate the correlation with primary cell profiles and confirm the technical improvements using Omni-ATAC-seq vs Fast-ATAC-seq. We used these profiles to evaluate the enrichment of COPD risk variants in lung-specific open chromatin regions (OCRs) and generated cell type-specific regulatory predictions for >6,500 variants corresponding to 82 COPD GWAS loci. Overall design: ATAC-seq profiles of 4 primary normal human lung cell types (alveolar type II pneumocytes, small airway epithelial cells, large airway [bronchial] epithelial cells, and lung fibroblasts) and 1 immortalized bronchial epithelial cell line (16HBE14o-). The complete data set contains a total of 14 samples.