A human cell atlas of fetal chromatin accessibility

We devised an improved assay for single cell profiling of chromatin accessibility with three-level combinatorial indexing (sci-ATAC-seq3). We applied this method to 53 fetal tissue samples representing 15 organs, altogether profiling approximately one million single cells. We leveraged cell types defined by gene expression in the same organs to annotate these data, and built a catalog of hundreds-of-thousands of candidate gene regulatory elements exhibiting cell type-specific accessibility. Our analyses focus on the properties of lineage-specific transcription factors, organ-specific specializations of broadly distributed cell types, and cell type-specific enrichments of complex trait heritability. Additional data formats are available at atlas.brotmanbaty.org. We profiled single cell chromatin accessibility in 53 human fetal samples (estimated gestational age 89-125d) spanning 15 organs. In total, we collected data on 1.6M individual cells, which were filtered down to ~800,000 cells after quality control. Please note that the downstream analyses were carried out on combined tissues/samples, which resulted in matrices of peak, cell metadata, motif enrichments, cell type specificity and cicero scores for the full dataset (included in the records as Series supplementary files). The raw data is to be made available through dbGaP (controlled access; phs002003.v1.p1): https://www.ncbi.nlm.nih.gov/gap/?term=phs002003