Abstract
A major drawback of single cell ATAC (scATAC) are the so-called dropout events, i.e. open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. We propose scOpen, a computational method for quantifying the open chromatin status of regulatory regions from scATAC-seq experiments. We demonstrate that scOpen improves all down-stream analysis steps of scATAC-seq data as clustering, visualisation and chromatin conformation. Moreover, we show the power of scOpen and single cell-based transcription factor footprinting analysis (scHINT) to dissect regulatory changes in the development of fibrosis in the kidney. This identified a novel role of Runx1 promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.
Competing Interest Statement
The authors have declared no competing interest.