| First Author | Li Z | Year | 2021 |
| Journal | Nat Commun | Volume | 12 |
| Issue | 1 | Pages | 6386 |
| PubMed ID | 34737275 | Mgi Jnum | J:339523 |
| Mgi Id | MGI:6826705 | Doi | 10.1038/s41467-021-26530-2 |
| Citation | Li Z, et al. (2021) Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen. Nat Commun 12(1):6386 |
| abstractText | A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis-regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis. |
