Human caudate cell type open chromatin regions and ortholog predictions in 240 mammals.
This track shows the ATAC-seq open chromatin regions from human postmortem brain scATAC-seq. These regions were obtained from Corces et al. Nature Genetics GSE147672. Astro caudate cell type.
We used ArchR to cluster caudate scATAC-seq samples to resolve medium spiny neuron subtypes (D1, D2, striatonigral), interneurons, and four glia cell types from the human caudate. We then mapped reproducible peaks of each cell type across 240 mammals using the Zoonomia Consortium multi-species cactus alignment of 241 mammals (including humans, hg38). We used cross-species cell type-specific machine learning models to predict open chromatin state of the DNA orthologs of each mappable peak to these species.
The Pfenning Lab, as well as the UCSC Genome Browser, provided the input data.
Please contact Andreas Pfenning or BaDoi Phan with questions.
Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet. 2021 Mar;53(3):403-411. PMID: 33633365; PMC: PMC8012210; DOI: 10.1038/s41588-021-00790-6
Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet. 2020 Nov;52(11):1158-1168. PMID: 33106633; PMC: PMC7606627; DOI: 10.1038/s41588-020-00721-x
Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. Nature. 2020 Nov;587(7833):240-245. PMID: 33177664; PMC: PMC7759459; DOI: 10.1038/s41586-020-2876-6
Phan, BN, Lawler AJ, He J, et al. Fine-mapping candidate neurological disorder-associated regulatory variants using cell type-aware comparative genomics, in preparation.