Joint profiling of chromatin accessibility and gene expression in thousands of single cells

• DOI: 10.1126/science.aau0730
• Publication Date: 2018-08-30T18:06:51Z
• Authors: Junyue Cao; Darren A. Cusanovich; Vijay Ramani; Delasa Aghamirzaie; Hannah A. Pliner; Andrew J. Hill; Riza M. Daza; Jose L. McFaline-...; Jonathan S. Packer; Lena Christiansen; Frank J. Steemers; Andrew C. Adey; Cole Trapnell; Jay Shendure
• Keywords: ChIA-PET

Although we can increasingly measure transcription, chromatin, methylation, and other aspects of molecular biology at single-cell resolution, most assays survey only one aspect cellular biology. Here describe sci-CAR, a combinatorial indexing-based coassay that jointly profiles chromatin accessibility mRNA (CAR) in each thousands single cells. As proof concept, apply sci-CAR to 4825 cells, including time series dexamethasone treatment, as well 11,296 cells from the adult mouse kidney. With resulting data, compare pseudotemporal dynamics gene expression, reconstruct cell types defined by RNA profiles, link cis-regulatory sites their target genes on basis covariance transcription across large numbers