Genome ResearchGenomicsPeer-reviewed journal article
Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility
Qiao Rui XingiD, Chadi A. El FarraniD, Ying Ying Zeng, Yao YiiD, Tushar WarrieriD, Pradeep GautamiD, James J. CollinsiD, Jian XuiD, Peter DrögeiD, Cheng-Gee KohiD, Hu LiiD, Li‐Feng ZhangiD, Yuin‐Han LohiD
Abstract
We developed ASTAR-Seq (Assay for Single-cell Transcriptome and Accessibility Regions) integrated with automated microfluidic chips, which allows for parallel sequencing of transcriptome and chromatin accessibility within the same single-cell. Using ASTAR-Seq, we profiled 192 mESCs cultured in serum+LIF and 2i medium, 424 human cell lines including BJ, K562, JK1, and Jurkat, and 480 primary cells undergoing erythroblast differentiation. Integrative analysis using Coupled NMF identified the distinct sub-populations and uncovered sets of regulatory regions and the respective target genes determining their distinctions. Analysis of epigenetic regulomes further unravelled the key transcription factors responsible for the heterogeneity observed.
- organism: human
- organism: mouse
- assay: scRNA-seq
- assay: scATAC-seq
- research focus: cell type annotation
- research focus: clustering
- research focus: differential expression
- research focus: gene regulatory network inference
- approach: experimental assay
- Citations
- 74
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