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Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility

Author(s)
Xing, Qiao Rui; Farran, Chadi A El; Zeng, Ying Ying; Yi, Yao; Warrier, Tushar; Gautam, Pradeep; Collins, James J; Xu, Jian; Dröge, Peter; Koh, Cheng-Gee; Li, Hu; Zhang, Li-Feng; Loh, Yuin-Han; ... Show more Show less
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Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/
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Abstract
© 2020 Xing et al. Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTARseq), for simultaneous measurement of whole-cell transcriptome and chromatin accessibility within the same single cell. To show the utility of ASTAR-seq, we profiled 384 mESCs under naive and primed pluripotent states as well as a two-cell like state, 424 human cells of various lineage origins (BJ, K562, JK1, and Jurkat), and 480 primary cord blood cells undergoing erythroblast differentiation. With the joint profiles, we configured the transcriptional and chromatin accessibility landscapes of discrete cell states, uncovered linked sets of cis-regulatory elements and target genes unique to each state, and constructed interactome and transcription factor (TF)-centered upstream regulatory networks for various cell states.
Date issued
2020
URI
https://hdl.handle.net/1721.1/136153
Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Synthetic Biology Center
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory

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