Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
Name
Genome Res.-2020-Xing-1027-39.pdf
Description
Accepted version
Size
7.21 MB
Format
Adobe PDF
Checksum (MD5)
0ed40f43c31c03909d05d6a3101df11c
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
Date Issued
2020
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory
Version
Final published version
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.
MIT 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
Terms of Use
Creative Commons Attribution NonCommercial License 4.0
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1101/GR.257840.119
