Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
© 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...
| Main Authors: | , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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Cold Spring Harbor Laboratory
2021
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| Online Access: | https://hdl.handle.net/1721.1/136153 |
| _version_ | 1811072872745009152 |
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| author | 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 |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science 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 |
| author_sort | Xing, Qiao Rui |
| collection | MIT |
| description | © 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. |
| first_indexed | 2024-09-23T09:18:32Z |
| format | Article |
| id | mit-1721.1/136153 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T09:18:32Z |
| publishDate | 2021 |
| publisher | Cold Spring Harbor Laboratory |
| record_format | dspace |
| spelling | mit-1721.1/1361532024-03-19T14:22:56Z Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility 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 Massachusetts Institute of Technology. Institute for Medical Engineering & Science Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Synthetic Biology Center © 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. 2021-10-27T20:31:07Z 2021-10-27T20:31:07Z 2020 2021-08-25T18:04:08Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136153 en 10.1101/GR.257840.119 Genome Research Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/ application/pdf Cold Spring Harbor Laboratory Cold Spring Harbor Laboratory Press |
| spellingShingle | 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 Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title | Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title_full | Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title_fullStr | Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title_full_unstemmed | Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title_short | Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility |
| title_sort | parallel bimodal single cell sequencing of transcriptome and chromatin accessibility |
| url | https://hdl.handle.net/1721.1/136153 |
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