Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells

Profiling multiple omic layers in a single cell enables the discovery and analysis of biological phenomena that are not apparent from analysis of mono-omic data. While methods for multiomic profiling have been reported, their adoption has been limited due to high cost and complex workflows. Here, a...

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Main Authors: Reyes, Miguel, Blainey, Paul C
Other Authors: Massachusetts Institute of Technology. Department of Biological Engineering
Format: Article
Language:English
Published: Wiley 2020
Online Access:https://hdl.handle.net/1721.1/125232
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author Reyes, Miguel
Blainey, Paul C
author2 Massachusetts Institute of Technology. Department of Biological Engineering
author_facet Massachusetts Institute of Technology. Department of Biological Engineering
Reyes, Miguel
Blainey, Paul C
author_sort Reyes, Miguel
collection MIT
description Profiling multiple omic layers in a single cell enables the discovery and analysis of biological phenomena that are not apparent from analysis of mono-omic data. While methods for multiomic profiling have been reported, their adoption has been limited due to high cost and complex workflows. Here, a simple method for joint profiling of gene expression and chromatin accessibility in tens to hundreds of single cells is presented. Assessed herein is the quality of resulting single cell ATAC- and RNA-seq data across three cell types, examining the link between accessibility and expression at the CD3G and FTH1 loci in human primary T cells and monocytes, and comparing the accuracy of clustering solutions for mono-omic and combined data. The new method allows biological laboratories to perform simultaneous profiling of gene expression and chromatin accessibility using standard reagents and instrumentation. This technique, in conjunction with other advances in multiomic profiling, will enable highly resolved cell state classification and more specific mechanistic hypothesis generation than is possible with mono-omic analysis.
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spelling mit-1721.1/1252322022-09-27T15:33:04Z Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells Reyes, Miguel Blainey, Paul C Massachusetts Institute of Technology. Department of Biological Engineering Profiling multiple omic layers in a single cell enables the discovery and analysis of biological phenomena that are not apparent from analysis of mono-omic data. While methods for multiomic profiling have been reported, their adoption has been limited due to high cost and complex workflows. Here, a simple method for joint profiling of gene expression and chromatin accessibility in tens to hundreds of single cells is presented. Assessed herein is the quality of resulting single cell ATAC- and RNA-seq data across three cell types, examining the link between accessibility and expression at the CD3G and FTH1 loci in human primary T cells and monocytes, and comparing the accuracy of clustering solutions for mono-omic and combined data. The new method allows biological laboratories to perform simultaneous profiling of gene expression and chromatin accessibility using standard reagents and instrumentation. This technique, in conjunction with other advances in multiomic profiling, will enable highly resolved cell state classification and more specific mechanistic hypothesis generation than is possible with mono-omic analysis. National Institute of Allergy and Infectious Diseases (U.S.) (Grant U24 AI118668) 2020-05-14T13:13:52Z 2020-05-14T13:13:52Z 2019-11 2020-03-04T17:44:11Z Article http://purl.org/eprint/type/JournalArticle 2366-7478 https://hdl.handle.net/1721.1/125232 Reyes, Miguel et al. “Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells.” Advanced biosystems 3 (2019) © 2019 The Author(s) en 10.1002/ADBI.201900065 Advanced biosystems Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Wiley PMC
spellingShingle Reyes, Miguel
Blainey, Paul C
Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title_full Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title_fullStr Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title_full_unstemmed Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title_short Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells
title_sort simultaneous profiling of gene expression and chromatin accessibility in single cells
url https://hdl.handle.net/1721.1/125232
work_keys_str_mv AT reyesmiguel simultaneousprofilingofgeneexpressionandchromatinaccessibilityinsinglecells
AT blaineypaulc simultaneousprofilingofgeneexpressionandchromatinaccessibilityinsinglecells