Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection

We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection...

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Published inScientific reports Vol. 7; no. 1; pp. 2776 - 8
Main Authors Gong, Haibiao, Wang, Xiaohui, Liu, Benjamin, Boutet, Stephane, Holcomb, Ilona, Dakshinamoorthy, Gajalakshmi, Ooi, Aik, Sanada, Chad, Sun, Gang, Ramakrishnan, Ramesh
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 05.06.2017
Nature Publishing Group
Nature Portfolio
Subjects
38
38/39
38/62
38/77
45
631/1647/2017
631/1647/2067
82
82/80
96/1
Biomarkers
Cell Line
Correlation analysis
Deoxyribonucleic acid
DNA
Gene expression
Gene Expression Profiling - methods
Humanities and Social Sciences
Humans
multidisciplinary
Proteins
Proteins - metabolism
Proteomics - methods
Real-Time Polymerase Chain Reaction
Reverse transcription
RNA, Messenger - genetics
RNA, Messenger - metabolism
Science
Science (multidisciplinary)
Single-Cell Analysis - methods
Single-cell protein
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Abstract We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
AbstractList We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
Abstract We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
Abstract We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
ArticleNumber 2776
Author Holcomb, Ilona
Sun, Gang
Gong, Haibiao
Dakshinamoorthy, Gajalakshmi
Ramakrishnan, Ramesh
Wang, Xiaohui
Boutet, Stephane
Liu, Benjamin
Sanada, Chad
Ooi, Aik
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Snippet We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is...
Abstract We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This...
Abstract We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This...
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SubjectTerms 38
38/39
38/62
38/77
45
631/1647/2017
631/1647/2067
82
82/80
96/1
Biomarkers
Cell Line
Correlation analysis
Deoxyribonucleic acid
DNA
Gene expression
Gene Expression Profiling - methods
Humanities and Social Sciences
Humans
multidisciplinary
Proteins
Proteins - metabolism
Proteomics - methods
Real-Time Polymerase Chain Reaction
Reverse transcription
RNA, Messenger - genetics
RNA, Messenger - metabolism
Science
Science (multidisciplinary)
Single-Cell Analysis - methods
Single-cell protein
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Title Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection
URI https://link.springer.com/article/10.1038/s41598-017-03057-5
https://www.ncbi.nlm.nih.gov/pubmed/28584233
https://www.proquest.com/docview/1955526738
https://search.proquest.com/docview/1906465114
https://pubmed.ncbi.nlm.nih.gov/PMC5459813
https://doaj.org/article/d53b4a806b534842a54ad55e4e3c21e5
Volume 7
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