Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering
Summary: Single-cell transcriptomics suffer from sensitivity limits that restrict low abundance transcript identification, affects clustering and can hamper downstream analyses. Here, we describe Constellation sequencing (Constellation-Seq), a molecular transcriptome filter that delivers two orders...
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doaj-122c5bb1f37a4254bb27f21fe7723e5a2021-03-22T12:51:45ZengElsevieriScience2589-00422021-03-01243102147Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filteringAndres F. Vallejo0James Davies1Amit Grover2Ching-Hsuan Tsai3Robert Jepras4Marta E. Polak5Jonathan West6Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK; Corresponding authorClinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UKGlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UKGlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, MA 02140, USAGlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UKClinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Corresponding authorInstitute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Corresponding authorSummary: Single-cell transcriptomics suffer from sensitivity limits that restrict low abundance transcript identification, affects clustering and can hamper downstream analyses. Here, we describe Constellation sequencing (Constellation-Seq), a molecular transcriptome filter that delivers two orders of magnitude sensitivity gains by maximizing read utility while reducing the data sparsity and sequencing costs. The technique reliably measures changes in gene expression and was demonstrated by resolving rare dendritic cell populations from a peripheral blood mononuclear cell sample sample and exploring their biology with extreme resolution. The simple and powerful method is fully compatible with standard scRNA-Seq library preparation protocols and can be used for hypothesis testing, marker validation or investigating pathways.http://www.sciencedirect.com/science/article/pii/S2589004221001152Biological SciencesOmicsTranscriptomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Andres F. Vallejo James Davies Amit Grover Ching-Hsuan Tsai Robert Jepras Marta E. Polak Jonathan West |
spellingShingle |
Andres F. Vallejo James Davies Amit Grover Ching-Hsuan Tsai Robert Jepras Marta E. Polak Jonathan West Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering iScience Biological Sciences Omics Transcriptomics |
author_facet |
Andres F. Vallejo James Davies Amit Grover Ching-Hsuan Tsai Robert Jepras Marta E. Polak Jonathan West |
author_sort |
Andres F. Vallejo |
title |
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
title_short |
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
title_full |
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
title_fullStr |
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
title_full_unstemmed |
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
title_sort |
resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering |
publisher |
Elsevier |
series |
iScience |
issn |
2589-0042 |
publishDate |
2021-03-01 |
description |
Summary: Single-cell transcriptomics suffer from sensitivity limits that restrict low abundance transcript identification, affects clustering and can hamper downstream analyses. Here, we describe Constellation sequencing (Constellation-Seq), a molecular transcriptome filter that delivers two orders of magnitude sensitivity gains by maximizing read utility while reducing the data sparsity and sequencing costs. The technique reliably measures changes in gene expression and was demonstrated by resolving rare dendritic cell populations from a peripheral blood mononuclear cell sample sample and exploring their biology with extreme resolution. The simple and powerful method is fully compatible with standard scRNA-Seq library preparation protocols and can be used for hypothesis testing, marker validation or investigating pathways. |
topic |
Biological Sciences Omics Transcriptomics |
url |
http://www.sciencedirect.com/science/article/pii/S2589004221001152 |
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