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Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering
Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering
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.
Biological Sciences, Omics, Transcriptomics
2589-0042
102147
Vallejo, Andres F.
27bc0b94-0c40-4fd1-9533-7e267d588c0a
Davies, James
a93b4fc9-80a2-4620-ada6-c12f05c5ee38
Grover, Amit
a45c5b79-5662-4496-a8d3-4f61e266267b
Tsai, Ching-hsuan
bd1cefe6-6509-4836-856a-afce7459a09f
Jepras, Robert
2268ceb7-0686-4af1-b387-a197fb6961cc
Polak, Marta E.
e0ac5e1a-7074-4776-ba23-490bd4da612d
West, Jonathan
f1c2e060-16c3-44c0-af70-242a1c58b968
Vallejo, Andres F.
27bc0b94-0c40-4fd1-9533-7e267d588c0a
Davies, James
a93b4fc9-80a2-4620-ada6-c12f05c5ee38
Grover, Amit
a45c5b79-5662-4496-a8d3-4f61e266267b
Tsai, Ching-hsuan
bd1cefe6-6509-4836-856a-afce7459a09f
Jepras, Robert
2268ceb7-0686-4af1-b387-a197fb6961cc
Polak, Marta E.
e0ac5e1a-7074-4776-ba23-490bd4da612d
West, Jonathan
f1c2e060-16c3-44c0-af70-242a1c58b968

Vallejo, Andres F., Davies, James, Grover, Amit, Tsai, Ching-hsuan, Jepras, Robert, Polak, Marta E. and West, Jonathan (2021) Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering. iScience, 24 (3), 102147, [102147]. (doi:10.1016/j.isci.2021.102147).

Record type: Article

Abstract

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.

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Accepted/In Press date: 31 January 2021
e-pub ahead of print date: 5 February 2021
Keywords: Biological Sciences, Omics, Transcriptomics

Identifiers

Local EPrints ID: 446773
URI: http://eprints.soton.ac.uk/id/eprint/446773
ISSN: 2589-0042
PURE UUID: 97f0311b-d67d-43bc-8dd5-4a32a9d7678e
ORCID for Andres F. Vallejo: ORCID iD orcid.org/0000-0002-4688-0598
ORCID for Jonathan West: ORCID iD orcid.org/0000-0002-5709-6790

Catalogue record

Date deposited: 22 Feb 2021 17:31
Last modified: 26 Nov 2021 03:10

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Contributors

Author: Andres F. Vallejo ORCID iD
Author: James Davies
Author: Amit Grover
Author: Ching-hsuan Tsai
Author: Robert Jepras
Author: Marta E. Polak
Author: Jonathan West ORCID iD

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