Single-cell transcriptomics in the context of long-read nanopore sequencing

Single cell transcriptomics were declared twice ‘Method of the year’ by Nature Methods journal, in 2013 and 2019. It marks the beginning of new avenue in fundamental and clinical research, as the classic biochemical approach is already seen as limited, as pooling up the contents of a large number of...

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Autores principales:	Soren Hayrabedyan, Petya Kostova, Viktor Zlatkov, Krassimira Todorova
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	single cell transcriptomics nanopore sequencing long-read sequencing Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/4f94f93611fa432c95d4a0499416751e
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spelling	oai:doaj.org-article:4f94f93611fa432c95d4a0499416751e2021-11-11T14:23:41ZSingle-cell transcriptomics in the context of long-read nanopore sequencing1310-28181314-353010.1080/13102818.2021.1988868https://doaj.org/article/4f94f93611fa432c95d4a0499416751e2021-01-01T00:00:00Zhttp://dx.doi.org/10.1080/13102818.2021.1988868https://doaj.org/toc/1310-2818https://doaj.org/toc/1314-3530Single cell transcriptomics were declared twice ‘Method of the year’ by Nature Methods journal, in 2013 and 2019. It marks the beginning of new avenue in fundamental and clinical research, as the classic biochemical approach is already seen as limited, as pooling up the contents of a large number of cells together depicts an averaged image that is missing the decision maker cells. Short-read sequencing has already revolutionized biology and medicine, providing an unsurpassed accuracy of the reads, and now third generation long-read nanopore sequencing completes and extends transcriptomics with the ability to discover all full-length isoforms at a single-cell level, providing a deeper insight in our understating of physiology and pathology of tissue functions. This review provides insight on how nanopore technological specifics and limitations have been explored so far in implementing the only direct nucleic acid sequencing platform in single cells sequencing. We review how single-cell sequencing was introduced, most widely used conventional and microfluidic approaches for single cell isolation, ways for further sequencing library generation tailored for Illumina, and how these were adopted for the nanopore technology.Soren HayrabedyanPetya KostovaViktor ZlatkovKrassimira TodorovaTaylor & Francis Grouparticlesingle cell transcriptomicsnanopore sequencinglong-read sequencingBiotechnologyTP248.13-248.65ENBiotechnology & Biotechnological Equipment, Vol 35, Iss 1, Pp 1439-1451 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	single cell transcriptomics nanopore sequencing long-read sequencing Biotechnology TP248.13-248.65
spellingShingle	single cell transcriptomics nanopore sequencing long-read sequencing Biotechnology TP248.13-248.65 Soren Hayrabedyan Petya Kostova Viktor Zlatkov Krassimira Todorova Single-cell transcriptomics in the context of long-read nanopore sequencing
description	Single cell transcriptomics were declared twice ‘Method of the year’ by Nature Methods journal, in 2013 and 2019. It marks the beginning of new avenue in fundamental and clinical research, as the classic biochemical approach is already seen as limited, as pooling up the contents of a large number of cells together depicts an averaged image that is missing the decision maker cells. Short-read sequencing has already revolutionized biology and medicine, providing an unsurpassed accuracy of the reads, and now third generation long-read nanopore sequencing completes and extends transcriptomics with the ability to discover all full-length isoforms at a single-cell level, providing a deeper insight in our understating of physiology and pathology of tissue functions. This review provides insight on how nanopore technological specifics and limitations have been explored so far in implementing the only direct nucleic acid sequencing platform in single cells sequencing. We review how single-cell sequencing was introduced, most widely used conventional and microfluidic approaches for single cell isolation, ways for further sequencing library generation tailored for Illumina, and how these were adopted for the nanopore technology.
format	article
author	Soren Hayrabedyan Petya Kostova Viktor Zlatkov Krassimira Todorova
author_facet	Soren Hayrabedyan Petya Kostova Viktor Zlatkov Krassimira Todorova
author_sort	Soren Hayrabedyan
title	Single-cell transcriptomics in the context of long-read nanopore sequencing
title_short	Single-cell transcriptomics in the context of long-read nanopore sequencing
title_full	Single-cell transcriptomics in the context of long-read nanopore sequencing
title_fullStr	Single-cell transcriptomics in the context of long-read nanopore sequencing
title_full_unstemmed	Single-cell transcriptomics in the context of long-read nanopore sequencing
title_sort	single-cell transcriptomics in the context of long-read nanopore sequencing
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/4f94f93611fa432c95d4a0499416751e
work_keys_str_mv	AT sorenhayrabedyan singlecelltranscriptomicsinthecontextoflongreadnanoporesequencing AT petyakostova singlecelltranscriptomicsinthecontextoflongreadnanoporesequencing AT viktorzlatkov singlecelltranscriptomicsinthecontextoflongreadnanoporesequencing AT krassimiratodorova singlecelltranscriptomicsinthecontextoflongreadnanoporesequencing
_version_	1718439034164871168

Single-cell transcriptomics in the context of long-read nanopore sequencing

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