Universität zu Köln

Wang, Qi ORCID: 0000-0002-7827-4808, Boenigk, Sven, Boehm, Volker ORCID: 0000-0001-7588-9842, Gehring, Niels, Altmueller, Janine and Dieterich, Christoph ORCID: 0000-0001-9468-6311 (2021). Single-cell transcriptome sequencing on the Nanopore platform with ScNapBar. RNA, 27 (7). S. 763 - 771. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. ISSN 1469-9001

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Abstract

The current ecosystem of single-cell RNA-seq platforms is rapidly expanding, but robust solutions for single-cell and single-molecule full-length RNA sequencing are virtually absent. A high-throughput solution that covers all aspects is necessary to study the complex life of mRNA on the single-cell level. The Nanopore platform offers long read sequencing and can be integrated with the popular single-cell sequencing method on the 10x Chromium platform. However, the high error-rate of Nanopore reads poses a challenge in downstream processing (e.g., for cell barcode assignment). We propose a solution to this particular problem by using a hybrid sequencing approach on Nanopore and Illumina platforms. Our software ScNapBar enables cell barcode assignment with high accuracy, especially if sequencing saturation is low. ScNapBar uses unique molecular identifier (UMI) or Naive Bayes probabilistic approaches in the barcode assignment, depending on the available Illumina sequencing depth. We have benchmarked the two approaches on simulated and real Nanopore data sets. We further applied ScNapBar to pools of cells with an active or a silenced nonsense-mediated RNA decay pathway. Our Nanopore read assignment distinguishes the respective cell populations and reveals characteristic nonsense-mediated mRNA decay events depending on cell status.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Wang, Qi UNSPECIFIED orcid.org/0000-0002-7827-4808 UNSPECIFIED Boenigk, Sven UNSPECIFIED UNSPECIFIED UNSPECIFIED Boehm, Volker UNSPECIFIED orcid.org/0000-0001-7588-9842 UNSPECIFIED Gehring, Niels UNSPECIFIED UNSPECIFIED UNSPECIFIED Altmueller, Janine UNSPECIFIED UNSPECIFIED UNSPECIFIED Dieterich, Christoph UNSPECIFIED orcid.org/0000-0001-9468-6311 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-582579
DOI:	10.1261/rna.078154.120
Journal or Publication Title:	RNA
Volume:	27
Number:	7
Page Range:	S. 763 - 771
Date:	2021
Publisher:	COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
Place of Publication:	COLD SPRING HARBOR
ISSN:	1469-9001
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language EXPRESSION Multiple languages Biochemistry & Molecular Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/58257