High throughput error corrected Nanopore single cell transcriptome sequencing
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Abstract
Droplet-based high throughput single cell sequencing techniques tremendously advanced our insight into cell-to-cell heterogeneity. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. In consequence, information on splicing and sequence heterogeneity is lost. To overcome this limitation, several approaches that use long-read sequencing were introduced recently. Yet, those techniques are limited by low sequencing depth and/or lacking or inaccurate assignment of unique molecular identifiers (UMIs), which are critical for elimination of PCR bias and artifacts. We introduce ScNaUmi-seq, an approach that combines the high throughput of Oxford Nanopore sequencing with an accurate cell barcode and UMI assignment strategy. UMI guided error correction allows to generate high accuracy full length sequence information with the 10x Genomics single cell isolation system at high sequencing depths. We analyzed transcript isoform diversity in embryonic mouse brain and show that ScNaUmi-seq allows defining splicing and SNVs (RNA editing) at a single cell level.
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- [5]Volden, R. & Vollmers, C. Highly multiplexed single-cell full-length cDNA sequencing of human immune cells with 10X genomics and R2C2. bioRxiv https://www.biorxiv.org/content/10.1101/2020.01.10.902361v1 (2020). · DOI
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Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing
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scTrends: A living review of commercial single-cell and spatial 'omic technologies
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Specific splice junction detection in single cells with SICILIAN
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Practical Considerations for Single‐Cell Genomics
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African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1
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Single-cell methods in myeloproliferative neoplasms: old questions, new technologies
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Single-Cell Analysis in the Omics Era: Technologies and Applications in Cancer
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Single-Cell Splicing Isoform Atlas of the Adult Human Heart and Heart Failure
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NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing
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From words to complete phrases: insight into single-cell isoforms using short and long reads
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Signature of m5C-Related lncRNA for Prognostic Prediction and Immune Responses in Pancreatic Cancer
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High-throughput full-length single-cell RNA-seq automation
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Isoform characterization of m6A in single cells identifies its role in RNA surveillance
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- Authors
- Lebrigand, K., Magnone, V., Barbry, P., & Waldmann, R.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Barbry, Pascal
- Waldmann, Rainer
- Venue
- Nature Communications
- Published
- 2020-08-12
- Volume
- 11
- Issue
- 1
- Pages
- 4025-4025
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7423900
- OpenAlex
- W3048389895
- Cited by
- 236
- References
- 19
- Citations by year
- 2026: 28 · 2025: 44 · 2024: 41 · 2023: 41 · 2022: 36 · 2021: 36 · 2020: 10
- FWCI
- 10.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Institut National Du Cancer (PLBIO2018-156)
- Conseil Départemental des Alpes Maritimes (2016-294DGADSH-CV)
- Fondation pour la Recherche Médicale (DEQ20180339158)
- Institut National de la Santé et de la Recherche Médicale (HuDeCA 2018)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- single-cell transcriptomics, Oxford Nanopore sequencing, unique molecular identifiers, error correction, cell barcoding, long-read sequencing, alternative splicing, RNA editing, single-cell RNA sequencing, 10x Genomics, embryonic mouse brain, cellular heterogeneity
- MeSH terms
- Nanopore Sequencing, Animals, Brain, Mice, Inbred C57BL, Gene Expression, Sequence Analysis, DNA, Sequence Analysis, RNA, Receptors, AMPA, Protein Isoforms, Gene Expression Profiling, Genomics, Mice, Nanopores, High-Throughput Nucleotide Sequencing, Transcriptome
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