Advances in long-read single-cell transcriptomics

Adewale BA (2020) Will long-read sequencing technologies replace short-read sequencing technologies in the next 10 years? African J Lab Med 9(1):1–5

Article  Google Scholar 

Adil A et al (2021) Single-cell transcriptomics: current methods and challenges in data acquisition and analysis. Front Neurosci 15:591122

Article  PubMed  Google Scholar 

Al’Khafaji AM et al (2023) High-throughput RNA isoform sequencing using programmed cDNA concatenation. Nat Biotechnol 42(4):582–586

Article  PubMed  Google Scholar 

Alquicira-Hernandez J, Sathe A, Ji HP, Nguyen Q, Powell JE (2019) scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biol 20:1–17

Article  Google Scholar 

Amarasinghe SL et al (2020) Opportunities and challenges in long-read sequencing data analysis. Genome Biol 21(1):1–16

Article  Google Scholar 

Andrews TS et al (2022) Single-cell, single-nucleus, and spatial RNA sequencing of the human liver identifies cholangiocyte and mesenchymal heterogeneity. Hepatol Commun 6(4):821–840

Article  CAS  PubMed  Google Scholar 

Angerer P et al (2017) Single cells make big data: new challenges and opportunities in transcriptomics. Cur Opin Syst Biol 4:85–91

Article  Google Scholar 

Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M (2019) Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol 20:163–172. https://doi.org/10.1038/s41590-018-0276-y

Article  CAS  PubMed  Google Scholar 

Bakken TE et al (2018) Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS ONE 13(12):e0209648

Article  PubMed  Google Scholar 

Baran-Gale J, Chandra T, Kirschner K (2018) Experimental design for single-cell RNA sequencing. Brief Funct Genomics 17(4):233–239

Article  CAS  PubMed  Google Scholar 

Boldogkői Z et al (2019) Long-read sequencing–a powerful tool in viral transcriptome research. Trends Microbiol 27(7):578–592

Article  PubMed  Google Scholar 

Bowden R et al (2019) Sequencing of human genomes with nanopore technology. Nat Commun 10(1):1869

Article  PubMed  Google Scholar 

Burja B et al (2022) An optimized tissue dissociation protocol for single-cell RNA sequencing analysis of fresh and cultured human skin biopsies. Front Cell Dev Biol 10:872688

Article  PubMed  Google Scholar 

Cavelier L et al (2015) Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer 15:1–12

Article  Google Scholar 

Chen Y, et al. (2021). A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. BioRxiv. p 2021.04. 21.440736.

Chung H, et al. (2022). SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue. bioRxiv. p 2022.08. 25.505257.

Cole C et al (2018) Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq. Nucleic Acids Res 46(10):e62–e62

Article  PubMed  Google Scholar 

Conesa A et al (2016) A survey of best practices for RNA-seq data analysis. Genome Biol 17(1):1–19

Google Scholar 

Davidson NM et al (2022) JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biol 23(1):1–20

Article  Google Scholar 

De Paoli-Iseppi R, et al. (2024). Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain. medRxiv. p 2024.02. 22.24303189.

Denisenko E et al (2020) Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol 21(1):1–25

Article  Google Scholar 

Denyer T, Timmermans MC (2022) Crafting a blueprint for single-cell RNA sequencing. Trends Plant Sci 27(1):92–103

Article  CAS  PubMed  Google Scholar 

Deshpande D et al (2023) RNA-seq data science: from raw data to effective interpretation. Front Genet 14:997383

Article  CAS  PubMed  Google Scholar 

Dobin A et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21

Article  CAS  PubMed  Google Scholar 

Dorney R et al (2023) Recent advances in cancer fusion transcript detection. Brief Bioinform 24(1):bbac519

Article  PubMed  Google Scholar 

Ebrahimi G et al (2022) Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments. Iscience 25(7):104530

Article  CAS  PubMed  Google Scholar 

Fan X et al (2020) Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing. PLoS Biol 18(12):e3001017

Article  CAS  PubMed  Google Scholar 

Felton C, et al. (2022). Detection of alternative isoforms of gene fusions from long-read RNA-seq with FLAIR-fusion. bioRxiv. p 2022.08. 01.502364.

Fu S, Wang A, Au KF (2019) A comparative evaluation of hybrid error correction methods for error-prone long reads. Genome Biol 20:1–17

Article  Google Scholar 

Fu Y, et al. (2023). Single cell and spatial alternative splicing analysis with long read sequencing. bioRxiv. p 2023.02. 23.529769.

Furlan M et al (2021) Computational methods for RNA modification detection from nanopore direct RNA sequencing data. RNA Biol 18(sup1):31–40

Article  CAS  PubMed  Google Scholar 

Gamaarachchi H et al (2022) Fast nanopore sequencing data analysis with SLOW5. Nat Biotechnol 40(7):1026–1029

Article  CAS  PubMed  Google Scholar 

Gao XH et al (2020) Comparison of fresh frozen tissue with formalin-fixed paraffin-embedded tissue for mutation analysis using a multi-gene panel in patients with colorectal cancer. Front Oncol 10:310

Article  PubMed  Google Scholar 

Garalde DR et al (2018) Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods 15(3):201–206

Article  CAS  PubMed  Google Scholar 

Gilpatrick T et al (2020) Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol 38(4):433–438

Article  CAS  PubMed  Google Scholar 

Gross A et al (2015) Technologies for single-cell isolation. Int J Mol Sci 16(8):16897–16919

Article  CAS  PubMed  Google Scholar 

Gupta I et al (2018) Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 36(12):1197–1202

Article  CAS  Google Scholar 

Hazzard B et al (2022) Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts. PLoS Negl Trop Dis 16(12):e0010991

Article  CAS  PubMed  Google Scholar 

Healey HM, Bassham S, Cresko WA (2022) Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis. Genetics 220(3):iyac017

Article  PubMed  Google Scholar 

Heberle BA, et al. (2023). Using deep long-read RNAseq in Alzheimer’s disease brain to assess medical relevance of RNA isoform diversity. bioRxiv

Helm M, Motorin Y (2017) Detecting RNA modifications in the epitranscriptome: predict and validate. Nat Rev Genet 18(5):275–291

Article  CAS  PubMed  Google Scholar 

Holmqvist I et al (2021) FLAME: long-read bioinformatics tool for comprehensive spliceome characterization. RNA 27(10):1127–1139

Article  CAS  PubMed  Google Scholar 

Huang KK et al (2021) Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer. Genome Biol 22:1–24

Article  Google Scholar 

Hwang B, Lee JH, Bang D (2018) Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med 50(8):1–14

Article  CAS  PubMed  Google Scholar 

Jabbari J, Tian L (2019). Massively parallel long-read sequencing of single cell RNA isoforms. Protocols. Io.

Jovic D et al (2022) Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 12(3):e694

Article  CAS  PubMed  Google Scholar 

Kaminow B, Yunusov D, Dobin A (2021). TARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. Biorxiv. p 2021.05. 05.442755.

Kim D et al (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37(8):907–915

Article  CAS  PubMed  Google Scholar 

Krishnaswami SR et al (2016) Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 11(3):499–524

Article  CAS  PubMed  Google Scholar 

Križanović K et al (2018) Evaluation of tools for long read RNA-seq splice-aware alignment. Bioinformatics 34(5):748–754

Article  PubMed  Google Scholar 

Lähnemann D et al (2020) Eleven grand challenges in single-cell data science. Genome Biol 21(1):1–35

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