ArticlePloS one2014
High-resolution transcriptome analysis with long-read RNA sequencing.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 68 citations in OpenAlex.
- Comprehensive visceral transcriptome profiling of three pig breeds along altitudinal gradients in Yunnan.Scientific data · 2025Article
- Long-read RNA sequencing reveals allele-specificGenome research · 2025Article
- Long-read sequencing reveals novel transcript diversity inAnimal cells and systems · 2025Article
- Long-read RNA sequencing reveals allele-specific NbioRxiv : the preprint server for biology · 2024Article
- RNA Sequencing in Disease Diagnosis.Annual review of genomics and human genetics · 2024Review
- Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum.G3 (Bethesda, Md.) · 2023Article
- Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking.International journal of molecular sciences · 2023Article
- Reversal of splicing infidelity is a pre-activation step in B cell differentiation.Frontiers in immunology · 2022Article
- TahcoRoll: fast genomic signature profiling via thinned automaton and rolling hash.Medical review (2021) · 2021Article
- Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets.BMC genomics · 2021Article
- Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.BMC genomics · 2021Article
- Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.Genome biology · 2021Article
- Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis.BMC genomics · 2021Article
- High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing.Nature communications · 2020Article
- Direct Metatranscriptome RNA-seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION - Promising Strategies for Multiplex Identification of Viable Pathogens in Food.Frontiers in microbiology · 2020Article
- Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.Genome biology · 2019Article
- Nanopore native RNA sequencing of a human poly(A) transcriptome.Nature methods · 2019Article
- PlanNET: homology-based predicted interactome for multiple planarian transcriptomes.Bioinformatics (Oxford, England) · 2018Article
- A Novel Functional Splice Variant ofCancer research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in read length influence various transcriptome analyses. In this study, we generated two paired-end RNA-seq datasets of differing read lengths (2×75 bp and 2×262 bp) for lymphoblastoid cell line GM12878 and compared the effect of read length on transcriptome analyses, including read-mapping performance, gene and transcript quantification, and detection of allele-specific expression (ASE) and allele-specific alternative splicing (ASAS) patterns. Our results indicate that, while the current long-read protocol is considerably more expensive than short-read sequencing, there are important benefits that can only be achieved with longer read length, including lower mapping bias and reduced ambiguity in assigning reads to genomic elements, such as mRNA transcript. We show that these benefits ultimately lead to improved detection of cis-acting regulatory and splicing variation effects within individuals.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.