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High-resolution transcriptome analysis with long-read RNA sequencing

ABSTRACT: Ongoing improvements to next generation sequencing technologies are leading to longer sequencing read lengths, but a thorough understanding of the impact of longer reads on RNA sequencing analyses is lacking. To address this issue, we generated and compared two RNA sequencing datasets of differing read lengths -- 2x75 bp (L75) and 2x262 bp (L262) -- and investigated the impact of read length on various aspects of analysis, including the performance of currently available read-mapping tools, gene and transcript quantification, and detection of allele-specific expression patterns. Our results indicate that, while the scalability of read-mapping tools and the cost-effectiveness of long read protocol is an issue that requires further attention, longer reads enable more accurate quantification of diverse aspects of gene expression, including individual-specific patterns of allele-specific expression and alternative splicing. Two RNA-Seq datasets of differing read lengths (2x262 bp and 2x75 bp)

ORGANISM(S): Homo sapiens  

SUBMITTER: Stephen B Montgomery   Kevin S Smith  Xin Li  Joe Davis  Alexis Battle  Hyunghoon Cho 

PROVIDER: E-GEOD-57862 | ArrayExpress | 2014-09-25



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High-resolution transcriptome analysis with long-read RNA sequencing.

Cho Hyunghoon H   Davis Joe J   Li Xin X   Smith Kevin S KS   Battle Alexis A   Montgomery Stephen B SB  

PloS one 20140924 9

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  ...[more]

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