Transcriptomics

Dataset Information

34

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. Overall design: Two RNA-Seq datasets of differing read lengths (2x262 bp and 2x75 bp)

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

ORGANISM(S): Homo sapiens  

SUBMITTER: Hyunghoon Cho  

PROVIDER: GSE57862 | GEO |

SECONDARY ACCESSION(S): PRJNA248285

REPOSITORIES: GEO

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