Virus Expression Database

GSE57862

High-resolution transcriptome analysis with long-read RNA sequencing

Submitted by Hyunghoon Cho (Massachusetts Institute of Technology, USA) on May 21 2014

Platform: ngs – Illumina HiSeq 2000 (Homo sapiens)

Pubmed: 25251678

Summary 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.

2 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1395233 GM12878 2x262 bp lymphoblastoid cell line  Human gammaherpesvirus 4
GSM1395234 GM12878 2x75 bp lymphoblastoid cell line  Human gammaherpesvirus 4