High-throughput mRNA sequencing (RNA-seq) uses massively parallel sequencing to allow an unbiased analysis of both genome-wide transcription levels and mutation status of a tumor. In the RNA-seq method, complementary DNA (cDNA) is used to generate short sequence reads by immobilizing millions of ampli fied DNA fragments onto a solid surface and performing the sequence reaction. The resulting sequences are aligned to a reference genome or transcript database to create a comprehensive description of the analyzed transcriptome. This chapter describes a protocol to perform RNA-seq using the Illumina sequencing platform, presents sequencing data quality metrics and outlines a bioinformatic pipeline for sequence alignment, digital gene expression, and mutation discovery. © Springer Science+Business Media, LLC 2013.
CITATION STYLE
Xiao, W., Tran, B., Staudt, L. M., & Schmitz, R. (2013). High-throughput RNA sequencing in B-cell lymphomas. Methods in Molecular Biology, 971, 295–312. https://doi.org/10.1007/978-1-62703-269-8_17
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