Work

High-Throughput RNA Sequencing in B-Cell Lymphomas

Year: 2012

Type: book-chapter

Abstract: 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 amplified 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.

Source: Methods in molecular biology

DOI: 10.1007/978-1-62703-269-8_17

Authors: Wenming Xiao, Bao Tran, Louis M. Staudt, Roland Schmitz

Institutions: National Institutes of Health, Center for Information Technology, National Cancer Institute, Center for Cancer Research

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

Funders: Dr. Mildred Scheel Stiftung für Krebsforschung, National Institutes of Health, National Cancer Institute