title: Quantitative transcriptome analysis using RNA-seq.
abstract: RNA-seq has emerged as the technology of choice to quantify gene expression. This technology is a convenient accurate tool to quantify diurnal changes in gene expression, gene discovery, differential use of promoters, and splice variants for all genes expressed in a single tissue. Thus, RNA-seq experiments provide sequence information and absolute expression values about transcripts in addition to relative quantification available with microarrays or qRT-PCR. The depth of information by sequencing requires careful assessment of RNA intactness and DNA contamination. Although the RNA-seq is comparatively recent, a standard analysis framework has emerged with the packages of Bowtie2, TopHat, and Cufflinks. With rising popularity of RNA-seq tools have become manageable for researchers without much bioinformatical knowledge or programming skills. Here, we present a workflow for a RNA-seq experiment from experimental planning to biological data extraction.
authors.affiliation: iGrad Plant, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.
authors.forename: Canan
authors.initials: C
authors.lastname: Külahoglu
authors.forename: Andrea
authors.initials: A
authors.lastname: Bräutigam
mesh_terms: D057906:Circadian Clocks / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods