title: Analyzing Prokaryotic RNA-Seq Data: A Case Study Identifying Holo-Fur Regulated Genes in Campylobacter jejuni.
abstract: In recent years, RNA-seq has become an important method in the process of measuring gene expression in various cells and organisms. This chapter will detail all the bioinformatic steps that should be undertaken to determine differentially expressed genes from a typical RNA-seq experiment. Each step will be clearly explained in "non-bioinformatic" terminology so that readers embarking on RNA-seq analysis will be able to understand the rationale and reasoning behind each step. Moreover, the exact command lines used to process the data will be presented along with a description of the various flags and commands.
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5.
authors.forename: Sophie
authors.initials: S
authors.lastname: Bérubé
authors.affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5.
authors.forename: James
authors.initials: J
authors.lastname: Butcher
authors.affiliation: Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5. astintzi@uottawa.ca.
authors.forename: Alain
authors.initials: A
authors.lastname: Stintzi
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D016123:Campylobacter jejuni / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D007501:Iron / Q000378:metabolism; D011381:Programming Languages; D012329:RNA, Bacterial / Q000032:analysis* / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; D007501:Iron
keywords: Bioinformatics; Campylobacter jejuni; Differential expression; RNA-seq