title: Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods.
abstract: Genomic tiling array transcriptomics and RNA-seq are two powerful and rapidly developing approaches for unbiased transcriptome analysis. Providing comprehensive identification and quantification of transcripts with an unprecedented resolution, they are leading to major breakthroughs in systems biology. Here we review each step of the analysis from library preparation to the interpretation of the data, with particular attention paid to the possible sources of artifacts. Methodological requirements and statistical frameworks are often similar in both the approaches despite differences in the nature of the data. Tiling array analysis does not require rRNA depletion and benefits from a more mature computational workflow, whereas RNA-Seq has a clear lead in terms of background noise and dynamic range with a considerable potential for evolution with the improvements of sequencing technologies. Being independent of prior sequence knowledge, RNA-seq will boost metatranscriptomics and evolutionary transcriptomics applications.
authors.affiliation: Ernst-Moritz-Arndt-University Greifswald, Institute for Microbiology and Interfaculty Institute for Genetics and Functional Genomics, F.-L.-Jahn-Strasse 15, Greifswald, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.forename: Hugues
authors.initials: H
authors.lastname: Richard
authors.forename: Philippe
authors.initials: P
authors.lastname: Bessières
authors.forename: Stéphane
authors.initials: S
authors.lastname: Aymerich
mesh_terms: D000818:Animals; D016477:Artifacts; D001419:Bacteria; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D005827:Genetics, Microbial / Q000379:methods*; D016678:Genome; D055106:Genome-Wide Association Study; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000235:genetics*; D012441:Saccharomyces cerevisiae; D017423:Sequence Analysis, RNA; D049490:Systems Biology
chemical_list: D012313:RNA