title: A Method for Bioinformatic Analysis of Transposon Insertion Sequencing (INSeq) Results for Identification of Microbial Fitness Determinants.
abstract: Transposon insertion sequencing is a process whereby microbial fitness determinants can be identified on a genome-wide scale. This process uses high-throughput next generation sequencing to screen for changes in the composition of a pool of transposon mutants after exposure to selective conditions. One commonly used process for generating transposon insertion sequencing libraries is called INSeq that works with mutant pools produced using a modified Mariner transposon. Libraries produced using the INSeq process are sequenced on the Illumina platform. In this chapter, we describe our method for processing the raw Illumina sequencing reads, aligning the reads to a reference sequence to determine read counts, and using the online transposon insertion sequencing data analysis server, ESSENTIALS, to interpret the results.
authors.affiliation: Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: Nengding
authors.initials: N
authors.lastname: Wang
authors.affiliation: Department of Medicine, Northwestern University Feinberg School of Medicine, 645 N Michigan Ave, Chicago, IL, USA. e-ozer@northwestern.edu.
authors.forename: Egon A
authors.initials: EA
authors.lastname: Ozer
mesh_terms: D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D016254:Mutagenesis, Insertional / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004251:DNA Transposable Elements
keywords: Bioinformatics; Gene function; INSeq; Microbial fitness; Next-generation sequencing; Transposon insertion sequencing