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Analyzing Immunity in Non-model insects Using De Novo Transcriptomics

  • With the advent of widely accessible and cost-effective next-generation sequencing technologies, it has become increasingly feasible to study insect immunity on a deep genomic or transcriptomic level. Here we introduce a protocol that is aimed at exploiting transcriptomic data to study immunity in non-model insect organisms. We provide instructions for an entire workflow, starting with successfiil extraction of insect RNA through to bioinformatic guidelines for the effective analysis of mRNA sequencing data. The RNA extraction procedure is based on TRIzol Reagent and a spin-column clean-up Step. The bioinformatic pipeline is intended to help users identify immune genes from de novo transcriptome data and includes guidelines for conducting differential gene expression analyses on transcriptomic data. The immune gene prediction method is based on inferring protein homologs with HMMERand Blastp and talces Advantage ofthe ImmunoDB database, which is a valuable resource for research onWith the advent of widely accessible and cost-effective next-generation sequencing technologies, it has become increasingly feasible to study insect immunity on a deep genomic or transcriptomic level. Here we introduce a protocol that is aimed at exploiting transcriptomic data to study immunity in non-model insect organisms. We provide instructions for an entire workflow, starting with successfiil extraction of insect RNA through to bioinformatic guidelines for the effective analysis of mRNA sequencing data. The RNA extraction procedure is based on TRIzol Reagent and a spin-column clean-up Step. The bioinformatic pipeline is intended to help users identify immune genes from de novo transcriptome data and includes guidelines for conducting differential gene expression analyses on transcriptomic data. The immune gene prediction method is based on inferring protein homologs with HMMERand Blastp and talces Advantage ofthe ImmunoDB database, which is a valuable resource for research on insect immune-related genes and gene families. The differential gene expression analysis procedure utilizes the DESeq2 package as imple� mented in R. We hope this protocol will serve as a usefi.il resource for researchers aiming to study immunity in non-model insect species.zeige mehrzeige weniger

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Metadaten
Autor*innen:S. He, P. R. Johnston, Dino Peter McMahon
Persönliche Herausgeber*innen:F. Sandrelli, G. Tettamanti
Dokumenttyp:Beitrag zu einem Sammelband
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):Immunity in Insects
Jahr der Erstveröffentlichung:2020
Organisationseinheit der BAM:4 Material und Umwelt
4 Material und Umwelt / 4.0 Abteilungsleitung und andere
Verlag:Springer Science+Business Media
Verlagsort:Luxemburg
Jahrgang/Band:2020
Aufsatznummer:Chapter 2
Erste Seite:35
Letzte Seite:49
DDC-Klassifikation:Technik, Medizin, angewandte Wissenschaften / Ingenieurwissenschaften / Sanitär- und Kommunaltechnik; Umwelttechnik
Freie Schlagwörter:De novo assembly; Differential gene expression analysis; Immune gene prediction; ImmunoDB; RNA extraction; mRNA-seq
Themenfelder/Aktivitätsfelder der BAM:Umwelt
DOI:10.1007/978-1-0716-0259-1_2
Verfügbarkeit des Dokuments:Datei im Netzwerk der BAM verfügbar ("Closed Access")
Datum der Freischaltung:06.12.2021
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:06.12.2021
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