title: Transcriptomes of whole blood and PBMC in chickens.
abstract: Global transcriptome analysis of chicken whole blood to discover biomarkers of different phenotypes or physiological disorders has never been investigated so far. Whole blood provides significant advantages, allowing large scale and non-invasive sampling. However, generation of gene expression data from the blood of non-mammalian species remains a challenge, notably due to the nucleated red blood cells, hindering the use of well-established protocols. The aim of this study was to analyze the relevance of using whole blood cells (WB) to find biomarkers, instead of Peripheral Blood Mononuclear Cells (PBMC), usually chosen for immune challenges. RNA sources from WB and PBMC was characterized by microarray analysis. Our results show that the quality and quantity of RNA obtained from WB was suitable for further analyses, although the quality was lower than that from PBMC. The transcriptome profiling comparison revealed that the majority of genes were expressed in both WB and PBMC. Hemoglobin subunits were the major transcripts in WB, whereas the most enriched biological process was related to protein catabolic process. Most of the over-represented transcripts in PBMC were implicated in functions specific to thrombocytes, like coagulation and platelet activation, probably due to the large proportion of this nucleated cell type in chicken PBMC. Functions related to B and T cells and to other immune functions were also enriched in the PBMC subset. We conclude that WB is more suitable for large scale immunity oriented studies and other biological processes that have been poorly investigated so far.
authors.affiliation: INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles, France; Agrocampus-Ouest, UMR1348, Rennes, France. Electronic address: colette.desert@agrocampus-ouest.fr.
authors.forename: Colette
authors.initials: C
authors.lastname: Désert
authors.affiliation: INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles, France; Agrocampus-Ouest, UMR1348, Rennes, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Merlot
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Zerjal
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Bed'hom
authors.affiliation: Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
authors.forename: Sonja
authors.initials: S
authors.lastname: Härtle
authors.affiliation: INRA, UR1037 Laboratoire de Physiologie et Génomique des Poissons, Rennes, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Le Cam
authors.affiliation: INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles, France; Agrocampus-Ouest, UMR1348, Rennes, France.
authors.forename: Pierre-François
authors.initials: PF
authors.lastname: Roux
authors.affiliation: INRA, UR83, Recherches Avicoles, Nouzilly, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Baeza
authors.affiliation: INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles, France; Agrocampus-Ouest, UMR1348, Rennes, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Gondret
authors.affiliation: INRA, UR83, Recherches Avicoles, Nouzilly, France.
authors.forename: Michel Jacques
authors.initials: MJ
authors.lastname: Duclos
authors.affiliation: INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'élevage, Saint-Gilles, France; Agrocampus-Ouest, UMR1348, Rennes, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000097:blood*; D001798:Blood Proteins / Q000235:genetics*; D002478:Cells, Cultured; D002645:Chickens / Q000235:genetics* / Q000254:growth & development; D019295:Computational Biology; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D008297:Male; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome / Q000235:genetics*
chemical_list: D015415:Biomarkers; D001798:Blood Proteins; D012333:RNA, Messenger
keywords: Chicken; Gene expression; Microarrays; PBMC; Whole blood