Sequencing Platform from Clermont-Ferrand
The GENTYANE (GEnoTYpage and sequencing in AuvergNE) platform is affiliated to INRAE (Centre de Clermont-Theix) and particularly to the Biology and Plant Improvement Department (BAP).
The scientific objectives of the platform are:
(1) to support the research conducted in the various teams of the UMR GDEC
(2) to carry out genotyping and sequencing services on behalf of other INRAE teams or other public and private bodies
(3) to ensure a technological watch enabling new tools to be implemented that respond better, more quickly and at a lower cost to users’ expectations
(4) training of students but also of staff of our partners within the framework of collaborative projects
The team is composed of engineers and technicians, experts in genotyping and sequencing. We have a building with all the safety features: electrical, fire and access control.
Expertise
- Genotyping :
- SNP in KASPar technology (384 plates or microfluidics)
- Genotyping by AgriSeq Thermo GBS sequencing (from 300 to 3000 SNPs on several thousand individuals)
- SNP with AXIOM technology (up to 675000 SNP in chip format 96 and up to 55000 SNP in chip format 384).
- Microsatellites on capillary sequencer (96)
- Gene expression study on Fluidigm 48*48 or 96*96Genomics chip
- Sequencing : de novo sequencing, amplicons, resequencing, mate-pair sequencing
- Optical mapping : ultra HMW DNA extraction, labelling and transfer to Bionano Genomics array, Saphyr equipment
- High throughput DNA extraction : the GENTYANE platform offers automated DNA extraction in Sbeadex or LifeStock chemistry (magnetic beads) on an oKtopure robot with a throughput of 1536 samples per day.
Equipments
- Sequencing : , 2 Sequel 8M (sept. 2019) Pacific Biosciences, IIon S5
- Genotyping : GENETITAN Affymetrix ; 3730xl DNA Analyzer, Biomark, JUNO, Biomark X, LightCycler 480, Genetitan, AgriSeq Thermo Solution (Ion Chef and S5 Prime)
- Optical mapping : 2 BionanoGenomics Saphyr
- Robotics : 3 Beckman FxP, 1 Biomek 4000, 1 Hamilton STARlet, Hamilton Vantage
- Others : Megaruptor 3, 1 BluePippin Sage, Tecan Infinite M1000, 2 Fragment Analyser Agilent, 1 Fragment Analyser Femto Pulse, 3 Integra ViaFlo 96 et 384, Qubit Flex Fluorometer
Main achievements
Completion of 300 projects (average annual turnover of €2.5 million) and ~25 scientific papers per year over the past 5 years
Saintenac, F. et al. A wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch, Nature Communications. (2021) 12:433. https://doi.org/10.1038/s41467-020-20685-0.
D’Ambrosio, R. et al. Genetic architecture and genomic selection of female reproduction traits in rainbow trout, BMC Genomics. (2020) 21 : 558. https://doi.org/10.1186/s12864-020-06955-7.
Rimbert H. et al. High throughput SNP discovery and genotyping in hexaploid wheat. PLOS ONE, (2018)13: e0186329.
Joulié A. et al. Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability. INFECTION, GENETICS AND EVOLUTION (2017) 48:142–149.
Bianco L. et al. Development and validation of the Axiom®Apple480K SNP genotyping array. THE PLANT JOURNAL (2016) 86:62-74.
Last update March 2022
Certification / Quality Assurance
Platform certified ISO9001 since 2012, and NFX50-900 since 2014
Labels
IBiSA platform certified as a strategic platform by INRAE.
Platform Managment
Charles Poncet
Gentyane Plateform
UMR INRAE 1095 Génétique Diversité et Ecophysiologie des Céréales
5 chemin de beaulieu,
63039 Clermont Ferrand cedex
Contacts
Charles Poncet : charles.poncet@clermont.inrae.fr
04 73 62 48 54
For further information
