Pascal Sirand-Pugnet and Patricia Fergelot
C. HUBERT (Sequencing), C. BRES (Tilling), V. GARCIA (Bioinformatics) F. Salin (Genotyping)
Plateforme Génome-Transcriptome de Bordeaux
Université Victor Segalen Bordeaux2
146 Rue Léo Saignat
33076 Bordeaux Cedex
The facility provides genotyping, sequencing and tilling services to a broad scientific community. It develops new technologies to answer the needs of a large variety of researchers involved in the study of plants, micro-organisms and humans.
Simplified list of equipments
Automated DNA isolation (Autogenflex 3000) Nucleic acids measurement by absorbance (Nanodrop) or fluorescence (Bioanalyzer) Automated robotic systems (Hamilton, Biomek 3000, Freedom EVO Tecan et Biomek NX Beckman) Thermocycler devices, real-time PCR ABI 7500 and LC 480 ROCHE Sequencing devices: capillary, ABI 3730 and ABI 3130 XL, plate, 3 LI-COR 4300 High-throughput genotyping system: BeadXpress Reader Next Generation Sequencing: Illumina Genome Analyzer II (GAIIX)
Detection of single base variations (SNP), of microsatellites or insertions/deletions by the most appropriate technique with regard to the number of samples, the type and the number of variations targeted: BeadXPress Goldengate - Veracode (Illumina), Mass array Sequenom, Hybridization by Taqman or Kspar probes using the LC480 Roche, HRM using the LC 480, Snap shot using the ABI 3730.
Implementation of low, medium or high throughput sequencing projects. In addition to Sanger technology, the facility provides next generation sequencing services since the end of 2010, allowing the acquisition of millions of sequences in a single run. The facility supports its users in every step of their projects from sample preparation to data processing.
Detection of unknown mutations in targeted genes in a population of tomato MicroTom mutants created by mutagenesis (EMS) by relying on a collection of 3,500 families of phenotyped M2 mutants.
Automated DNA Extraction (for whole blood and plant DNA) Provision of equipment Nucleic acids quantification Copy number variation Technical assistance to users Education and training
The facility supports the research of a broad community with diverse fields of interest and expertise. Specific strengths are in human genetics, plant sciences and microbiology-virology analyses.
Automation of the handling of biological samples (tube – plate, plate – plate, plate normalization) used for the preparation and purification of sequencing reactions and for the preparation of next generation sequencing libraries.
Optimisation of genotyping and sequencing methods (quality, costs, throughput, multiplexing).
Inauguration and opening of the next generation sequencing service to users in 2010. Participation in 7 ANR projects, 8 European projects, 3 international projects, 8 national projects and 4 INRA or CIVB projects in 2010. Launching of the facility’s new web site in 2010. Inauguration of new dedicated building in September 2011 in Cestas.