The Bordeaux Transcriptome Genome Platform is an academic structure specialized in sequencing and genotyping. It was born from the desire of the University of Bordeaux and INRA to pool skills, technological and human resources at the service of the scientific community. A member of France Génomique, it is part of a network of seven integrated technological platforms in the Centre de Génomique Fonctionnelle de Bordeaux (CGFB), and is a component of INRA’s Distributed Genomic Research Infrastructure currently under construction, which brings together the four INRA platforms in the field of genomics.

In the field of genomics, the PGTB aims to satisfy the genotyping and sequencing needs related to laboratory research activities, and to be a centre open to the entire academic scientific community (INRA, CNRS, INSERM, IFREMER, CHU, Universities…) and industrial stakeholders. It provides its services and know-how for regional, national and international projects in fields as varied as health, agronomy and the environment.

Expertise

Equipments

Sequencing

The PGTB offers different sequencing solutions for a wide range of applications: transcriptomics, targeted metagenomics, de novo sequencing, resequencing and targeted sequencing (capture). Projects are carried out on Illumina® short-read sequencers and GridION long-read sequencers (Oxford Nanopore Technologies), for which the PGTB is “Nanopore Service Certified”.

The PGTB also has a Fluidigm® Access Array System 48.48 for resequencing amplicons (up to 480 samples) in combination with the MiSeq.

Genotyping

The MassARRAY® System (Agena Bioscience™), allows to analyze di, tri and tetra-allel SNPs as well as INDELs (up to 40 bp). Different combinations are possible: 40 SNPs on 380 samples, 80 SNPs on 190 samples, and 160 SNPs on 95 samples.

Quantification & Robotics

A Roche® LC480 II qPCR and a Droplet Digital PCR QX200 (Bio-Rad®) are available for the absolute detection and quantification of copies in small quantities.

The PGTB has a ChemagicSTAR robot (Hamilton) equipped with a 96 pipette head and 8 individual pipettes. This robot can dilute, rearrange and pool samples, primers and PCR products in 96 and 384 plates, distribute PCR and qPCR mixes in 96 and 384 plates, and also a Dragonfly (TTP Labtech) is available for ultra-fast and contactless distribution of mixes.

Confined laboratory

This laboratory is equipped with clean rooms with filtered air, positive pressure and UV radiation. It is dedicated to the study of environmental DNA and “sensitive” samples (wood, herbarium…). It has complete molecular biology equipment and several rooms for sample preparation, DNA extraction and PCR preparation.

Main achievments

About 100 projects carried out each year since 2009 in the fields of sequencing and genotyping. The PGTB provides its services and know-how for regional, national and international projects in fields as varied as health, forestry research, vines and wine, microbiology, agronomy and the environment.