The Genome Transcriptome Platform of Bordeaux (PGTB) is a technological infrastructure supported by the UMR BIOGECO and open to the entire academic scientific community and to industrial companies.
The PGTB is part of the INRAE Genomics Research Infrastructure, with the GeT and CNRGV platforms in Toulouse, the Gentyane platform in Clermont-Ferrand and the EPGV platform in Evry. The PGTB is also a member of the France Genomics network, which brings together the main genomics platforms at national level.

The PGTB develops and offers services using medium- and high-throughput technologies based on sequencing (sequencing of short and long DNA fragments, targeted metagenomics, sequencing of genomes and transcriptomes, total metagenomics and metatranscriptomics, gene capture, etc.), mutation search and genotyping (SNP, INDEL and microsatellites), quantification of gene expression, and analysis of environmental, sensitive or ancient DNA in a confined laboratory.

Expertise

Equipments

Sequencing

PGTB offers different sequencing solutions for a wide range of applications: targeted and global metagenomics, de novo sequencing, transcriptomics and metatranscriptomics, resequencing and targeted capture sequencing. Projects are carried out on llumina’s NetSeq 2000, MiSeq and iSeq 100 short-read sequencers and on P2solo and MinION (long-read sequencers (Oxford Nanopore Technologies). PGTB also offers ready-to-load sequencing on NextSeq 2000 of pools of RNAseq, single-cell, ATAC-seq, Chip-seq, WGS, etc. libraries.

Genotyping

PGTB has developed an innovative method of microsatellite genotyping  using Illumina high-throughput sequencing and offers a turnkey service including (1) the development of microsatellite markers from random sequencing data performed by PGTB or from pre-existing genomic resources, (2) amplification tests and Illumina sequencing of these markers, (3) bioinformatics analysis to validate the markers and to generate a  table of genotypes.

The PGTB also has a MassARRAY® System (Agena Bioscience™), which allows the analysis of di-, tri- and tetra-allelic 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.

Robotics

The PGTB has a STAR 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. A Dragonfly (TTP Labtech) is also available for ultra-fast and contactless distribution of mixes in 96 and 384 plates.

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 and sequencing library preparations .

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.

Last update February 2024