Activities

All our activities are available here.

Sequencing

PGTB offers various NGS sequencing solutions adapted to many types of research projects:

  • Whole transcriptome (RNA-Seq)
  • Sequencing of microbial genomes
  • ddRAD sequencing (double digest restriction associated DNA)
  • Targeted sequencing (SureSelect technologies, Ion AmpliSeq)
  • Targeted gene expression and small RNA profiling
  • Amplicon resequencing (Fluidigm Access Array System 48.48)
  • Metagenomic and metabarcoding

PGTB have four benchtop next-generation sequencers:

Oxford Nanopore Technologies MinION

Long-reads sequencer which generates 5 to 10Gb of sequences. Maximum read length up to hundreds of kb..

MinION

 

Illumina MiSeq

1 to 25 M reads. Read length from 2x75 to 2x300 bp paired-end.

Specif_MiSeq

 

 

Illumina MiSeq

 

Ion Torrent PROTON

1 microchip generating 100 M reads. Read length from 100 to 200 bp single-end.

 

Ion Torrent PROTON

 

Ion Torrent PGM

3 microchips generating 0.5, 2.5 and 5M reads. Read length from100 to 700 bp single-end.

 

Ion Torrent PGM

 

Genotyping

Multiple genotyping techniques are available within the PGTB

SNP AND INDEL GENOTYPING

This technology is based on mass spectrometry (MassArray System of Agena Biosciences, formely Sequenom) allowing the analyse of di, tri and tetra-allelic SNPs and Indel (up to 40 bp). Different combinations are available : 40 SNPs on 380 samples, 80 SNPs on 190 samples or 160 SNPs on 95 samples.

Sequenom

 

HRM

High Resolution Melt analysis on Roche LightCycler 480

MICROSATELLITES

Simplex or multiplex analysis of labelled microsatellites (FAM, PET, VIC and NED) on ABI 3730 (48 capillaries).

 

Bioinformatics

Four dedicated workstations are available for data storage and analysis of genotyping and sequencing data. One workstation is exclusively dedicated to NGS analysis with CLC Genomics Workbench
PGTB allows the free access to its own Galaxy instance

For more specific requests in bioinformatics, please contact the Bioinformatics Center of Bordeaux: http://www.cbib.u-bordeaux2.fr/

Bioinformatique

 

Support services

Several equipment are available for:

Usage Equipment
Quantification of nucleic acids Fluorimeters Qubit (tubes) and Infinite 200 Tecan Quant-it (96 or 384-well plates)
Spectrophotometer NanoDrop ND1000 et ND8000 (1 to 8 DNA/RNA analyzed simultaneously)
Quality control of samples and librairies Bioanalyzer 2100 (Agilent Technologies)
DNA shearing Covaris M220

 

Robotics

Automation for the dilution, rearrangement and pooling of samples and for the distribution of PCR/qPCR mix and DNA (96 or 384-well plates) on Hamilton ChemagicSTAR robotic station

Robotics