All our activities are available here.
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..
1 to 25 M reads. Read length from 2x75 to 2x300 bp paired-end.
Ion Torrent PROTON
1 microchip generating 100 M reads. Read length from 100 to 200 bp single-end.
Ion Torrent PGM
3 microchips generating 0.5, 2.5 and 5M reads. Read length from100 to 700 bp single-end.
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.
High Resolution Melt analysis on Roche LightCycler 480
Simplex or multiplex analysis of labelled microsatellites (FAM, PET, VIC and NED) on ABI 3730 (48 capillaries).
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/
Several equipment are available for:
|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|
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