The “Genomics and Transcriptomics” facility is currently evolving from a concentration of self-service devices dedicated to nucleic acids analyses to an expanded facility with the addition of a next-generation sequencing service run by a dedicated technical staff, Julien Daligault, and offering access to bioinformatics tools installed on a local server. This latter service is about to emerge with the aim of being operational in 2013.
Currently, the facility hosts a number of instruments that are used on a self-service basis. The equipment available allows the quantification and analysis of nucleic acids in a sequence-specific manner using either an ultrasensitive format with real-time PCR or a high-throughput format with microarrays.
Real-time PCR allows the reliable, sensitive and specific quantification of nucleic acid sequences, the characterisation of PCR products by melting curve analysis and genotyping of single nucleotide polymorphism (SNP) in less than one hour.
For real-time PCR, five real-time PCR thermocyclers are available: two capillary Roche Light Cycler 1.5, two 96-well plate Stratagene Mx and one 384-well plate Roche Light Cycler 480. The system is complemented by a pipetting robot Eppendorf Epmotion 5070 to load the plates and a preparation robot Tecan Freedom Evo 100 for high-throughput sample preparation.
With DNA chips it is possible to measure in a single step the changes in relative abundance of a large number of nucleic acid sequences.
They can be used to quantify the mRNAs expressed in cells, to analyse the distribution of chromosomal proteins along the genome, and to identify the amplification and deletions of chromosomal regions as well as genetic polymorphisms.
Hybridization robots and device are available to use microarrays from Agilent, Nimblegen and other suppliers. A high density scanner, the Tecan PowerScanner, is available to analyze the arrays.
The facility also offer access to a microspectrophotometer Nanodrop that can be used to acquire the absorbance spectra of very small samples (1 µl), a lab on a chip electrophoresis system Agilent Bioanalyzer 2100, a lab on a chip electrophoresis system for DNA sizing and purification (Caliper Labchip XT), a 96-well Luminometer Berthold Centro, a 96-well plate reader Dynex MRX and a 96 well spectrophotometer and fluorimeter Tecan Infinite 200.
The facility will soon offer a high throughput next-generation DNA sequencing service based on two benchtop DNA sequencers offering complementary options for rapid turnover medium capacity sequencing. Both the Ion Torrent (PGM) and Illumina (Miseq) technology will be available.
Computer servers for NGS data storage and analyses are being installed within the Ressource Parisienne en Bioinformatique Structurale (RPBS) facility. A Galaxy-based server will be available.
Supervisor: Thierry Grange, CNRS