PF GenoBiRDThe two core facilities that compose GenoBiRD offer a complete service from the laboratory bench to the analysis of the data :
  • sequencing
  • genotyping
  • genome expression analysis projects
GenoBiRD also provides open-access to wet-lab equipment and IT resources for bioinformatics.




Photo credit : Stéphane Bellanger

Know-how

génomiqueThe Genomics core facility is recognized for its expertise in the following applications:
  • transcriptome analysis (RNA-seq, 3'seq RNA Profiling, DNA chips)
  • massive sequencing (NGS): whole genomes or exomes, capture of targeted genes.
  • high-speed genotyping (on Affymetrix Axiom chips)
The BiRD Bioinformatics platform has expertise in large-scale data analysis and develops dedicated bioinformatics pipelines to standardize analysis.bird
  • analysis of NGS sequencing data (detection of genetic variations)
  • transcriptome data analysis (RNA-seq, 3'seq RNA Profiling, DNA chips)
  • primary analysis of high throughput genotyping data
  • microbiota data analysis (16S, Shotgun Metagenomics in development)

Photos crédit : Université de Nantes

Types of services

GenoBiRD offers two types of services:
  • project management : all project requests are discussed during a meeting with the project leader and his colleagues, in order to establish a engagement sheet in which is described the specifications, as well as the modalities for delivering results and the timeframe of the service.
  • Provision:
    • genomics equipment : their use includes training and technical support by platform staff, if necessary. Initial training is organized for all new users;
    • of bioinformatics resources : cluster computing and storage, SnakeMake pipelines. Their use requires an account and the approval of the BiRD charter.

Examples of achievements

GenoBiRD supports about thirty projects per year. In particular, it is a partner in projects :
 
  • SysMics : integrated genomics research cluster labelled by the I-SITE NExT, which is based on the GenoBiRD infrastructure. SysMics aims to federate the NExT community with a shared objective: to anticipate the emergence of systemic medicine by co-developing 3 large-scale genomic screening approaches: genome sequencing of patient populations, genomic profiling on single cells and metagenomics applied to microbiota(s). The first mission of SysMics is to build on site all the resources necessary to implement or consolidate these 3 approaches. The second step will be to combine these approaches in the context of pilot projects in immunology, oncology and pathophysiology of cardiovascular, metabolic, respiratory and neuro-digestive diseases.
  • INEX-MED : INtegration and EXploration of heterogeneous bio-MEDical data. The objective of this pilot project supported by the IFB is to develop a sustainable infrastructure for integration, exploitation and modelling (semantic/statistical) on heterogeneous data sources and multi-site computing infrastructures in the biomedical area.
  • RegioCard : the genetic team of l’institut du thorax develops strategies based on whole genome for cardiac arrhythmia disorders and sudden death. Furthermore they particularly interested in investigating the role of variants in the non-coding region of the genome, seat of the gene regulation. They developed research programs on cardiac epigenetics to functionally annotate the gene regulatory regions of the genome.
  • SIRIC ILIAD : Integrated Cancer Research Site. The PISTER program brings together teams of clinicians, academics and researchers from CHUN, ICO, CHUA, CRCINA, LS2N, LAREMA and the Jean Leray mathematics laboratory. It is based on the multidisciplinary expertise of Pays de la Loire actors in clinical and translational oncology research (molecular mechanisms of apoptosis, tumor resistance and heterogeneity, oncoimmunology, oncolytic viruses, etc.) associated with a network of mathematicians and bioinformaticians.
  • RHU CHOPIN : The first goal of the team 4 of l’institut du thorax is to improve deciphering of the hepatic and intestinal metabolism of LDL in order to identify new pathways and ultimately new drug targets for hypercholesterolemia (RHU CHOPIN).
  • Ceph Recherche : Pilot project for the secure storage of massive research data using CEPH technology on a principle of sharing equipment and staff of partner members : CCIPL, BiRD (Institut du Thorax/SFR-santé), LS2N, CEISAM, DSIN.
  • IFB Biosphère : French Institute of Bioinformatics (IFB) provides life scientists with a federation of clouds, Biosphere, and bioinformatics cloud services to analyze life science data. Biosphere is used for scientific production in the life sciences, developments, and to support events like cloud and scientific training sessions, hackathons or workshops.
  • ELIXIR Interoperabillity Platform : The goal of the Interoperability Platform is to help people and machines to discover, access, integrate and analyse biological data. It encourages the life science community to adopt standardised file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals.
  • MIBIOGATE : Mibiogate is a project to study biological barriers and their microbiota in the development of chronic diseases, supported by the Pays de la Loire Region. The consortium created aims to structure a research network specialized in the study of the dysfunctions of the biological barriers of the different organs in chronic pathologies of interest.

Equipments

  • 3 high throughput sequencers (Illumina NovaSeq, HiSeq and MiSeq)
  • 1 genotyping and expression profiling station (Affymetrix GeneTitan MC)
  • 1 real-time PCR device (Roche LC480)
  • Compute clusters for bioinformatics representing 1600 cores and 800 TB of storage

Applications

The multiple applications in genomics are not limited in terms of the species studied. They can be applied in marine, agronomy, environment and health fields.