Mutualisation des compétences et des équipements français
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the GenoBiRD platform

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Since the revolution of high throughput sequencing technologies, the study of genomes, whether structural or functional, has become easier, faster and less expensive. These cutting-edge technologies are accompanied by a deluge of data that must be analyzed with appropriate tools. These two areas of expertise (genomics and bioinformatics) must constantly stay in phase to keep pace with the extremely rapid evolution of technologies.
Thanks to the skills of a dedicated and highly qualified staff, GenoBiRD is recognized for its technical and analytical expertises for the following applications :
- High Throughput Sequencing (HTS)
- High throughput genotyping
- Microarrays
- Sanger sequencing

GenoBiRD includes two modules :
- Thanks to the expertise of a dedicated and highly qualified staff, the genomics core facility advise, propose and develop genomic services : high-throughput sequencing (genomes, exomes, gene capture...), high-throughput genotyping, transcriptome study (RNA-Seq,DGE-Seq and expression microarrays), and capillary sequencing. Trained users also have direct access to state of the art equipments.
- The bioinformatics core facility, BiRD is co-managed by the ITX and the LS2N, employs six computational biologists. BiRD advises, proposes and develops genomic and bioinformatics services : high-throughput sequencing for variant detection, high-throughput genotyping, transcriptome studies as a service to academic and private laboratories. For all of these applications, BiRD has expertise in large-scale data analysis and developed dedicated bioinformatics workflows that standardize processing from raw data to biological significance.
The core facility is supported by a dedicated computing and storage infrastructure (1456 cores, 5.5 TB RAM, 600 TB storage), directly connected to the sequencers and allowing remote access to all SysMics members, regardless of their host institution.
These services are supported by a dedicated computing and storage infrastructure directly connected to the sequencers, accessible remotely through several and open to the scientific community regardless of its supervision.

These services in genomics and bioinformatics are open to academics and private laboratories.

Service

GenoBiRD provides different types of services :
• Genomics project management : From experimentation to data analysis
• Provision of resources (Equipment and IT)
• Training

> Project management in Genomics
• Realization of a project only by an experimental approach
• Realization of bioinformatic data analysis project
• Realization of a project combining experimentation and analysis

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

> Resources provision
GenoBiRD provides different types of resources :
- Equipment to carry out genomics projects
- A high-performance, tooled and secure IT infrastructure for computing and hosting your scientific data. The software environment is constantly evolving with the regular addition of new tools according to your requests.

>GenoBiRD accompanies you for the use of resources by user training.

Expertise
NGS sequencing and data analysis up to variants calling for :
- Whole genome
- Exome
- Gene panels

High throughput genotyping
- Axiom Affymetrix microarrays (GeneTitan Station)
- Primary data analysis

Transcriptome study
- RNA Sequencing (NGS), Microarrays
- Data analysis up to differentially expressed genes<

Variants detection
PCR product sequencing
Sanger sequencing

Equipment
Sequencing : MiSeq Illumina, Hiseq2500 Illumina
Quantitative PCR : LightCycler480, Roche

Nucleic Acid quality control
(DNA, RNA, PCR products, Librairies, …) : Bioanalyzer2100 Agilent, TapeStation2200 Agilent

IT Resources
Compute Cluster :
- 560 cores, 1.4 To de RAM, 400 To storage
- Software environnement : BiRD Cluster provides several bioinformatics tools dedicated to genomic fields (NGS, genotyping, GWAS, systems biology, metagenomics…)
- Authenticated access (SSH) to launch analysis via a scheduler or for bioinformatics developments
- Galaxy web portal

Training
GenoBiRD organizes open courses for public and private research laboratories.
- Analysis of RNAseq data with GALAXY (3 days)
- Introduction to the programming language R (1 day)
- Introduction to Linux (1 day)

Each course consists of a theoretical part and practical exercises

Certification / Quality Assurance
Good practices according to the ISO9001 v2015 standards
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Labels
IBiSA core facilty
The bioinformatics core facility (BiRD) is part of the IFB bioinformatics national research infrastructure.

Platform Managment

Genomic core facility Bioinformatic core facility
Scientific leaders Richard Redon
Solena Le Scouarnec
Richard Redon
Jérémie Bourdon
Technical managers Françoise Gros
Stéphanie Bonnaud
Audrey Bihouée

IR SUN,
Institut du thorax
8 quai Moncousu
44007 NANTES

Contacts
genomique@univ-nantes.fr
pf-bird@univ-nantes.fr

For further information :
www.pf-genomique.univ-nantes.fr/
www.pf-bird.univ-nantes.fr

last update : 2017


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