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Biomics
Responsable : Dr. Sean Kennedy • Responsable Tech. : Dr. Sean P Kennedy
Adresse : INSTITUT PASTEUR
28, rue du Docteur Roux
75724 Paris Cedex 15
Téléphone : +33 (0)1 44 38 95 35
75724 Paris

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Site web

http://citech.pasteur.fr/team/biomics/

Presentation de la plate-forme

The Biomics Pole (http://citech.pasteur.fr/team/biomics/) regroups expertise in genomics, transcriptomics, genotyping and epigenetics within the Center of Innovation and Technology (http://citech.pasteur.fr/) at the Pasteur Institute (http://www.pasteur.fr). The NGS activities of the Pole are part of the France Genomique PIA, and provide access to the latest in NGS technologies. We have installed 2XMiSeq, NextSeq500, HiSeq2500 and iScan equipment.
The main mode of operation of the platform is the realization of collaborative projects where the platform provides access to advanced equipment and the corresponding technological and scientific expertise. The primary themes of the projects on the platform cover all components of the study of infectious diseases epidemiology and clinical research in cognitive research on pathogens and their hosts. The platform also handles numerous projects in very diverse areas such as development, cancer or fundamental microbiology.
An important aspect of NGS data is that the volume and complexities of multi-omics data represent an important challenge. The C3BI (https://c3bi.pasteur.fr/) and the Bioinformatics HUB, as well as the informatics services throughout the Pasteur Network, play an important role in analyzing the data for researchers. Several individuals of the HUB are integrated with teams to assist in project design, implementation and analysis.
Activities include
Bacterial Sequencing:
- Séquençage of bacterial and viral complete genomes by NGS
- Resequencing genomes by NGS
- NGS Sequencing Service: Production sequencing for National Reference Centres, WHO Collaborating Centres and the cell biological emergency response, management of migration reaction sequence

Transcriptome:

-Study of virulence factors
-Study of host-pathogen interactions, and host response to infection
-Study of the effect of environmental pressures (stress, immune pressure, drug pressure …) on the pathogen
-Comparison of inter-species transcriptomes
-Identification of regulatory targets (virulence, motility...)
-Developmental Biology

Epigenetics:
-High-throughput BeadArray technology for genotyping and Next-gen DNA sequencing.
Immunoprecipitation sequencing products (ChIP-SEQ) by NGS
- Human Genome-wide DNA methylation profiling (480,000 CpG positions)

Eukaryote Genotyping:
- Whole genome genotyping: Single Nucleotide Polymorphism (SNP) and Copy Number Variants (CNV): Illumina Infinium and Affymetrix
- Genotyping average flow: Illumina GoldenGate
- Whole Exome Sequencing running on high output mode (V4) HiSeq2500

Genotyping microorganisms and molecular epidemiology:

-Génotypage By sequencing (Multi Locus Sequence Typing - MLST and microarray) analysis of variations in copy number of tandem repeats (VNTR) and SNP analysis (Bioplex technology).
- Comparative Genomic Hybridization and Genotyping by DNA microarray approach
- Launch of MLST data (www.pasteur.fr/mlst) and VNTR (www.pasteur.fr/mlva)

Metagenomics:
-Whole genome shotgun sequencing of complex samples
-16S community analysis
-Bioinformatic and differential statistical analysis software and pipelines

The Biomics Pole offers services for ongoing research as well as advice for constructing research proposals. We are also open to establishing collaborations for the development of new techniques and analyses. Our technical, informatics and statistical experts are available to advise on all aspects of what the Biomics Pole can provide. Teams interested in making use our equipment and services are encouraged to contact us to understand the full range of what we can offer for both sequencing and proteomics analyses.

Moyens et equipements

- LabChip Caliper
- BioAnalyzer Agilent (commun)
- BioAnalyzer Agilent (Platform Only)
- Illumina Hiseq 2500
- NextSeq500
- Illumina MiSeq X 2
- PacBio SEQUEL

- Hydridization Station and scanner from Affymetrix

- Illumina Genotyping system iScan and automation (Illumina et TECAN). (2008); Module Goldengate (2009)

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