Genomic platform of Nantes GenoA
The GenoA (GEnomics Atlantic) platform is open to the scientific community including academic laboratories, hospital services and private companies.
The GenoA platform advises, offers and develops services in genomics: ready-to-use high-throughput sequencing, preparation of libraries and sequencing of the genome, transcriptome and microbiome.
For all these applications, the GenoA platform works in conjunction with the BiRD platform (member of the IFB), which has expertise in large-scale data analysis and develops dedicated bioinformatics analysis pipelines to standardise the analysis of raw data through to biological interpretation.
The GenoA platform provides genomics equipment: its use includes training and technical support by platform staff, if required. Initial training is organised for all new users.
The multiple applications of genomics are not limited in terms of species studied. They can be applied in the fields of marine, agronomy, environment and health.
Expertise
- Genome studies :
- whole genome
- Primary analysis: demultiplexing, QC, DRAGEN primary analysis (alignment, variant detection)
- Transcriptomics studies:
- 3'SRP (3'seq-RNA Profiling) RNA Sequencing
- Primary analysis: demultiplexing, QC, alignment and read counting
- Microbiome study
- 16s
- Primary analysis (16s): demultiplexing, QC, ASV abundance table, read distribution, alpha and beta diversity analysis, taxonomic assignment
- Shotgun (fastq)
- Ready-to-use (user prepared libraries)
- Genome: exomes, target region genes
- Regulome (ATAC-seq, ChIP-seq, HiChIP-seq, Cut&Run, Cut&Tag, miRNA)
- single cell (scRNA-seq, scATAC-seq, scChIP-seq, scCNV-seq, scTCR-seq, scVDJ-seq)
Services offered
- Project management services in the field of genomics, from experimentation to data analysis, in collaboration with the BiRD platform.
- Project implementation using an experimental approach only
- Implementation of a project through a complete formula combining experimentation and primary analysis.Provision of resources (equipment)
- All project requests are discussed at a meeting with the project leader and his collaborators, in order to establish a commitment form in which the specifications are described, as well as the terms of delivery of the results and the deadline for the service.
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- Provision of equipment
- Training in the use of resources
Equipments
- Sequencers: MiSeq (Illumina), NovaSeq (Illumina)
- Chromium (10X Genomics)
- Robotics: Biomek NXP Span-8 (Beckman), Biomek 4000 (Beckman)
- Nucleic acid quality control: Bioanalyzer2100 (Agilent), TapeStation2200 (Agilent), QuBit (ThermoFischer)
- Sonicators: Bioruptor Diagenode, M220 Covaris
Computing resources
The computing and storage resources of the BiRD platform are accessible and open for projects from the GenoA platform.
Computing cluster with authenticated access (SSH) for launching complex analyses or development
Software environment: BiRDCluster has many bioinformatics tools dedicated to the different fields of genomics (NGS, genotyping, GWAS, systems biology, metagenomics…)
Training
Last update February 2022
Quality Certification / Label / Partnership
In quality process according to ISO9001, v2015
Labels
IBISA
Platform Managment
Scientific Manager
Julien Barc
Technical Manager
Marine Cornec
IRS- SUN
Institut du thorax
8 quai Moncousu
44007 NANTES cedex 1
Contacts
For further information
