Sequencing Platform of Strasbourg
Expertise
- High throughput technologies to survey genomes, their expression and their regulation.
- Illumina high-throughput sequencing: ChIP-seq, RNA-seq, small RNA-seq, DNA-seq (exomes, targeted regions), ATAC-seq, MEDIP-seq. For RNA-seq, we propose a large variety of protocols adapted to different quality and quantity of starting material and to different aims of the studies.
- Single cell studies: RNA-seq and Q-PCR
- High-throughput Q-PCR
- Full services from quality check of starting material up to data analysis using standardized methodologies.
Equipments
- High-throughput sequencing : Illumina Hiseq4000
- High-throughput nanofluidics : 10X Genomics Chromium Controller, Fluidigm Biomark and C1 Single-Cell Auto Prep systems
- Quality control : Varioskan Flash Reader, Qubit 2.0 Fluorometer, Agilent 2100 Bioanalyzer and AATI Fragment Analyzer
- Sonicator : Covaris E220 AFA system
- IT Infrastructure : computing power (Dell): 304 cores, storage (Isilon): 325 TB
Bioinformatics Analysis
Personalized support for data analysis (ChIP-seq, RNA-seq, small RNA-seq, DNA-seq, ATAC-seq, MEDIP-seq), from primary analysis to a large panel of in-depth secondary analysis through scientific collaborations. In particular, we have established RNA-seq, ChIP-seq and targeted DNA-seq pipelines using publicly available tools or in-house software.
Regular organization of trainings on Next Generation Sequencing data analysis.
Access and training on GalaxEast (http://www.galaxeast.fr/), a local instance of the Galaxy platform opened to the scientific community.
Main achievements
Members of the platform are co-authors of 45 publications from 2016 to 2018 (mainly on ChIP-seq, RNA-seq, DNA-seq projects or on integrative analysis of data from several applications).
Over the past two years, the platform worked each year on about 300 projects (corresponding each year to more than 4,000 sequenced libraries, more than 1,500 RNA-seq and more than 500 ChIP-seq libraries prepared), and the bioinformaticians from the platform analysed each year about 160 projects.
Quality Certification/ Label/Partnership
The platform is ISO 9001 certified since January 2007 and NFX 50-900 since January 2016.
IBiSA platform since 2008.
Partner of the French Foundation for rare diseases (Fondation Maladies Rares) since 2011.
Platform Managment
Scientific Committee :
Irwin Davidson, Philippe Kastner, Gérard Gradwohl et Jamel Chelly
Technical coordinator :
Christelle Thibault-Carpentier
GenomEast platform
IGBMC UMR 7104 CNRS-Univertité de Strasbourg / INSERM U1258
1, rue Laurent Fries,
67404 ILLKIRCH Cedex, France
Contacts
Christelle Thibault Carpentier
thibault@igbmc.fr
For further information
