A national research infrastructure that brings together French expertise and equipment for genomic analysis and bioinformatics

Home > France Genomic Platforms > Sequencing Platform of Strasbourg

Sequencing Platform of Strasbourg

JPEG - 43.6 kb

Since its opening in 2000, our platform is dedicated to providing researchers access to state-of-the-art high throughput technologies to survey genomes, their expression and their regulation. We offer full services from quality check of starting material up to data analysis using standardized methodologies.

Expertise
We provide comprehensive services for two complementary technologies: Illumina high-throughput sequencing (HiSeq 4000) and Fluidigm Biomark and C1 Single-Cell Auto Prep systems. We routinely perform ChIP-seq, DNA-seq, RNA-seq and small RNA-seq analyses using a large variety of protocols adapted to different quality and quantity of starting material and to different aims of the studies. We have also developed dedicated bioinformatic pipelines to analyse the corresponding results. Using Fluidigm technology, we are able to study gene expression down to the single-cell level by Q-PCR or RNA-seq.

Equipment

- High-throughput sequencing: Illumina Hiseq4000 and cBot
- High-throughput nanofluidics: 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:
Our bioinformaticians offer personalized support for basic or in-depth data analysis through scientific collaborations and propose a large panel of analysis. We also regularly organize trainings on Next Generation Sequencing data analysis. We have established RNA-seq, ChIP-seq and targeted DNA-seq pipelines using publically available tools or in-house software. We have also set up GalaxEast (http://www.galaxeast.fr/), a local instance of the Galaxy platform, opened to the scientific community.

Main achievements
Over the past ten years, we have acquired solid experience on library preparation and data analysis for ChIP-seq, RNA-seq, small RNA-seq, DNA-seq, CaptureBS-seq and MNAse-seq. As an example, in 2017, we have prepared and sequenced more than 500 ChIP-seq and more than 1500 RNA-seq libraries. For RNA-seq library preparation, we propose a large panel of protocols depending on the quantity and quality of starting material and on the types of studied RNA. Expert in ChIP-seq data analysis, we have developed the seqMINER software to establish qualitative and quantitative correlations between multiple ChIP-seq datasets. We are co-authors of 79 publications from 2013 to 2017, mainly on projects using ChIP-seq, RNA-seq, smallRNA-seq or DNA-seq and on integrative analysis from several sequencing applications. Since 2011, we are involved in a national research program from the French Foundation for rare diseases (Fondation Maladies Rares) aimed at identifying causative genes responsible for rare diseases using next generation sequencing technologies such as whole exome, whole genome, transcriptome and epigenome sequencing. The foundation financially supports investigators through the launch of specific calls for projects.

Certification / Quality Assurance
The platform is ISO 9001 certified since January 2007 and NFX 50-900 since January 2016.

JPEG - 7.6 kb

Platform managment
Scientific Committee : Irwin Davidson, Philippe Kastner, Gérard Gradwohl and Jamel Chelly
Technical coordinator: Christelle Thibault-Carpentier

GenomEast platform
IGBMC UMR 7104 CNRS-UdS / INSERM U964
1, rue Laurent Fries,
67404 ILLKIRCH Cedex, France

Contact
Christelle Thibault Carpentier
thibault@igbmc.fr

For further information
http://genomeast.igbmc.fr/

last update : 20/06/2018


All the versions of this article: [English] [français]