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Sequencing Platform of Strasbourg

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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.

We provide comprehensive services for three complementary technologies : Illumina high-throughput sequencing (HiSeq 4000), Affymetrix DNA microarrays 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
- Microarrays : Affymetrix GeneChip System
- 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
.

Main achievements :
Over the past 9 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 2016, we have prepared and sequenced 600 ChIP-seq and more than 1000 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 69 publications from 2012 to 2016, 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.
RNA-Seq : Since the year 2000, we have participated in multiple national programmes dedicated to transcriptome analyse using DNA chips, including the « Affymetrix call for proposals », the LNCC Programme « Carte d’Identité des tumeurs » and the Programme « RESOGEN ». In 2009, a change of technology from biochips to RNA-Seq was initiated, and the platform has now sequenced more than 700 samples using RNA-Seq.
DNA-Seq : Since 2011, we have been service providers to the Programme “Initiative Plateforme Mutation” of the Fondation Maladies Rares (Rare Diseases Foundation), for exome sequencing and targeted sequencing for identification of variants.

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.

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

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

Platform Managers :
Scientific Committee : Irwin Davidson, Philippe Kastner, Gérard Gradwohl, Jean Louis Mandel
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


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