Sequencing Platform of Strasbourg GenomEast
Introduction
The GenomEast Platform is hosted at the IGBMC (CNRS / University of Strasbourg / INSERM). With an experience of over 20 years, we offer a wide range of services to survey genomes, their expression and their regulation, from quality check of starting material up to data analysis. These services are intended for the entire scientific community, national and international, public and private.
Expertise
- Transcriptome analysis: RNA-seq (using various protocols adapted to different quality and quantity of starting material and to different aims of the studies), small RNA-seq, single-cell RNA-seq, spatial transcriptomics.
- Epigenome analysis: ChIP-seq, Cut&Run, MeDIP-seq, single cell ATAC-seq, sequencing of ATAC-seq or Cut&Tag libraries.
- Genome analysis: targeted regions (exome, regions of interest), whole genome sequencing.
Over the past years, we have gained expertise in single-cell sequencing technologies (six members of the platform have been awarded the University of Strasbourg’s collective Research Expertise 2021 prize in the Life and Health category for their expertise in single cell transcriptomics), and would like to further develop this expertise (especially single cell multiomics).
Equipments
- High-throughput sequencing : Illumina NextSeq2000
- High-throughput nanofluidics : 10X Genomics Chromium Controller
- Quality control : Varioskan Flash Reader, Qubit Fluorometer, Agilent 2100 Bioanalyzer and AATI Fragment Analyzer
- Sonicator : Covaris E220 AFA system
- IT Infrastructure : computing power (Dell): 304 cores, storage (Lenovo, GPFS): 750 TB
Bioinformatics
Personalized support for data analysis (RNA-seq, single cell RNA-seq, small RNA-seq, ChIP-seq, Cut&Run, Cut&Tag, ATAC-seq, MEDIP-seq, DNA-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 training sessions on Next Generation Sequencing data analysis.

Main achievements
Over the past three years, the platform worked each year on about 300 projects (corresponding each year to about 3,000 sequenced libraries, 1,500 RNA-seq and 500 ChIP-seq libraries prepared), and the bioinformaticians from the platform analysed each year about 150 projects.
Members of the platform are co-authors of 50 publications over the last three years. Four of them are listed below:
Abu El Maaty et al. Hypoxia-mediated stabilization of HIF1A in prostatic intraepithelial neoplasia promotes cell plasticity and malignant progression. Science Advances (2022) 8(29):eabo2295.
Ibrahim et al. MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion. Science (2021) 372(6549):eabd5581.
Zhang et al. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nature communications (2021) 12(1):5446.
Vernet et al. Meiosis occurs normally in the fetal ovary of mice lacking all retinoic acid receptors. Science Advances (2020) 6(21):eaaz1139.
Last update September 2022

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, Gérard Gradwohl and Amélie Piton
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