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.

Equipments

Bioinformatics

Personalized support for data analysis (RNA-seq, single cell RNA-seq and ATAC-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 analyses 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), and the bioinformaticians from the platform analysed each year about 150 projects.

Members of the platform are co-authors of 47 publications over the last three years. A selection is listed below:

Ramos-Alonso L, Holland P, Le Gras S, Zhao X, Jost B, Bjørås M, Barral Y, Enserink JM, Chymkowitch P. Mitotic chromosome condensation resets chromatin to safeguard transcriptional homeostasis during interphase. PNAS. 2023 ; 120(4):e2210593120.

Abu El Maaty MA, Terzic J, Keime C, Rovito D, Lutzing R, Yanushko D, Parisotto M, Grelet E, Namer IJ, Lindner V, Laverny G, Metzger D. Hypoxia-mediated stabilization of HIF1A in prostatic intraepithelial neoplasia promotes cell plasticity and malignant progression. Science Advances. 2022 ; 8(29):eabo2295.

Zhao X, Hendriks IA, Le Gras S, Ye T, Ramos-Alonso L, Nguéa P A, Lien GF, Ghasemi F, Klungland A, Jost B, Enserink JM, Nielsen ML, Chymkowitch P. Waves of sumoylation support transcription dynamics during adipocyte differentiation. Nucleic Acids Research. 2022 ; 50(3):1351-1369.

Paiva I, Cellai L, Meriaux C, Poncelet L, Nebie O, Saliou JM, Lacoste AS, Papegaey A, Drobecq H, Le Gras S, Schneider M, Malik EM, Müller CE, Faivre E, Carvalho K, Gomez-Murcia V, Vieau D, Thiroux B, Eddarkaoui S, Lebouvier T, Schueller E, Tzeplaeff L, Grgurina I, Seguin J, Stauber J, Lopes LV, Buée L, Buée-Scherrer V, Cunha RA, Ait-Belkacem R, Sergeant N, Annicotte JS, Boutillier AL, Blum D. Caffeine intake exerts dual genome-wide effects on hippocampal metabolism and learning-dependent transcription. The Journal of Clinical Investigation. 2022 ; 132(12):e149371.

Ibrahim A, Papin C, Mohideen-Abdul K, Le Gras S, Stoll I, Bronner C, Dimitrov S, Klaholz BP, Hamiche A. MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion. Science. 2021 ; 372(6549):eabd5581.

Zhang J, Le Gras S, Pouxvielh K, Faure F, Fallone L, Kern N, Moreews M, Mathieu AL, Schneider R, Marliac Q, Jung M, Berton A, Hayek S, Vidalain PO, Marçais A, Dodard G, Dejean A, Brossay L, Ghavi-Helm Y, Walzer T. Sequential actions of EOMES and T-BET promote stepwise maturation of natural killer cells. Nature Communications. 2021 ; 12(1):5446.

Abu El Maaty MA, Grelet E, Keime C, Rerra AI, Gantzer J, Emprou C, Terzic J, Lutzing R, Bornert JM, Laverny G, Metzger D. Single-cell analyses unravel cell type-specific responses to a vitamin D analog in prostatic precancerous lesions. Science Advances. 2021 ; 7(31):eabg5982.

Last update April 2023