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 advice on experimental design and 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, ChIP-seq, Cut&Run, Cut&Tag, ATAC-seq, MEDIP-seq, DNA-seq, spatial transcriptomics), 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 250 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 52 publications over the last three years. A selection is listed below:

• Cai Q, Sahu R, Ueberschlag-Pitiot V, Souali-Crespo S, Charvet C, Silem I, Cottard F, Ye T, Taleb F, Metzger E, Schuele R, Billas IML, Laverny G, Metzger D, Duteil D. LSD1 inhibition circumvents glucocorticoid-induced muscle wasting of male mice. Nature Communications. 2024 ; 15(1):3563.
• Bertacchi M, Maharaux G, Loubat A, Jung M, Studer M. FGF8-mediated gene regulation affects regional identity in human cerebral organoids. Elife. 2024 ; 13:e98096.
• Dupré N, Gueniot F, Domenga-Denier V, Dubosclard V, Nilles C, Hill-Eubanks D, Morgenthaler-Roth C, Nelson MT, Keime C, Danglot L, Joutel A. Protein aggregates containing wild-type and mutant NOTCH3 are major drivers of arterial pathology in CADASIL. The Journal of Clinical Investigation. 2024 ;134(8):e175789.
• Davidson G, Helleux A, Vano YA, Lindner V, Fattori A, Cerciat M, Elaidi RT, Verkarre V, Sun CM, Chevreau C, Bennamoun M, Lang H, Tricard T, Fridman WH, Sautes-Fridman C, Su X, Plassard D, Keime C, Thibault-Carpentier C, Barthélémy P, Oudard SM, Davidson I, Malouf GG. Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma. Cancer Research, 2023;83(17):2952-2969.
• Terzic J, Abu el Maaty M, Lutzing R, Vincent A, El Bizri R, Jung M, Keime C, Metzger D. Hypoxia-inducible factor 1A inhibition overcomes castration resistance of prostate tumors. EMBO Molecular Medicine, 2023;15(6):e17209.
• Scutenaire J, Plassard D, Matelot M, Villa T, Zumsteg J, Libri D, Séraphin B. The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts. Nucleic Acids Research. 2023 ; 51(2):517-535.
• 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.

Last update Jan 2025