IRCAN Genomics Core Facility, GenoMed, is dedicated to the analysis of genetic variation, gene expression and its regulation. It provides knowledge and access to cutting-edge, medium-to-high throughput tools and technologies. It is open to all members of IRCAN, as well as to external academic or non-academic members of the scientific community.
Expertise/ Service offer/ Applications
The genomic analyses carried out on the platform aim to characterize and quantify the diversity of DNA or RNA species, their variations and epigenetic modifications, at the level of the entire genome or at targeted loci.
GenoMed, is equipped to provide the following services:
- Quality control of RNA or DNA
- Sequencing library preparation
- Illumina (short reads) and nanopore (long reads) sequencing
Other services (panels, ChIP-seq, TT-seq) are possible on request.
Members
Gaël CRISTOFARI, DR Inserm Scientific manager
Equipment
Sequencing
1 NextSeq500 Sequencer (short-reads, Illumina)
1 MinION Mk1c Nanopore sequencer (long-reads, Oxford Nanopore Technologies)
Quality control and library preparation
1 Pippin prep (Sage Science). Preparative electrophoresis of nucleic acids with automated size selection
1 Bioruptor Pico. Sonicator for microvolumes 6- to 12-samples in parallel)
1 digital droplet PCR machine (ddPCR, QX200 Bio-Rad). Absolute DNA and RNA quantification
1 Bionalyzer 2100 (Agilent). Sensitive RNA and DNA size profiling and quantification by microfluidic electrophoresis
1 IP-Star Compact Automated System (Diagenode). Pipetting robot for automated chromatin-IP (ChIP)
1 qPCR StepOne Plus (Thermofisher) with 96-wells block. Real-time quantitative PCR for library quantification
Getting started/Access
Anyone wishing to use a device must contact Christian Baudoin christian.baudoin@univ-cotedazur.fr. Training on the device will be provided. Use of the devices is subject to training and the signing of the platforer charter.
Access & Booking
With the exception of next-generation sequencing, Genomics Core Facility equipment is open-access after signature of the charter and online mandatory reservation. A small fee to cover the operating costs is charged by IRCAN to research teams based on their use.
Sequencing
Deep-sequencing projects are treated as a service or on a collaborative basis.
1) Send a brief description (few lines max) of the experiments and number of samples to: gael.cristofari@univ-cotedazur.fr
2) We will define with the demanding team: the feasibility, the costs, the degree of contribution of the Core Facility, the needs in bioinformatics for analyzing the results.
3) Library preparations and deep-sequencing can be performed by Christian Baudoin or by the
demanding team. Bioinformatic analyses can be performed by the bioinformatic service or by the demanding team.
Acknowledgment and publications
The Genomics Core Facility must be acknowledged in the acknowledgment section of any publication for which its equipment was used. For instance, you can use the sentence: « We thank the IRCAN Genomics Core Facility for providing access to [Illumina sequencing]. » If the contribution to the work is significant, particularly for custom genomic approaches, the facility members involved will be included as co-authors in the publication, in agreement with the project leader.
Publications
A ganglioside-based immune checkpoint enables senescent cells to evade immunosurveillance during aging
Charlène Iltis, Iryna Moskalevska, Antoine Debiesse, Laetitia Seguin, Christina Fissoun, Ludovic Cervera, Lyvia Moudombi, Maude Ardin, Anthony Ferrari, Coline Eliott, Didier Pisani, Alexandre Ottaviani, Manon Bourinet, Carmelo Luci, Philippe Gual, Gabriela Makulyte, David Bernard, Manon Durandy, Lou C. Duret, Tynhinane Hamidouche, Sarah Kunz, Olivier Croce, Clément Delannoy, Yann Guérardel, Fabrice Allain, Paul Hofman, Delphine Benarroch-Popivker, Laurence Bianchini, Berengère Dadone-Montaudie, Estelle Cosson, Julien Guglielmi, Thierry Pourcher, Véronique M. Braud, Marina Shkreli, Yves-Marie Pers, Christian Jorgensen, Jean-Marc Brondello, Chloé C. Féral, Marie-Cécile Michallet, Eric Gilson, Julien Cherfils-Vicini
Nat Aging. 2025; 5(2): 219–236. Published online 2024 Dec 27. doi: 10.1038/s43587-024-00776-z
PMCID: PMC11839482
p16High immune cell – controlled disease tolerance as a broad defense and healthspan extending strategy
Francisco Triana-Martinez, Alessandra Pierantoni, Daisy Graca, Veronica Bergo, Alexander Emelyanov, Bogdan B Grigorash, Shunya Tsuji, Sosuke Nakano, Laurent Grosse, Vesna Brglez, Pierre Marty, Jean Dellamonica, Albert J Fornace, Jr, Eirini Trompouki, Eiji Hara, Barbara Seitz-Polski, Dmitry V Bulavin
Version 1. bioRxiv. Preprint. 2024 Jul 15. doi: 10.1101/2024.07.15.603540
PMCID: PMC11257523
Lack of telomerase reduces cancer incidence and increases lifespan of zebrafish tp53M214K mutants
Naz Şerifoğlu, Bruno Lopes-Bastos, Miguel Godinho Ferreira
Sci Rep. 2024; 14: 5382. Published online 2024 Mar 5. doi: 10.1038/s41598-024-56153-8
PMCID: PMC10914805
Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites
Sophie Lanciano, Claude Philippe, Arpita Sarkar, David Pratella, Cécilia Domrane, Aurélien J. Doucet, Dominic van Essen, Simona Saccani, Laure Ferry, Pierre-Antoine Defossez, Gael Cristofari
Cell Genom. 2024 Feb 14; 4(2): 100498. Published online 2024 Feb 2. doi: 10.1016/j.xgen.2024.100498
PMCID: PMC10879037
Gut-specific telomerase expression counteracts systemic aging in telomerase-deficient zebrafish
Mounir El Maï, Malia Bird, Asma Allouche, Seniye Targen, Naz Şerifoğlu, Bruno Lopes-Bastos, Jean-Marie Guigonis, Da Kang, Thierry Pourcher, Jia-Xing Yue, Miguel Godinho Ferreira
Nat Aging. 2023; 3(5): 567–584. Published online 2023 May 4. doi: 10.1038/s43587-023-00401-5
PMCID: PMC10191862
Senescence‐associated transcriptional derepression in subtelomeres is determined in a chromosome‐end‐specific manner
Martin Rey‐Millet, Mélanie Pousse, Chan Soithong, Jing Ye, Aaron Mendez‐Bermudez, Eric Gilson
Aging Cell. 2023 May; 22(5): e13804. Published online 2023 Mar 15. doi: 10.1111/acel.13804
PMCID: PMC10186611
Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence
Aaron Mendez-Bermudez, Liudmyla Lototska, Melanie Pousse, Florent Tessier, Oliver Croce, Chrysa M Latrick, Veronica Cherdyntseva, Joe Nassour, Jiang Xiaohua, Yiming Lu, Corinne Abbadie, Sarantis Gagos, Jing Ye, Eric Gilson
Nucleic Acids Res. 2022 Jul 22; 50(13): 7493–7510. Published online 2022 Jul 12. doi: 10.1093/nar/gkac603
PMCID: PMC9303393
Locus-specific chromatin profiling of evolutionarily young transposable elements
Darren Taylor, Robert Lowe, Claude Philippe, Kevin C L Cheng, Olivia A Grant, Nicolae Radu Zabet, Gael Cristofari, Miguel R Branco
Nucleic Acids Res. 2022 Apr 8; 50(6): e33. Published online 2021 Dec 15. doi: 10.1093/nar/gkab1232
PMCID: PMC8989514
Longevity strategies in response to light in the reef coral Stylophora pistillata
Alexandre Ottaviani, Rita Eid, Didier Zoccola, Mélanie Pousse, Jean-Marc Dubal, Edwige Barajas, Karine Jamet, Kevin Lebrigand, Pascal Lapébie, Christian Baudoin, Marie-Josèphe Giraud-Panis, Alice Rouan, Gallic Beauchef, Christelle Guéré, Katell Vié, Pascal Barbry, Sylvie Tambutté, Eric Gilson, Denis Allemand
Sci Rep. 2020; 10: 19937. Published online 2020 Nov 17. doi: 10.1038/s41598-020-76925-2
PMCID: PMC7673115
Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters
Agata Oruba, Simona Saccani, Dominic van Essen
Nat Commun. 2020; 11: 1075. Published online 2020 Feb 26. doi: 10.1038/s41467-020-14950-5
PMCID: PMC7044431
Human RAP1 specifically protects telomeres of senescent cells from DNA damage
Liudmyla Lototska, Jia‐Xing Yue, Jing Li, Marie‐Josèphe Giraud‐Panis, Zhou Songyang, Nicola J Royle, Gianni Liti, Jing Ye, Eric Gilson, Aaron Mendez‐Bermudez
EMBO Rep. 2020 Apr 3; 21(4): e49076. Published online 2020 Feb 25. doi: 10.15252/embr.201949076
PMCID: PMC7132343
Mitochondrial function in skeletal myofibers is controlled by a TRF2‐SIRT3 axis over lifetime
Jérôme D. Robin, Maria‐Sol Jacome Burbano, Han Peng, Olivier Croce, Jean Luc Thomas, Camille Laberthonniere, Valerie Renault, Liudmyla Lototska, Mélanie Pousse, Florent Tessier, Serge Bauwens, Waiian Leong, Sabrina Sacconi, Laurent Schaeffer, Frédérique Magdinier, Jing Ye, Eric Gilson
Aging Cell. 2020 Mar; 19(3): e13097. Published online 2020 Jan 28. doi: 10.1111/acel.13097
PMCID: PMC7059141
The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection
Sultana T, van Essen D, Siol O, Bailly-Bechet M, Philippe C, Zine El Aabidine A, Pioger L, Nigumann P, Saccani S, Andrau JC, Gilbert N, Cristofari G. Mol Cell. 2019 May 2;74(3):555-570.e7. doi: 10.1016/j.molcel.2019.02.036. Epub 2019 Apr 4.
PMCID: 30956044
Cancer cells induce immune escape via glycocalyx changes controlled by the telomeric protein TRF2
Julien Cherfils‐Vicini, Charlene Iltis, Ludovic Cervera, Sabrina Pisano, Olivier Croce, Nori Sadouni, Balázs Győrffy, Romy Collet, Valérie M Renault, Martin Rey‐Millet, Carlo Leonetti, Pasquale Zizza, Fabrice Allain, Francois Ghiringhelli, Nicolas Soubeiran, Marina Shkreli, Eric Vivier, Annamaria Biroccio, Eric Gilson
EMBO J. 2019 Jun 3; 38(11): e100012. Published online 2019 Apr 18. doi: 10.15252/embj.2018100012
PMCID: PMC6545744
Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales
Jing Li, Ignacio Vázquez-García, Karl Persson, Asier González, Jia-Xing Yue, Benjamin Barré, Michael N Hall, Anthony Long, Jonas Warringer, Ville Mustonen, Gianni Liti
Mol Biol Evol. 2019 Apr; 36(4): 691–708. Published online 2019 Jan 17. doi: 10.1093/molbev/msz006
PMCID: PMC6445301
Tumor-stroma mechanics coordinate amino acid availability to sustain tumor growth and malignancy
Thomas Bertero, William M. Oldham, Eloise M. Grasset, Isabelle Bourget, Etienne Boulter, Sabrina Pisano, Paul Hofman, Floriant Bellvert, Guerrino Meneguzzi, Dmitry V. Bulavin, Soline Estrach, Chloe C. Feral, Stephen Y. Chan, Alexandre Bozec, Cedric Gaggioli
Cell Metab. Author manuscript; available in PMC 2020 Jan 8.Published in final edited form as: Cell Metab. 2019 Jan 8; 29(1): 124–140.e10. Published online 2018 Oct 4. doi: 10.1016/j.cmet.2018.09.012
PMCID: PMC6432652