
Genomeast
GenomEast
PLATFORM LEADER
With over 20 years of experience, we offer a wide range of services to explore genomes, their expression and regulation, from quality control of starting samples to data analysis. These services are intended for the entire scientific community, national and international, public and private.
The platform is a member of the central core of the France Genomics National Research Infrastructure
The platform is IBISA certified.
Currently equipped with an Illumina NextSeq 2000 and a MGI DNBSEQ-G400 sequencers, we are carrying out projects to analyse :
of the transcriptome :
- RNA-seq
- Single cell RNA-seq (scRNA-seq)
- Spatial transcriptomics
of the epigenome :
- ChIP-seq
- Cut & Run
- MeDIP-seq
- We also have experience in sequencing your ATAC-seq or Cut & Tag libraries
of the genome :
- Targeted regions of the genome (exome, regions of interest)
- Full genome sequencing
multiomics :
- Single Cell Multiome ATAC + Gene Expression
For these projects, we prepare and sequence your libraries, performing quality controls at each step. We can also perform the bioinformatics analysis of your data. We have expertise in a wide variety of applications and have developed dedicated bioinformatics pipelines to analyze the corresponding results.
Alternatively, you can use our sequencing capabilityto sequence your own libraries as long as they are compatible with Illumina technology.
How to submit a project to GenomEast?
Via our web interface
All our services are governed by the general terms and conditions of sale, which take precedence over any conditions of purchase, unless otherwise agreed in writing by us. You can also consult our Data Management Plan.
We regularly share our knowledge and expertise through various courses and training sessions, including:
- The "High Throughput Approaches" course at the Ecole Supérieure de Biotechnologie de Strasbourg (ESBS)
- The "Omics 2" course of the Master 2 Biology-Health, Biomedicine Research course at the University of Strasbourg
- The PhD Program of the IMCBio University Research School in Strasbourg
- The DU "High-throughput sequencing and rare diseases" at the University of Dijon
- The AVIESAN IFB Inserm bioinformatics school
- The organisation of training courses in bioinformatics for high-throughput sequencing with Inserm and the CNRS
Other equipments:
- High-throughput sequencing: iSeq100 (Illumina)
- High-throughput nanofluidics: Chromium Controller (10X Genomics)
- Spatial transcriptomics: GeoMx Digital Spatial Profiler (NanoString)
- Quality control : Varioskan Flash Reader and Qubit Fluorometer (Thermo Fisher), 2100 Bioanalyzer and AATI Fragment Analyzer (Agilent)
- Sonicator : E220 AFA system (Covaris)
- IT Infrastructure : computing power (Dell): 304 cores, storage (Lenovo, GPFS): 750 TB
France Génomique
Our platform has been a partner of the France Genomics network since the initial selection of the project within the framework of the "Investissements d'avenir" in 2011. This network brings together and shares the resources of the main French genomics and bioinformatics platforms.
Fondation maladies rares
Since 2011, we have been one of the partner platforms of the Fondation maladies rares for the implementation of the "GenOmics: high throughput sequencing & rare diseases" programme, which aims to unravel the genetic and molecular basis of rare diseases using high throughput sequencing.
IBiSA and CoRTecS
Since 2008, we have been part of the national network of platforms and resource centers in biology, health, and agronomy of the GIS IBiSA, and since 2021, part of the regional CoRTecS network, which brings together the scientific research and service platforms of the University of Strasbourg.
New applications and technologies
Over the past years, we have gained a strong expertise in single-cell sequencing technologies (Research Expertise 2021 prize from the University of Strasbourg). We further implement new applications each year. At the same time, we are implementing two complementary technologies dedicated to spatial transcriptomics: Visium (10X Genomics) and GeoMx (NanoString).
Publications
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2022
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Concurrent CDX2 cis -deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL
- Marie Passet
- Rathana Kim
- Stéphanie Gachet
- François Sigaux
- Julie Chaumeil
- Ava Galland
- Thomas Sexton
- Samuel Quentin
- Lucie Hernandez
- Lise Larcher
- Hugo Bergugnat
- Tao Ye
- Nezih Karasu
- Aurélie Caye
- Beate Heizmann
- Isabelle Duluc
- Patrice Chevallier
- Philippe Rousselot
- Françoise Huguet
- Thibaut Leguay
- ...
Blood ; Volume: 139 ; Page: 3505-3518
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Caffeine intake exerts dual genome-wide effects on hippocampal metabolism and learning-dependent transcription
- Isabel Paiva
- Lucrezia Cellai
- Céline Meriaux
- Lauranne Poncelet
- Ouada Nebie
- Jean-Michel Saliou
- Anne-Sophie Lacoste
- Anthony Papegaey
- Hervé Drobecq
- Stéphanie Le Gras
- Marion Schneider
- Enas Malik
- Christa Müller
- Emilie Faivre
- Kevin Carvalho
- Victoria Gomez-Murcia
- Didier Vieau
- Bryan Thiroux
- Sabiha Eddarkaoui
- Thibaud Lebouvier
- ...
The Journal of clinical investigation ; Volume: 132
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Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning
- Andrea Riba
- Attila Oravecz
- Matej Durik
- Sara Jiménez
- Violaine Alunni
- Marie Cerciat
- Matthieu Jung
- Céline Keime
- William M Keyes
- Nacho Molina
Nature Communications ; Volume: 13 ; Page: 2865
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Nivolumab, nivolumab–ipilimumab, and VEGFR-tyrosine kinase inhibitors as first-line treatment for metastatic clear-cell renal cell carcinoma (BIONIKK): a biomarker-driven, open-label, non-comparative, randomised, phase 2 trial
- Yann-Alexandre Vano
- Réza Elaidi
- Mostefa Bennamoun
- Christine Chevreau
- Delphine Borchiellini
- Diane Pannier
- Denis Maillet
- Marine Gross-Goupil
- Christophe Tournigand
- Brigitte Laguerre
- Philippe Barthélémy
- Elodie Coquan
- Gwenaelle Gravis
- Nadine Houédé
- Mathilde Cancel
- Olivier Huillard
- Philippe Beuzeboc
- Laure Fournier
- Arnaud Méjean
- Xavier Cathelineau
- ...
Lancet Oncology ; Volume: 23 ; Page: 612-624
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The S. cerevisiae m6A-reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts
- Jérémy Scutenaire
- Damien Plassard
- Mélody Matelot
- Tommaso Villa
- Julie Zumsteg
- Domenico Libri
- Bertrand Séraphin
Nucleic Acids Research
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Waves of sumoylation support transcription dynamics during adipocyte differentiation
- Xu Zhao
- Ivo A Hendriks
- Stéphanie Le Gras
- Tao Ye
- Lucía Ramos-Alonso
- Aurélie Nguéa P
- Guro Flor Lien
- Fatemeh Ghasemi
- Arne Klungland
- Bernard Jost
- Jorrit M Enserink
- Michael L Nielsen
- Pierre Chymkowitch
Nucleic Acids Research ; Volume: 50 ; Page: 1351-1369
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2021
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Androgen receptor-mediated transcriptional repression targets cell plasticity in prostate cancer
- Eva Erdmann
- Pauline Ould Madi-Berthélémy
- Félicie Cottard
- Charlotte Zoe Angel
- Edwige Schreyer
- Tao Ye
- Bastien Morlet
- Luc Negroni
- Bruno Kieffer
- Jocelyn Ceraline
Molecular Oncology ; Volume: 16 ; Page: 2518-2536
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Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells
- Wiruntita Chankeaw
- Sandra Lignier
- Christophe Richard
- Theodoros Ntallaris
- Mariam Raliou
- Yongzhi Guo
- Damien Plassard
- Claudia Bevilacqua
- Olivier Sandra
- Göran Andersson
- Patrice Humblot
- Gilles Charpigny
BMC Genomics ; Volume: 22
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Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network
- Valérie Schreiber
- Reuben Mercier
- Sara Jiménez
- Tao Ye
- Emmanuel García-Sánchez
- Annabelle Klein
- Aline Meunier
- Sabitri Ghimire
- Catherine Birck
- Bernard Jost
- Kristian Honnens de Lichtenberg
- Christian Honoré
- Palle Serup
- Gérard Gradwohl
Molecular metabolism ; Volume: 53 ; Page: 101313
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Photoreceptor cKO of OTX2 Enhances OTX2 Intercellular Transfer in the Retina and Causes Photophobia
- Pasquale Pensieri
- Annabelle Mantilleri
- Damien Plassard
- Takahisa Furukawa
- Kenneth Moya
- Alain Prochiantz
- Thomas Lamonerie
eNeuro ; Volume: 8 ; Page: ENEURO.0229-21.2021
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