Genomic and Transcriptomic Platform

Before and after sequencing, the platform is designed to support teams in the implementation, analysis and valorization of their projects based on NGS approaches (e.g. RNA-Seq, ChiP-Seq, ATAC-Seq).
Our team
Bioinformatics : Margot ZAHM (Engineer)
Wet Lab : Adeline CHAUBET (Engineer)
Scientific Supervision : Olivier JOFFRE (PhD, Associate-Lecturer)

Service offering

From the outset of the project, the platform supports teams in setting up an experimental design adapted to the question posed. It offers two types of complementary services:

  • Upstream of sequencing: RNA extraction, creation of libraries and library pools, interfacing with sequencing platforms
  • Downstream of sequencing: bioinformatics analysis of a wide range of NGS data, staff training, tool development, etc

The platform works on a wide range of sequencing data: RNAseq bulk, scRNAseq, ATACseq, ChIPseq, CITEseq and participates in the development of new technologies and data analyses.

 

Training & expertise

  • Help in setting up or optimizing an experimental protocol
  • Help in analyzing and interpreting results
  • Staff training

Operating

To meet the needs of teams, we offer two operating modes.

Project management

The project leader fills in a project sheet to initiate an initial discussion with the platform. Plateau members can then help set up an experimental design adapted to the project’s biological question. The platform then carries out the services requested by the project sponsor. Finally, the deliverables are sent to the user, with a full summary of the quality controls and results obtained.

Project supervision

A member of the requesting team is trained in bioinformatics analysis (routine analyses) by the platform’s bioinformatician. This person then carries out the analyses on the project. This responsibility includes sending the forms (project, technical and library) and quality control to the platform for monitoring the project’s progress.

 

It is possible to set up a hybrid project with project management prior to sequencing and project supervision after sequencing.

 

Equipment

Instruments

  • Chromium iX (10X Genomics)
  • 4150 TapeStation system (Agilent)
  • M220 focused-ultrasonicator (Covaris)
  • Bioruptor Pico sonication device (Diagenode)
  • LightCycler 480 (Roche)
Softwares

 

Autres informations


Steering comittee
  • Jean-Charles Guery (Team 01)
  • Stéphane Galiacy (Team 02)
  • Lilian Basso (Team 03)
  • Anne Dejean (Team 04)
  • Stéphanie Trudel-Ausseil (Team 05)
  • Nicolas Blanchard (Team 06)
  • Cécile Malnou (Team 07)
  • Sébastien Lhomme (Team 08)
  • Nabila Jabrane-Ferrat (Team 09)
  • Véronique Adoue (Team 10)
  • José Enrique Méjia (Team 11)
  • Isabelle Lamsoul (Team 12)
  • Manuel Diaz-Munoz (Team 13)
  • Jasper Kamphuis (Team 14)
Publications

2024

Maire, Kilian; Chamy, Léa; Ghazali, Samira; Carratala-Lasserre, Manon; Zahm, Margot; Bouisset, Clément; Métais, Arnaud; Combes-Soia, Lucie; Fuente-Vizuete, Lidia; Trad, Hussein; Chaubet, Adeline; Savignac, Magali; de Peredo, Anne Gonzalez; Subramaniam, Arun; Joffre, Olivier; Lutz, Pierre G.; Lamsoul, Isabelle

Fine-tuning levels of filamins a and b as a specific mechanism sustaining Th2 lymphocyte functions Journal Article

In: Nature Communications, vol. 15, no. 1, pp. 10574, 2024, ISSN: 2041-1723.

Abstract | Links | BibTeX

Dias, Chloé; Ballout, Nissrine; Morla, Guillaume; Alileche, Katia; Santiago, Christophe; Guerrera, Ida Chiara; Chaubet, Adeline; Ausseil, Jerome; Trudel, Stephanie

Extracellular vesicles from microglial cells activated by abnormal heparan sulfate oligosaccharides from Sanfilippo patients impair neuronal dendritic arborization Journal Article

In: Molecular Medicine, vol. 30, no. 1, pp. 197, 2024, ISSN: 1528-3658.

Abstract | Links | BibTeX

Morandi, Elena; Adoue, Véronique; Bernard, Isabelle; Friebel, Ekaterina; Nunez, Nicolas; Aubert, Yann; Masson, Frederick; Dejean, Anne S; Becher, Burkhard; Astier, Anne; Martinet, Ludovic; Saoudi, Abdelhadi

Impact of the Multiple Sclerosis-Associated Genetic Variant CD226 Gly307Ser on Human CD8 T-Cell Functions Journal Article

In: Neurol Neuroimmunol Neuroinflammation, vol. 11, no. 6, 2024.

Abstract | Links | BibTeX

Joulia, Emeline; Michieletto, Michaël F.; Agesta, Arantxa; Peillex, Cindy; Girault, Virginie; Dorze, Anne-Louise Le; Peroceschi, Romain; Bucciarelli, Florence; Szelechowski, Marion; Chaubet, Adeline; Hakim, Nawad; Marrocco, Rémi; Lhuillier, Emeline; Lebeurrier, Manuel; Argüello, Rafael J.; Saoudi, Abdelhadi; Costa, Hicham El; Adoue, Veronique; Walzer, Thierry; Sarry, Jean-Emmanuel; Dejean, Anne S.

Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation Journal Article

In: Journal of Experimental Medicine, vol. 221, no. 2, 2024, ISSN: 0022-1007.

Links | BibTeX

2023

Osma-Garcia, Ines C.; Mouysset, Mailys; Capitan-Sobrino, Dunja; Aubert, Yann; Turner, Martin; Diaz-Muñoz, Manuel D.

The RNA binding proteins TIA1 and TIAL1 promote Mcl1 mRNA translation to protect germinal center responses from apoptosis Journal Article

In: Cellular & Molecular Immunology, 2023, ISSN: 2042-0226.

Abstract | Links | BibTeX

2018

Dupain, Célia; Harttrampf, Anne C.; Boursin, Yannick; Lebeurrier, Manuel; Rondof, Windy; Robert-Siegwald, Guillaume; Khoueiry, Pierre; Geoerger, Birgit; Massaad-Massade, Liliane

Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse and relevance for personalized medicine Journal Article

In: Molecular Therapy, 2018.

Abstract | Links | BibTeX

Partenaires Cytométrie

CNRS

CNRS

TRI-Genotoul

TRI-Genotoul