Transcriptomic & Genomic Platform Marseille Luminy

Logo TGML 

The TGML provides access for public research and business to functional genomics studies using a wide range of experimental and bioinformatic methods.

The platform "Transcriptomics and Genomics of Marseille-Luminy" (TGML) is integrated into the laboratory "Theory and Approaches of Genomic Complexity" (TAGC, Pr. Pascal Rihet, UMR 1090, Inserm / Aix-Marseille University) Of Luminy.
The platform has been labeled as a National Platform by GIS IBiSA, previously RIO, and is a founding member of the National Infrastructure for genomic analysis and bioinformatics France Génomique.
The TGML platform and the TAGC provide a recognized expertise in the analysis of different types of DNA chips and sequencing data. Our researchers and engineers actively contribute to the development of new tools for integrated analysis and processing of genomic, epigenomic and transcriptomic data.

 

Activities / Specialties

  • Transcriptomics: mRNA-seq and DNA chips (DGE, miRNA, CGH)
  • Genomics: Targeted re-sequencing, complete exome, SNV, small / large IndDels, etc.
  • Epigenomics: ChIP-seq, FAIRE-seq / ATAC-seq, Mnase-seq, 3C-seq, 4C-seq

 

 

 

 

 

Developments

  • Chromium controller : single-cell and long-read
  • Targeted CRISPR for single cell
  • High throughput CapStarr-seq

 

 

 

 

Main facilities

  • NextSeq-500 Sequencer Illumina (20-120Gb)
  • Ion PGM Thermo Sequencer (10Mb-2Gb)
  • Agilent High-Resolution Microarray Scanner
  • Robots: EVO-150 Tecan; Apollo-324 WaferGen; Ion Chef System, Fragment analyzer

The high-speed sequencing service is equipped with an Illumina NextSeq-500 sequencer and all the equipment and controllers needed to prepare the libraries.
The NextSeq-500 can produce up to 120 gigabases (Gb), from 130 to 400M reads, in single-end (from 75 to 300nt) or pair-end reads (from 75 to 150nt), up to 96 samples per session.
The Agilent DNA chip service allows transcriptomic studies of many organisms. It also allows miRNA, CGH, and analysis of DNA methylation profiling.
Platform staff can provide sample preparation advice and follow-up on selected projects. Users can benefit from the services offered by the TGML as a service or collaboration, on the basis of a predefined contract.

 

Computer cluster

  • Computing power:
    • 18 nodes
    • 288 cores
    • 1.5 TB RAM
  • Data storage : 1 bay with gpfs of 220 TB

 

Computer tools

  • In development: Workflow for transcriptome, genome and epigenome analysis
  • Available:
    • GeVarA software for the analysis of genomic variants
    • Custom conversion and analysis tools (wig, bed, sam, etc.)

 

Quality approach

The entire activity of the platform is certified ISO 9001:2015 and NFX 50-900:2016. You can download the quality policy document here.

Labels

GIS IBiSA, Cancéropôle PACA, CoReBio PACA, Plateforme technologique AMU (see charter).

 

 

Contact

Responsible for the scientific and technical platform: Béatrice Loriod
beatrice.loriod@inserm.fr
+33 (0) 6 17 25 70 34 / +33 (0) 4 91 82 87 13

TGML/TAGC U1090
Inserm - Aix Marseille Université
163 Avenue de Luminy
13288 Marseille cedex 9

If you want to Submit a service request, Click here !

Publications

2017

Ragheb R, Chuyen A, Torres M, Defaye A, Seyres D, Kremmer L, Fernandez-Nunez N, Tricoire H, Rihet P, Nguyen C, Röder L, Perrin L. Interplay between trauma and Pseudomonas entomophila infection in flies: a central role of the JNK pathway and CrebA. Sci Rep. 2017 Nov 24. PMID: 29176735

Ragheb R, Venton G, Chelbi R, Bonnet N, Le Treut T, Ivanov V, Mercier C, Poulin P, Beaufils N, Gabert J, Suchon P, Rihet P, Loriod B, Kahn-Perlès B, Costello RT. Vorinostat and Mithramycin A in combination therapy as an interesting strategy for the treatment of Sézary T lymphoma: a transcriptomic approach. Arch Dermatol Res. 2017 Oct. PMID 28695331

Hervé M, Bergon A, Le Guisquet AM, Leman S, Consoloni JL, Fernanadez-Nunez N, Lefebvre MN, El-Hage W, Belzeaux R, Belzung C, Ibrahim EC. Translational identification of transcriptional signatures of major depression and antidepressant response. Front Mol Neurosci. 2107 Aug 8. PMID : 28848385

Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, Van Helden J, Spicuglia S. Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Gene. 2017 Jul. PMID: 28581502

Tsagmo Ngoune JM, Njiokou F, Loriod B, Kame-Ngasse G, Fernandez-Nunez N, Rioualen C, Van Helden J, Geiger A. Transcriptional profiling of midguts prepared from Trypanosoma/T. congolense-positive Glossina palpalis palpalis collected from two distinct cameroonian Foci: coordinated signatures of the midguts’ remodeling as T. congolense-supportive niches. Front Immunol. 2017 Jul 28. PMID: 28804485

Barral S, Morozumi Y, Tanaka H, Montellier E, Govin J, De Dieuleveult M, Charbonnier G, Couté Y, Puthier D, Buchou T, Boussouar F, Urahama T, Fenaille F, Curtet S, Héry P, Fernandez-Nunez N, Shiota H, Gérard M, Rousseaux S, Kurumizaka H, Khochbin S. Histone variants H2A.L.2 guides transition protein-dependent assembly in male germ cells. Mol Cell. 2017 Apr 6. PMID: 28366643

Paban V, Loriod B, Villard C, Buee L, Blum D, Pietropaolo S, Cho YH, Gory-Faure S, Mansour E, Gharbi A, Alescio-Lautier B. Omics analysis of mouse brain models of human diseases. Gene. 2017 Feb 5. PMID: 27871923

See more publications