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 !

 

JOURNAL DU TGML

 

 

Publications

2019

Saadi W, Kermezli Y, Dao LTM, Mathieu E, Santiago-Algarra D, Manosalva I, Torres M, Belhocine M1, Pradel L, Loriod B, Aribi M, Puthier D, Spicuglia S. A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation. Sci Rep. 2019 Mar 18. PMID: 30886319

Kermezli Y, Saadi W, Belhocine M, Mathieu EL, Garibal MA, Asnafi V, Aribi M, Spicuglia S, Puthier D. A comprehensive catalog of LncRNAs expressed in T-cell acute lymphoblastic leukemia. Leuk Lymphoma. 2019 Jan 16. PMID: 30648438

2018

Shiota H, Barral S, Buchou T, Tan M, Couté Y, Charbonnier G, Reynoird N, Boussouar F, Gérard M, Zhu M, Bargier L, Puthier D, Chuffart F, Bourova-Flin E, Picaud S, Filippakopoulos P, Goudarzi A, Ibrahim Z, Panne D, Rousseaux S, Zhao Y, Khochbin S.Nut Directs p300-Dependant, Genome-Wide H4 Hyperacetylation in Male Germ Cells. Cell Rep. 2018 Sep 25. PMID: 30257209

Labiad Y, Venton G, Farnault L, Baier C, Colle J, Mercier C, Ivanov V, Nicolino C, Loriod B, Fernandez-Nunez N, Torres M, Mattei JC, Rihet P, Nguyen C, Costello R. A transcriptomic signature predicting septic outcome in patients undergoing autologous stem cell transplantation. Exp Hematol. 2018 Sep. PMID: 29885947.

Aigle A, Bonin P, Fernandez-Nunez N, Loriod B, Guasco S, Bergon A, Armougom F, Iobbi-Nivol C, Imbert J, Michotey V.The nature of electron acceptor (MnIV/NO3) triggers differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3. FEMS Microbiol Lett. 2018 Jul 1. PMID: 29566166

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