Transcriptomic & Genomic Platform Marseille Luminy

State of the art high throughput genomics with certified quality processes for academics and private companies.

TAGC (UMR_S 1090 Inserm/Aix-Marseille) is a laboratory with a very strong expertise in the field of genomics. For 20 years now, it has been offering its state-of-the-art services to the scientific community. This service has been structured over the years to give rise to the TGML platform (Transcriptomics and Genomics Marseille-Luminy).

As part of the structuring of the offer, the platform has obtained the IBiSA label (Infrastructure in Biology, Health and Agronomy) in 2008, and then integrated the France Genomics distributed infrastructure, which brings together and pools the resources of the main French genomics and bioinformatics platforms. In 2015, it was awarded the AMU technology platform label (renewal obtained in 2019). The confidence of the institutions is linked in particular to the model developed by the platform, which is based on strong expertise, standardization of procedures and complete openness to the national and international scientific community.

In this sense, the platform obtained, in 2015, the certification "ISO 9001: 2015 & NFX 50-900: 2016" which, after an external audit, was renewed in January 2021. More recently, the platform has integrated the Marseille Institute for Rare Diseases (MarMaRa), of which it hopes to become one of the actors in the long term. Since its creation, the platform has been very strongly involved in teaching. In 2014, the platform began, via CoreBio PACA funding, to offer practical work to Master 2 students (Structural Biology and Genomics). More recently, the platform has become involved in the Master of Excellence project (led by C. Bordi). Through its involvement in training towards Master's degrees, the TGML is a key player in education. Finally, the platform's staff is involved in training on a national scale by training dozens of researchers each year at the Roscoff Bioinformatics School for one week (D. Puthier) and on an international scale (Mexico, Algeria, Thailand, Brazil...).

EXPERTISE

Since its creation in 2010, the TGML has followed the technological evolutions of the field in order to offer its customers state-of-the-art services based on an adapted pricing system validated by Inserm. In particular, the platform offers its expertise for the analysis of different types of projects related to high-throughput sequencing. The main services offered are :

Molecular biology :

Transcriptomics: single cell RNA-seq (w/ or w/o cell hashing), bulk mRNA-seq (polyA, total) and DNA chips (DGE, miRNA, CGH)
Genomics: Targeted re-sequencing, complete exome, SNV, small / large IndDels, etc.
Epigenomics: ChIP-seq, FAIRE-seq / ATAC-seq, MNnase-seq, 3C-seq, 4C-seq

Bioinformatics :

Metaworkflow : Routine data processing workflow following the FAIR (Findable, Accessible, Interoperable and Reusable) principle for data generation.
OLOGRAM (OverLap Of Genomic Regions Analysis using Monte Carlo) : performs overlap statistics between sets of genomic regions described in BEDs or GTF.
PyGTFtk (Python GTF tool kit) : A Python package intended to ease handling of GTF/GFF2.0 files (Gene Transfer Format).

Developments

Single-cell on nucleus and fixed cell on Chromium controller
Continuous integration of the Metaworkflow

Main EQUIPMENTS

NextSeq-500 Sequencer Illumina (20-120Gb)
Agilent High-Resolution Microarray Scanner
Robots: EVO-150 Tecan; Apollo-324 WaferGen; Ion Chef System, Fragment analyzer
Computing power : 18 nodes, 288 cores, 1.5 TB RAM
Data storage : 1 bay with gpfs of 220 TB

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) respectively with up to 96 samples per run.
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.

JOURNAL OF TGML

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

Contact

Platform managers: Béatrice Loriod & Denis Puthier

denis.puthier@univ-amu.fr
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

2020

Vivien Suteraa, Aurélie Hennebique, Lopez F, Fernandez N, Schneider D, Maurina M., Genomic trajectories to fluoroquinolone resistance in Francisella tularensis subsp. holarctica live vaccine strain, International Journal of Antimicrobial Agents, Volume 56, Issue 6, December 2020. PMID: 32911069; https://doi.org/10.1016/j.ijantimicag.2020.106153

M. Seipelt E, Tourniaire F, Couturier C, Astier J, Loriod B, Vachon H, Pucéat M, Mounien L, Landrier JF, Prenatal maternal vitamin D deficiency sex‐dependently programs adipose tissue metabolism and energy homeostasis in offspring, The faseb Journal 2020. PMID: 32924159; https://doi.org/10.1096/fj.201902924rr

Jean-Philippe Mevy , Beatrice Loriod , Xi Liu 3, Erwan Corre 3, Magali Torres 2,Michael Büttner , Anne Haguenauer , Ilja Marco Reiter , Catherine Fernandez and Thierry Gauquelin. Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics. Plants 2020, 9(9), 1149; https://doi.org/10.3390/plants9091149

Darely Y Gutiérrez-Reyna 1, Alejandra Cedillo-Baños 1, Linda A Kempis-Calanis 1, Oscar Ramírez-Pliego 1, Lisa Bargier 2, Denis Puthier 2 3, Jose D Abad-Flores 2 3, Morgane Thomas-Chollier 4, Denis Thieffry 4, Alejandra Medina-Rivera 5, Salvatore Spicuglia 2 3, Maria A Santana 1. IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8 + T Cells. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2020.01089

2019

Swayden M, Alzeeb G, Masoud R, Berthois Y, Audebert S, Camoin L, Hannouche L, Vachon H, Gayet O, Bigonnet M, Roques J, Silvy F, Carrier A, Dusetti N, Iovanna JL, Soubeyran P. PML hyposumoylation is responsible for the resistance of pancreatic cancer. The FASEB journal. PMID: 31557059 https://doi.org/10.1096/fj.201901091R

Tran, T.T., Mathieu, C., Torres, M. et al. Effect of landiolol on sex-related transcriptomic changes in the myocardium during sepsis. ICMx 7, 50 (2019). https://doi.org/10.1186/s40635-019-0263-0

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