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).

https://plateformes-aix-marseille.univ-amu.fr/tgml.html

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...).

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). 

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

• 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.

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