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 :

Collaboration / Prestation :

• Transcriptomics: single cell RNA-seq (w/ or w/o cell hashing), bulk mRNA-seq (polyA, total), miRNA-seq and capture
• 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 :

• TGMLcore : NF-core based pipeline for quality control of high-throughput sequencing data generated in the platform.
• SciGeneX identifies modules of co-expressed genes. The pipeline first selects informative genes based on neighborhood analysis, then constructs a gene–gene neighborhood graph, partitions this graph using MCL (Markov Cluster Algorithm), and derives modules of co-expressed genes. These modules can subsequently be combined to characterize distinct cell populations, including rare cell populations. 

• Single-cell on fixed cell and single-nucleus on Chromium X
• Continuous integration of the Metaworkflow : Nf-core
• Spatial Visium HD on tissue on CytAssist
• Single-cell on frozen and fixed cell with  « Illumina single-cell » kit
• Long read on plasmid and ADNg on MinION (Oxford Nanopore technologies) 

• NextSeq-2000 Sequencer Illumina (10-540Gb)

The high-speed sequencing service is equipped with an Illumina NextSeq-2000 sequencer and all the equipment and controllers needed to prepare the libraries.

The NextSeq-2000 can produce up to 540 gigabases (Gb), from 100 M to 1.8 B reads, in single-end (from 50 to 300nt) or pair-end reads (from 50 to 300nt) respectively with up to 384 samples per run.

• Chromium X (10X)

The Chromium X allows transcriptomic profiling of up to a million single cells with multiomic capabilities to reveal cellular diversity.

• Visium CytAssist (10X)

The Visium Spatial enables whole transcriptome analysis of FFPE & fresh frozen tissue within morphological context.

• MinION  Mk1D (ONT)

  The MinION Mk1D is a cutting-edge, palm-sized sequencer enabling real-time long-read sequencing in diverse environments. Designed to connect with modern laptops via its USB-C port

• Agilent  5200 Fragment Analyzer

  The 5200 Fragment Analyzer system is a capillary electrophoresis instrument that can separate up to 48 or 96 samples in parallel. Using automated parallel capillary electrophoresis, the 5200 Fragment Analyzer system enables DNA & RNA quality control for a range of applications (NGS libraries, gDNA, cfDNA, large DNA fragments,  small RNA, total RNA, and mRNA vaccines). 

• Computing power : 24 nodes, 384 cores, 3 TB RAM
• Data storage : 1 bay with gpfs of 293 TB

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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