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

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

•    N°1, June 2019
•    N°2, February 2020
•    N°3, June 2020
•    N°4, April 2021
•    N°5, April 2023

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

Publications

2023

Lamia Madaci, Charlyne Gard, Sébastien Nin, Alexandre Sarrabay, Céline Baier, Geoffroy Venton, Pascal Rihet, Denis Puthier, Béatrice Loriod, and Régis Costello. Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation. Diseases, 12(1):1,December 2023a. doi: 10.3390/diseases12010001. URL https://amu.hal.science/hal-04501292.

Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, and Catherine N’Guyen. Cross-species analysis of differential transcript usage in humans and chickens with fatty liver disease. Veterinary World, 16(9):1964–1973, September 2023. doi:10.14202/vetworld.2023.1964-1973. URL https://hal.science/hal-04289438.

Domenico Iuso, Isabel Garcia-Saez, Yohann Couté, Yoshiki Yamaryo-Botté, Elisabetta Boeri Erba, Annie Adrait, Nour Zeaiter, Malgorzata Tokarska-Schlattner, Zuzana Macek Jilkova, Fayçal Boussouar, Sophie Barral, Luca Signor, Karine Couturier, Azadeh Hajmirza, Florent Chuffart, Ekaterina Bourova-Flin, Anne-Laure Vitte, Lisa Bargier, Denis Puthier, Thomas Decaens, Sophie Rousseaux, Cyrille Botté, Uwe Schlattner, Carlo Petosa, and Saadi Khochbin. Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. Science Advances , 9(36):eadh0140, September 2023. doi: 10.1126/sciadv.adh0140. URL https://hal.science/hal-04216158.

Lamia Madaci, Charlyne Gard, Sébastien Nin, Geoffroy Venton, Pascal Rihet, Denis Puthier, Béatrice Loriod, and Régis Costello. The Contribution of Multiplexing Single Cell RNA Sequencing in Acute Myeloid Leukemia. Diseases, 11(3):96, July 2023b. doi: 10.3390/diseases11030096. URL https://amu.hal.science/hal-04161267.

2022

Mohamed Belhocine, Mathieu Simonin, José David Abad Flores, Agata Cieslak, Iris Manosalva, Lydie Pradel, Charlotte Smith, Eve-Lyne Mathieu, Guillaume Charbonnier, Joost H A Martens, Hendrik G Stunnenberg, Muhammad Ahmad Maqbool, Aneta Mikulasova, Lisa J Russell, Daniel Rico, Denis Puthier, Pierre Ferrier, Vahid Asnaf, and Salvatore Spicuglia. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes. Genome Research, 32(7):
1328–1342, July 2022. doi: 10.1101/gr.266924.120. URL https://amu.hal.science/hal-03831947.

Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, and Catherine Nguyen. A novel crossspecies differential tumor classifcation method based on exosome-derived microRNA biomarkers established by human-dog lymphoid and mammary tumor cell lines’ transcription profles. Veterinary World, 15(5):1163–1170, May 2022. doi: 10.14202/vetworld.2022.1163-1170. URL https://amu.hal.science/hal-03831863.

Florian Rosier, Nicolas Fernandez Nunez, Magali Torres, Béatrice B. Loriod, Pascal Rihet, and Lydie C Pradel. Transcriptional Response in a Sepsis Mouse Model Reflects Transcriptional Response in Sepsis Patients. International Journal of Molecular Sciences, 23(2):821, January 2022. doi:10.3390/ijms23020821. URL https://amu.hal.science/hal-03528060.

2021

Lamia Madaci, Julien Colle, Geoffroy Venton, Laure Farnault, Béatrice Loriod, and Régis Costello. The contribution of single-cell analysis of acute leukemia in the therapeutic strategy. Biomarker Research, 9(1), December 2021. doi: 10.1186/s40364-021-00300-0. URL https://amu.hal.science/hal-03358838.

Tao Wang, Daniel Perazza, Fayçal Boussouar, Matteo Cattaneo, Alexandre Bougdour, Florent Chuffart, Sophie Barral, Alexandra Vargas, Ariadni Liakopoulou, Denis Puthier, Lisa Bargier, Yuichi Morozumi, Mahya Jamshidikia, Isabel Garcia-Saez, Carlo Petosa, Sophie Rousseaux, A Verdel, and Saadi Khochbin. ATAD2 controls chromatin-bound HIRA turnover. Life Science Alliance, September 2021. doi: 10.26508/lsa.202101151. URL https://hal.science/hal-03359419.

Mengqing Gao, Jin Wang, Sophie Rousseaux, Minjia Tan, Lulu Pan, Lijun Peng, Sisi Wang, Wenqian Xu, Jiayi Ren, Yuanfang Liu, Martin Spinck, Sophie Barral, Tao Wang, Florent Chuffart, Ekaterina Bourova-Flin, Denis Puthier, Sandrine Curtet, Lisa Bargier, Zhongyi Cheng, Heinz Neumann, Jian Li, Yingming Zhao, Jian-Qing Mi, and Saadi Khochbin. Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution. Cell Reports, 36(4):109460, 2021. doi:10.1016/j.celrep.2021.109460. URL https://hal.science/hal-03335489.

2020

Vivien Sutera, Aurélie Hennebique, Fabrice Lopez, Nicolas Fernandez, Dominique Schneider, and Max Maurin. Genomic trajectories to fluoroquinolone resistance in Francisella tularensis subsp. holarctica live vaccine strain. International Journal of Antimicrobial Agents, 56, December 2020. doi: 10.1016/j.ijantimicag.2020.106153. URL https://amu.hal.science/hal-03139160.

Eva Seipelt, Franck Tourniaire, Charlène Couturier, Julien Astier, Béatrice B. Loriod, Hortense Vachon, Michel Puceat, Lourdes Mounien, and Jean-Francois Landrier. Prenatal maternal vitamin D defciency sex-dependently programs adipose tissue metabolism and energy homeostasis in offspring. FASEB Journal, 34(11):14905–14919, November 2020. doi: 10.1096/fj.201902924RR. URL https://hal.inrae.fr/hal-03156949.

Agata Cieslak, Guillaume Charbonnier, Melania Tesio, Eve-Lyne Mathieu, Mohamed Belhocine, Aurore Touzart, Charlotte Smith, Guillaume Hypolite, Guillaume Andrieu, Joost H.A. Martens, Eva Janssen-Megens, Marta Gut, Ivo Gut, Nicolas Boissel, Arnaud Petit, Denis Puthier, Elizabeth Macintyre, Hendrik Stunnenberg, Salvatore Spicuglia, and Vahid Asnaf. Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specifc TCR enhancer activation. Journal of Experimental Medicine, 217(9), September 2020. doi: 10.1084/jem.20192360. URL https://amu.hal.science/hal-03015052.

J.P. Mevy, Béatrice B. Loriod, Xi Liu, Erwan Corre, Magali Torres, Michael Büttner, Anne Haguenauer, Ilja M. 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, 9(9):1149, September 2020. doi: 10.3390/plants9091149. URL https://amu.hal.science/hal-02945417.

Darely Gutiérrez-Reyna, Alejandra Cedillo-Banos, Linda Kempis-Calanis, Oscar Ramirez-Pliego, Lisa Bargier, Denis Puthier, Jose Abad-Flores, Morgane Thomas-Chollier, Denis Thieffry, Alejandra Medina-Rivera, Salvatore Spicuglia, and Maria Santana. IL-12 Signaling Contributes to the Reprogramming of Neonatal CD8+ T Cells. Frontiers in Immunology, 11, June 2020. doi:10.3389/fmmu.2020.01089. URL https://hal.science/hal-02935693.

Jaafar Alomairi, Anne Molitor, Nori Sadouni, Saadat Hussain, Magali Torres, Wiam Saadi, Lan Dao, Guillaume Charbonnier, David Santiago-Algarra, Jean Christophe Andrau, Denis Puthier, Tom Sexton, and Salvatore Spicuglia. Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene. PLoS ONE, 15(5):e0233191, May 2020. doi: 10.1371/journal.pone.0233191. URL https://amu.hal.science/hal-02773600.

Naghmeh Hoghoughi, Sophie Barral, Sandrine Curtet, Florent Chuffart, Guillaume Charbonnier, Denis Puthier, Thierry Buchou, Sophie Rousseaux, and Saadi Khochbin. RNA-Guided Genomic Localization of H2A.L.2 Histone Variant. Cells, 9(2):474, February 2020. doi: 10.3390/cells9020474. URL https://amu.hal.science/hal-02773006.

2019

Mirna Swayden, George Alzeeb, Rawand Masoud, Yolande Berthois, Stéphane Audebert, Luc Camoin, Laurent Hannouche, Hortense Vachon, Odile Gayet, Martin Bigonnet, Julie Roques, Françoise Silvy, Alice Carrier, Nelson Dusetti, Juan Iovanna, and Philippe Soubeyran. PML hyposumoylation is responsible for the resistance of pancreatic cancer. FASEB Journal, 33(11):12447–12463, November 2019. doi: 10.1096/fj.201901091R. URL https://inserm.hal.science/inserm-02439811.

Thi Tran, Calypso Mathieu, Magali Torres, Béatrice B. Loriod, Linh Thuy Lê, Catherine Nguyen, Monique Bernard, Marc Leone, and Nathalie Lalevee. Effect of landiolol on sex-related transcriptomic changes in the myocardium during sepsis. Intensive Care Medicine Experimental, 7(1), August 2019. doi: 10.1186/s40635-019-0263-0. URL https://amu.hal.science/hal-02279120.

Wiam Saadi, Yasmina Kermezli, Lan Dao, Evelyne Mathieu, David Santiago-Algarra, Iris Manosalva, Magali Torres, Mohamed Belhocine, Lydie Pradel, Béatrice B. Loriod, Mourad Aribi, Denis Puthier, and Salvatore Spicuglia. A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation. Scientifc Reports, 9(1), March 2019. doi:10.1038/s41598-019-41247-5. URL https://amu.hal.science/hal-02078114.

Yasmina Kermezli, Wiam Saadi, Mohamed Belhocine, E. L. Mathieu, Marc-Antoine Garibal, Vahid Asnaf, Mourad Aribi, Salvatore Spicuglia, and Denis Puthier. A comprehensive catalog of LncRNAs expressed in T-cell acute lymphoblastic leukemia. Leukemia & lymphoma, pages 1–13, January 2019. doi: 10.1080/10428194.2018.1551534. URL https://amu.hal.science/hal-02078367.

2018

Hitoshi Shiota, Sophie Barral, Thierry Buchou, Minjia Tan, Yohann Couté, Guillaume Charbonnier, Nicolas Reynoird, Fayçal Boussouar, Matthieu G´erard, Mingrui Zhu, Lisa Bargier, Denis Puthier, Florent Chuffart, Ekaterina Bourova-Flin, Sarah Picaud, Panagis Filippakopoulos, Afsaneh Goudarzi, Ziad Ibrahim, Daniel Panne, Sophie Rousseaux, Yingming Zhao, and Saadi Khochbin. Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells. Cell Reports, 24(13):3477
– 3487.e6, September 2018. doi: 10.1016/j.celrep.2018.08.069. URL https://amu.hal.science/hal-01887337.

Axel Aigle, Patricia Bonin, Nicolas Fernandez Nunez, Béatrice B. Loriod, Sophie Guasco, Aurélie Bergon, Fabrice Armougom, Chantal Iobbi-Nivol, Jean Imbert, and Valerie Michotey. The nature of electron acceptor (MnIV/NO3) triggers differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3. FEMS Microbiology Letters, July 2018. doi: 10.1093/femsle/fny068. URL https://amu.hal.science/hal-01766209.

Yasmine Labiad, Geoffroy Venton, Farnault Laure, Céline Baier, Julien Colle, Cédric Mercier, Ivanov Vadim, Corinne Nicolino-Brunet, Loriod Béatrice, Nicolas Fernandez-Nunez, Magali Torres, JeanCamille Mattei, Pascal Rihet, Catherine Nguyen, and Régis Costello. A transcriptomic signature predicting septic outcome in patients undergoing autologous stem cell transplantation. Experimental Hematology, June 2018. doi: 10.1016/j.exphem.2018.06.001. URL https://amu.hal.science/hal-01850637.

Jonathan Bond, Christine Tran Quang, Guillaume Hypolite, Mohamed Belhocine, Aurélie Bergon, Gaëlle Cordonnier, Jacques Ghysdael, Elizabeth Macintyre, Nicolas Boissel, Salvatore Spicuglia, and Vahid Asnaf. Novel Intergenically Spliced Chimera, NFATC3-PLA2G15 , Is Associated with Aggressive T-ALL Biology and Outcome. Molecular Cancer Research, February 2018. doi: 10.1158/1541-7786.MCR-17-0442. URL https://amu.hal.science/hal-01716815.

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