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Plateforme Transcriptomique & Génomique Marseille Luminy

La plateforme « Transcriptomique et Génomique de Marseille-Luminy » (TGML) est intégrée au laboratoire « Technologies Avancées pour le Génome et la Clinique » (TAGC, Dr Catherine Nguyen, UMR 1090, Inserm  / Aix-Marseille Université) sur le Parc des Sciences de Luminy.

Cette plateforme offre un accès pour la recherche publique et les entreprises à des études de génomique fonctionnelle en utilisant un large ensemble de méthodes expérimentales et bioinformatiques.

La plateforme a été labélisée comme Plateforme Nationale par le GIS IBiSA, précédemment RIO, et est un membre fondateur de l'Infrastructure Nationale en Biologie et Santé France Génomique.

La plateforme TGML et le TAGC fournissent une expertise reconnue dans l'analyse des différents types de puces à ADN et des données de séquençage. Nos chercheurs et ingénieurs contribuent activement au développement de nouveaux outils d'analyse et de traitement intégré des données génomiques, épigénomiques et transcriptomiques.

Activités / Spécialités

- Transcriptomique : mRNA-seq et puces à ADN (DGE, miRNA, CGH)

- Génomique : Re-séquençage ciblé, exome complet, SNV, small/large IndDels, etc.

- Épigénomique : ChIP-seq, FAIRE-seq / ATAC-seq, Mnase-seq, 3C-seq

 

Développements

- Single-Cell (C1 fluidigm / Icell8 WaferGen)

- Long reads (MinION Oxford nanopore /Sequel PacBio)

 

Équipements principaux

- Séquenceur NextSeq-500 Illumina (20-120Gb)

- Séquenceur Ion PGM Thermo (10Mb-2Gb)

- Scanner Microarray Haute-Résolution Agilent

- Robots : EVO-150 Tecan ; Apollo-324 WaferGen ; Ion Chef  System

 

Le service de séquençage à haut débit est équipé d'un séquenceur Illumina NextSeq-500  ainsi que de tous les équipements et automates nécessaires pour la préparation des librairies.

Le NextSeq-500 peut produire jusqu’à 120 gigabases (Gb), issues de 130 à 400M de clusters, en lectures single-end ou paire-end, de 75 à 150 nt et jusqu’à 96 échantillons par session.

Le service puce à ADN Agilent permet des études transcriptomique de nombreux organismes. Il permet également des études miRNA, CGH, et l'analyse du profil de méthylation de l'ADN.

Le personnel de la plateforme peut fournir des conseils pour la préparation des échantillons et assure le suivi des projets sélectionnés. Les utilisateurs peuvent bénéficier des prestations offertes par le TGML sous forme de service ou de  collaboration, sur la base d'un contrat prédéfini.

 

Ferme de calcul

- une machine maître

Dell PowerEdge R720

2 CPUs Xeon E5-2640 (2.5 GHz) -> 12 cœurs

64 Gb de mémoire

- 12 nœuds de calcul

Dell C6220

2 CPUs Xeon E5-2670 (2.6 GHz) -> 12x16 cœurs = 192 cœurs

128 Gb de mémoire par nœud

- une baie de stockage

Dell MD3260

36 disques de 3 Tb -> 82 Tb utiles (formatés)

- Stockage : 4 volumes (baies Dell MD1000, MD1200 et MD3260) de 140 à 220 Tb

 

Outils informatiques en développement

- Développement de workflow pour l’analyse du transcriptome, du génome et de l’épigénome

- Logiciel GeVarA pour l’analyse des variants génomiques

- Outils de conversion et analyse à façon (wig, bed, sam, etc.)

 

Démarche qualité

L’ensemble de l’activité de la plate-forme est certifié ISO 9001:2008 et NF X 50-900

 

Labels

GIS IBiSA, Cancéropôle PACA, CoReBio PACA

 

Responsable de la plateforme scientifique et technique : Béatrice Loriod

beatrice.loriod@ inserm.fr

+33 (0)4 91 82 87 13

Campus Universitaire de Luminy 13009 Marseille

TAGC U1090

Inserm, Aix Marseille Université

 

 

Publications TGML 2016-2008

Les noms des membres permanents et associés de la plateforme TGML sont soulignés.

2016

Venton G, Labiad Y, Colle J, Fino A, Afridi S, Torres M, Monteuil S, Loriod B, Fernandez-Nunez N, Farnault L, Suchon P, Mattei JC, Rihet P, Bergon A, Nguyen C, Baier C, Costello R. Natural killer cells in acute myeloid leukemia patients: from phenotype to transcriptomic analysis. Immunol Res. 2016 Aug 1.PMID: 27481509

Belzeaux R, Lin CW, Ding Y, Bergon A, Ibrahim EC, Turecki G, Tseng G, Sibille E. Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. J Psychiatr Res. 2016 Jul 9;81:119-126. PMID: 27438688

Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla A. Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. Environ Microbiol Rep. 2016 Jun 6. PMID: 27264199

Sakakini N, Turchi L, Bergon A, Holota H, Rekima S, Lopez F, Paquis P, Almairac F, Fontaine D, Baeza-Kallee N, Van Obberghen-Schilling E, Junier MP, Chneiweiss H, Figarella-Branger D, Burel-Vandenbos F, Imbert J, Virolle T. A positive feed-forward loop associating EGR1 and PDGFA promotes proliferation and self-renewal in glioblastoma stem cells. J Biol Chem. 2016 Mar 21. PMID: 27002148

Landel V, Millet P, Baranger K, Loriod B, Féron F. Vitamin D interacts with Esr1 and Igf1 to regulate molecular pathways relevant to Alzheimer's disease. Mol Neurodegener. 2016 Mar 1;11(1):22. PMID: 26932723

2015

Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation.Nucleic Acids Res. 2015 Dec 15. PMID: 26673693

Sanchez C, Baier C, Colle JG, Chelbi R, Rihet P, Le Treut T, Imbert J, Sébahoun G, Venton G, Costello RT. Natural killer cells in patients with polycythemia vera. Hum Immunol. 2015 Sep 23.PMID: 26407910

Bergon A, Belzeaux R, Comte M, Pelletier F, Hervé M, Gardiner EJ, Beveridge NJ, Liu B, Carr V, Scott RJ, Kelly B, Cairns MJ, Kumarasinghe N, Schall U, Blin O, Boucraut J, Tooney PA, Fakra E, Ibrahim EC. CX3CR1 is dysregulated in blood and brain from schizophrenia patients. Schizophr Res. 2015 Aug 15. PMID: 26285829

Féron F, Gepner B, Lacassagne E, Stephan D, Mesnage B, Blanchard MP, Boulanger N, Tardif C, Devèze A, Rousseau S, Suzuki K, Izpisua Belmonte JC, Khrestchatisky M, Nivet E, Erard-Garcia M. Olfactory stem cells reveal MOCOS as a new player in autism spectrum disorders. Mol Psychiatry. 2015 Aug 4. PMID:26239292

Vanhille L, Griffon A, Maqbool MA, Zacarias-Cabeza J, Dao LT, Fernandez-Nunez N, Ballester B, Andrau JC, Spicuglia S. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Nat Commun. 2015 Apr 15;6:6905. PMID: 25872643

Metzler-Guillemain C, Victorero G, Lepoivre C, Bergon A, Yammine M, Perrin J, Sari-Minodier I, Boulanger N, Rihet P, Nguyen C. Sperm mRNAs and microRNAs as candidate markers for the impact of toxicants on human spermatogenesis: an application to tobacco smoking. Syst Biol Reprod Med. 2015 Mar 30:1-11.PMID: 25821920

Zacarías-Cabeza J, Belhocine M, Vanhille L, Cauchy P, Koch F, Pekowska A, Fenouil R, Bergon A, Gut M, Gut I, Eick D, Imbert J, Ferrier P, Andrau JC, Spicuglia S. Transcription-Dependent Generation of a Specialized Chromatin Structure at the TCRβLocus. J Immunol. 2015 March 2. PMID: 25732733

2014

Bond J, Bergon A, Durand A, Tigaud I, Thomas X, Asnafi V, Spicuglia S, Macintyre E. Cryptic XPO1-MLLT10 translocation is associated with HOXA locus deregulation in T-ALL. Blood. 2014 Nov 6;124(19):3023-5. PMID: 25377562

Amrani A, Bergon A, Holota H, Tamburini C, Garel M, Ollivier B, Imbert J, Dolla A, Pradel N. Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure. PLoS One. 2014 Sep 12;9(9):e106831. PMID: 25215865

Landel V, Baranger K, Virard I, Loriod B, Khrestchatisky M, Rivera S, Benech P, Féron F. Temporal gene profiling of the 5XFAD transgenic mouse model highlights the importance of microglial activation in Alzheimer's disease. Mol Neurodegener. 2014 Sep 11;9(1):33. PMID: 25213090

Mathieu EL, Belhocine M, Dao LT, Puthier D, Spicuglia S. Functions of lncRNA in development and diseases.Med Sci (Paris). 2014 8-9;30(8-9):790-796. Epub 2014 Sep 1. PMID: 25174757

Rommelaere S, Millet V, Vu Manh TP, Gensollen T, Andreoletti P, Cherkaoui-Malki M, Bourges C, Escalière B, Du X, Xia Y, Imbert J, Beutler B, Kanai Y, Malissen B, Malissen M, Tailleux A, Staels B, Galland F, Naquet P. Sox17 regulates liver lipid metabolism and adaptation to fastin. PLoS One. 2014 Aug 20;9(8):e104925. PMID: 25141153

Di Gregorio E, Borroni B, Giorgio E, Lacerenza D, Ferrero M, Lo Buono N, Ragusa N, Mancini C, Gaussen M, Calcia A, Mitro N, Hoxha E, Mura I, Coviello DA, Moon YA, Tesson C, Vaula G, Couarch P, Orsi L, Duregon E, Papotti MG, Deleuze JF, Imbert J, Costanzi C, Padovani A, Giunti P, Maillet-Vioud M, Durr A, Brice A, Tempia F, Funaro A, Boccone L, Caruso D, Stevanin G, Brusco A. ELOVL5 Mutations Cause Spinocerebellar Ataxia 38. Am J Hum Genet. 2014 Jul 23. PMID: 25065913

Hamidou Soumana I, Tchicaya B, Loriod B, Rihet P, Geiger A. Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies. Front Microbiol. 2014 May 27. PMID: 24904565

Cornen,S., Guille,A., Adelaide,J., Addou-Klouche,L., Finetti,P., Saade,M.R., Manai,M., Carbuccia,N., Bekhouche,I., Letessier,A., Raynaud,S., Charafe-Jauffret,E., Jacquemier,J., Spicuglia,S., de The,H., Viens,P., Bertucci,F., Birnbaum,D., and Chaffanet,M. (2014). Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling. PLoS. ONE. 9, e81843.

Soumana Hamidou,I., Loriod,B., Ravel,S., Tchicaya,B., Simo,G., Rihet,P., and Geiger,A.(2014) The transcriptional signatures of Sodalis glossinidius in the Glossina palpalis gambiensis flies negative for Trypanosoma brucei gambiense contrast with those of this symbiont in tsetse flies positive for the parasite: Possible involvement of a Sodalis-hosted prophage in fly Trypanosoma refractoriness? Infect.Genet.Evol. 24C:41-56.

2013

Grange,M., Verdeil,G., Arnoux,F., Griffon,A., Spicuglia,S., Maurizio,J., Buferne,M., Schmitt-Verhulst,A.M., and Auphan-Anezin,N. (2013). Active STAT5 regulates T-bet and eomesodermin expression in CD8 T cells and imprints a T-bet-dependent Tc1 program with repressed IL-6/TGF-beta1 signaling. J Immunol. 191, 3712-3724.

Lepoivre,C., Belhocine,M., Bergon,A., Griffon,A., Yammine,M., Vanhille,L., Zacarias-Cabeza,J., Garibal,M.A., Koch,F., Maqbool,M.A., Fenouil,R., Loriod,B., Holota,H., Gut,M., Gut,I., Imbert,J., Andrau,J.C., Puthier,D., and Spicuglia,S. (2013). Divergent transcription is associated with promoters of transcriptional regulators. BMC. Genomics 14, 914.

Liang,Y., Cucchetti,M., Roncagalli,R., Yokosuka,T., Malzac,A., Bertosio,E., Imbert,J., Nijman,I.J., Suchanek,M., Saito,T., Wulfing,C., Malissen,B., and Malissen,M. (2013). The lymphoid lineage-specific actin-uncapping protein Rltpr is essential for costimulation via CD28 and the development of regulatory T cells. Nat. Immunol. 14, 858-866.

Lortet,S., Lacombe,E., Boulanger,N., Rihet,P., Nguyen,C., Goff,L.K., and Salin,P. (2013). Striatal molecular signature of subchronic subthalamic nucleus high frequency stimulation in parkinsonian rat. PLoS. ONE. 8, e60447.

Montellier,E., Boussouar,F., Rousseaux,S., Zhang,K., Buchou,T., Fenaille,F., Shiota,H., Debernardi,A., Hery,P., Curtet,S., Jamshidikia,M., Barral,S., Holota,H., Bergon,A., Lopez,F., Guardiola,P., Pernet,K., Imbert,J., Petosa,C., Tan,M., Zhao,Y., Gerard,M., and Khochbin,S. (2013). Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev. 27, 1680-1692.

Paban,V., Billard,J.M., Bouet,V., Freret,T., Boulouard,M., Chambon,C., Loriod,B., and Alescio-Lautier,B. (2013). Genomic transcriptional profiling in LOU/C/Jall rats identifies genes for successful aging. Brain Struct. Funct. 218, 1501-1512.

Sawan,C., Hernandez-Vargas,H., Murr,R., Lopez,F., Vaissiere,T., Ghantous,A.Y., Cuenin,C., Imbert,J., Wang,Z.Q., Ren,B., and Herceg,Z. (2013). Histone acetyltransferase cofactor trrap maintains self-renewal and restricts differentiation of embryonic stem cells. Stem Cells 31, 979-991.

Spicuglia,S., Maqbool,M.A., Puthier,D., and Andrau,J.C. (2013). An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods.

2012

Belzeaux,R., Bergon,A., Jeanjean,V., Loriod,B., Formisano-Treziny,C., Verrier,L., Loundou,A., Baumstarck-Barrau,K., Boyer,L., Gall,V., Gabert,J., Nguyen,C., Azorin,J.M., Naudin,J., and Ibrahim,E.C. (2012). Responder and nonresponder patients exhibit different peripheral transcriptional signatures during major depressive episode. Transl. Psychiatry 2, e185.

Boone,N., Bergon,A., Loriod,B., Deveze,A., Nguyen,C., Axelrod,F.B., and Ibrahim,E.C. (2012). Genome-wide analysis of familial dysautonomia and kinetin target genes with patient olfactory ecto-mesenchymal stem cells. Hum. Mutat. 33, 530-540.

de Bentzmann,S., Giraud,C., Bernard,C.S., Calderon,V., Ewald,F., Plesiat,P., Nguyen,C., Grunwald,D., Attree,I., Jeannot,K., Fauvarque,M.O., and Bordi,C. (2012). Unique Biofilm Signature, Drug Susceptibility and Decreased Virulence in Drosophila through the Pseudomonas aeruginosa Two-Component System PprAB. PLoS. Pathog. 8, e1003052.

Gaucher,J., Boussouar,F., Montellier,E., Curtet,S., Buchou,T., Bertrand,S., Hery,P., Jounier,S., Depaux,A., Vitte,A.L., Guardiola,P., Pernet,K., Debernardi,A., Lopez,F., Holota,H., Imbert,J., Wolgemuth,D.J., Gerard,M., Rousseaux,S., and Khochbin,S. (2012). Bromodomain-dependent stage-specific male genome programming by Brdt. EMBO J 31, 3809-3820.

Lepoivre,C., Bergon,A., Lopez,F., Perumal,N.B., Nguyen,C., Imbert,J., and Puthier,D. (2012). TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC. Bioinformatics. 13, 19.

2011

Barbier,M., Faille,D., Loriod,B., Textoris,J., Camus,C., Puthier,D., Flori,L., Wassmer,S.C., Victorero,G., Alessi,M.C., Fusai,T., Nguyen,C., Grau,G.E., and Rihet,P. (2011). Platelets alter gene expression profile in human brain endothelial cells in an in vitro model of cerebral malaria. PLoS. ONE  6, e19651.

Pekowska,A., Benoukraf,T., Zacarias-Cabeza,J., Belhocine,M., Koch,F., Holota,H., Imbert,J., Andrau,J.C., Ferrier,P., and Spicuglia,S. (2011). H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. 30, 4198-4210.

Sananmuang,T., Tharasanit,T., Nguyen,C., Phutikanit,N., and Techakumphu,M. (2011). Culture medium and embryo density influence on developmental competence and gene expression of cat embryos. Theriogenology 75, 1708-1719.

Terrier,O., Josset,L., Textoris,J., Marcel,V., Cartet,G., Ferraris,O., Nguyen,C., Lina,B., Diaz,J.J., Bourdon,J.C., and Rosa-Calatrava,M. (2011). Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway. Virol. J. 8, 285.

Textoris,J., Loriod,B., Benayoun,L., Gourraud,P.A., Puthier,D., Albanese,J., Mantz,J., Martin,C., Nguyen,C., and Leone,M. (2011). An evaluation of the role of gene expression in the prediction and diagnosis of ventilator-associated pneumonia. Anesthesiology 115, 344-352.

Wurmser,F., Ogereau,D., Mary-Huard,T., Loriod,B., Joly,D., and Montchamp-Moreau,C. (2011). Population transcriptomics: insights from Drosophila simulans, Drosophila sechellia and their hybrids. Genetica 139, 465-477.

2010

Boone,N., Loriod,B., Bergon,A., Sbai,O., Formisano-Treziny,C., Gabert,J., Khrestchatisky,M., Nguyen,C., Feron,F., Axelrod,F.B., and Ibrahim,E.C. (2010). Olfactory stem cells, a new cellular model for studying molecular mechanisms underlying familial dysautonomia. PLoS ONE 5, e15590.

Costello,R., Sanchez,C., Le Treut,T., Rihet,P., Imbert,J., and Sebahoun,G. (2010). Peripheral T-cell lymphoma gene expression profiling and potential therapeutic exploitations. Br. J. Haematol. 150, 21-27.

Donate,P.B., Fornari,T.A., Junta,C.M., Magalhaes,D.A., Macedo,C., Cunha,T.M., Nguyen,C., Cunha,F.Q., and Passos,G.A. (2010). Collagen induced arthritis (CIA) in mice features regulatory transcriptional network connecting major histocompatibility complex (MHC H2) with autoantigen genes in the thymus. Immunobiology.

Josset,L., Textoris,J., Loriod,B., Ferraris,O., Moules,V., Lina,B., Nguyen,C., Diaz,J.J., and Rosa-Calatrava,M. (2010). Gene expression signature-based screening identifies new broadly effective influenza a antivirals. PLoS. ONE 5.

Lesur,I., Textoris,J., Loriod,B., Courbon,C., Garcia,S., Leone,M., and Nguyen,C. (2010). Gene expression profiles characterize inflammation stages in the acute lung injury in mice. PLoS. ONE 5, e11485.

2009

Benoukraf,T., Cauchy,P., Fenouil,R., Jeanniard,A., Koch,F., Jaeger,S., Thieffry,D., Imbert,J., Andrau,J.C., Spicuglia,S., and Ferrier,P. (2009). CoCAS: a ChIP-on-chip analysis suite. Bioinformatics 25, 954-955.

Simoncini,S., Njock,M.S., Robert,S., Camoin-Jau,L., Sampol,J., Harle,J.R., Nguyen,C., Dignat-George,F., and Anfosso,F. (2009). TRAIL/Apo2l Mediates the Release of Procoagulant Endothelial Microparticles Induced by Thrombin In Vitro. A Potential Mechanism Linking Inflammation and Coagulation. Circ. Res.

2008

Lopez,F., Textoris,J., Bergon,A., Didier,G., Remy,E., Granjeaud,S., Imbert,J., Nguyen,C., and Puthier,D. (2008). TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS ONE 3, e4001.

Ritchie,W., Theodule,F.X., and Gautheret,D. (2008). Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics 24, 1394-1396.

Vendrell,J.A., Robertson,K.E., Ravel,P., Bray,S.E., Bajard,A., Purdie,C.A., Nguyen,C., Hadad,S.M., Bieche,I., Chabaud,S., Bachelot,T., Thompson,A.M., and Cohen,P.A. (2008). A candidate molecular signature associated with tamoxifen failure in primary breast cancer. Breast Cancer Res. 10, R88.


Firstname Name Status Phone E-mail Web link
/nfernandez.jpg Nicolas Fernandez-Nuñez Research Engineer +33(0)491 82 87 04 nicolas.fernandez-nunez@inserm.fr TGML
Léonard Hérault Research Engineer +33(0)491 82 87 04 Leonard.Herault@inserm.fr TGML
bloriot.jpg Béatrice Loriod IRHC Inserm +33(0)491 82 87 13 beatrice.loriod@inserm.fr TGML
/vanhille.jpg Hortense Vachon Research Engineer +33(0)491 82 87 04 hortence.vachon@inserm.fr TGML