Transcriptomic & Genomic Platform Marseille Luminy

The platform "Transcriptomics and Genomics of Marseille-Luminy" (TGML) is integrated into the laboratory "Theory and Approaches of Genomic Complexity" (TAGC, Dr. Catherine Nguyen, UMR 1090, Inserm / Aix-Marseille University) Of Luminy.
This platform provides access for public research and business to functional genomics studies using a wide range of experimental and bioinformatic methods.
The platform has been labeled as a National Platform by GIS IBiSA, previously RIO, and is a founding member of the National Infrastructure in Biology and Health France Genomics.
The TGML platform and the TAGC provide a recognized expertise in the analysis of different types of DNA chips and sequencing data. Our researchers and engineers actively contribute to the development of new tools for integrated analysis and processing of genomic, epigenomic and transcriptomic data.

Activities / Specialties

  • Transcriptomics: mRNA-seq and DNA chips (DGE, miRNA, CGH)
  • Genomics: Targeted re-sequencing, complete exome, SNV, small / large IndDels, etc.
  • Epigenomics: ChIP-seq, FAIRE-seq / ATAC-seq, Mnase-seq, 3C-seq

 

Developments

  • Single-Cell (C1 fluidigm / Icell8 WaferGen)
  • Long reads (Minion Oxford nanopore / Sequel PacBio)

 

Main facilities

  • NextSeq-500 Sequencer Illumina (20-120Gb)
  • Ion PGM Thermo Sequencer (10Mb-2Gb)
  • Agilent High-Resolution Microarray Scanner
  • Robots: EVO-150 Tecan; Apollo-324 WaferGen; Ion Chef System

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 clusters, in single-end or pair-end reads, from 75 to 150 nt and up to 96 samples per session.
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.
 

Computer cluster

  • a master machine:

Dell PowerEdge R720
2 CPUs Xeon E5-2640 (2.5 GHz) -> 12 cores
64 Gb of memory

  • 12 computation nodes:

Dell C6220
2 CPUs Xeon E5-2670 (2.6 GHz) -> 12x16 cores = 192 cores
128 Gb of memory per node

  • a storage bay:

Dell MD3260
36 disks of 3 Tb -> 82 Tb useful (formatted)

  • Storage:

4 volumes (Dell MD1000, MD1200 and MD3260) from 140 to 220 Tb

 

Computer tools in development

  • Workflow development for transcriptome, genome and epigenome analysis
  • GeVarA software for the analysis of genomic variants
  • Custom conversion and analysis tools (wig, bed, sam, etc.)

 

Quality approach

The entire activity of the platform is certified ISO 9001: 2008 and NF X 50-900
 

Labels

GIS IBiSA, Cancéropôle PACA, CoReBio PACA
 

Contact

Responsible for the scientific and technical platform: Béatrice Loriod
Beatrice.loriod @ inserm.fr
+33 (0) 4 91 82 87 13
Campus University of Luminy 13009 Marseille
TAGC U1090
Inserm, Aix Marseille University

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Publications

 

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.