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MAD Dutch Genomics Service & Support Provider University of Amsterdam

Contact Details

University of Amsterdam

Science Park 904 (room C2.273) 1098 XH Amsterdam The Netherlands

Dr. T.M. Breit

0031 (020) 5257058

Hotel Description

MAD Dutch Genomics Service & Support Provider (Previously known as MicroArray Department), is an applied genome technology and bioinformatics expertise centre within the Swammerdam Institute for Life Sciences (SILS) of the Faculty of Science (FNWI) at the University of Amsterdam (UvA).

• Genomics technology – The MAD was founded in 1999 with funding from the Dutch government plus major investments from several industrial food and pharma partners. The tasks of the expertise centre include: the design, production and use of (custom-made) microarrays (Affymetrix GeneChip® & GeneTitan®, Agilent), plus bioinformatics analysis of the experimental results. In 2012, next-generation sequencing technology (Ion Proton–Life Technologies) and associated bioinformatics for genome re-sequencing and RNAseq were added. Our NGS platform is especially suited for small-RNAseq.

• Set-up – Nowadays, the MAD comprises of a “Wet-Lab” for molecular-biology analyses and a “Dry-Lab” for bioinformatics service and support. With a staff of ~18 multidisciplinary experts, the MAD has all the necessary know-how and expertise (biology, molecular biology, statistics, bioinformatics, scientific programming, computer science, informatics, e-science, etc.) to perform, analyse, and interpret genomics experiments. Our activities are: technology and applied-bioinformatics research, genomics and transcriptomics service and support, as well as education. Our specialty is genome-wide gene-expression analysis.

• Service and support – The MAD has always operated as a core-facility for UvA researchers, as well as a service and support provider for external customers and collaborators. Throughout the years we have cooperated with numerous: academic groups (AMC, VU, UMCU, LU and more), companies (DSM, Unilever, Solvay, Philips, Organon, Rijk Zwaan, Bejo zaden and more), and not-for-profit organisations (RIVM, NAKtuinbouw and more). The yearly service and support revenues fund a significant portion of our staff and overhead.

• DTL Hotel – In the first DTL hotel call we had a 100% success rate for our 3 submitted hotel projects. Our secret is simply our customer centric approach: value for money, (= a lot of high-quality samples), expert advice on experiment design (= the right experiment), and over a decade of dedicated bioinformatics support experience (= the correct results). Do you want to feel like a research celebrity? Just visit our DTL hotel!

Genomics
Public
  • Agri & Food
  • Biomedical & health
  • Applied Bioinformatics
  • Genomics
  • Transcriptomics
  • Microarray technology (Affymetrix GeneChip® & GeneTitan®, Agilent)
  • Next-generation sequencing (Ion Proton –Life Technologies)
  • Red Life Sciences
  • Green Life Sciences
  • Fundamental Research
  • Applied Research
  • All Others

Expertise and Track Record

435000001 Deconstructing the plant immune system by using a Fusarium effector protein as a probe with Dr. M. Rep (UvA) 435000019 Genome Sequencing of Evolved Strains of Synechocystis PCC6803 with dr. F. Branco dos Santos (UvA). 435000027 Transcriptomics analysis and bioinformatics approaches for the identification of in vitro molecular early signatures for immunogenicity with dr. B.O. Fabriek (TNO)

The MAD is one of the largest combined genomics technology and bioinformatics groups in the Netherlands. We have a unique know-how on how to provide service and support in the complex environment of academic and industrial life sciences research. Due to our over 14 year experience we also created a wide-spread network of collaborating experts as well as life-sciences collaborators. As far as we know we are the only not-for-profit genomics and
bioinformatics service and support group in the Netherlands that professionally operates at a nation-wide scale.

As we are already for over 14 years a service and support group, we have performed numerous collaborative projects. This ranges from small experiments in which we just supply genomics technology support, to large projects in which we are the genomics technology and bioinformatics partner. The past years, we ran ~60-70 service and support projects per year. Evidence of our support activities can be found in our 60+ collaborative publications at: http://www.ncbi.nlm.nih.gov/pubmed/?term=breit+t

We have only limited experience with qualitative cross-technology integration.

  • 1. Melis JPM, Derks KWJ, Pronk T, Wackers P, Schaap MM, Zwart E, van IJcken WF, Jonker M, Breit TM, Pothof J, van Steeg H, Luijten M In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Archives of Toxicology 2014
  • 2. Tulinski P; Duim B; Wittink FR; Jonker MJ; Breit TM; van Putten JP; Wagenaar JA; Fluit AC. Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium. BMC genomics
  • 3. Jonker MJ, Melis JPM, Kuiper RV, van der Hoeven TV, Robinson J, van der Horst GTJ, Breit TM, Vijg J, Dolle M, Hoeijmakers JHJ, van Steeg H Lifelong murine gene expression profiles in relation to chronological and biological aging in multiple organs. Aging Cell. 2013 Oct;12(5):901-9.
  • 4. Sasidharan R, Mustroph A, Boonman A, Akman M, Ammerlaan AM, Breit T, Schranz ME, Voesenek LA, van Tienderen P.Root transcript profiling of two Rorippa (Brassicaceae) species reveals gene clusters associated with extreme submergence tolerance. Plant Physiol. 2013 Nov;163(3):1277-92.
  • 5. Surdova K, Gamba P, Claessen D, Siersma T, Jonker MJ, Errington J, Hamoen LW. The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis. Journal of Bacteriology 2013 Dec;195(24):5450-60.
  • 6. Röschmann K, van Kuijen A-M, Luiten S; Jonker M, Breit T, Fokkens W, Petersen A, van Drunen . M Purified Timothy grass pollen major allergen Phl p 1 may contribute to the modulation of allergic responses through a pleiotropic induction of cytokines and chemokines from airway epithelial cells. Clin Exp Immunol. 2012 Mar;167(3):413-21.
  • 7. Doroszuk A, Jonker MJ, Pul N, Breit TM, Zwaan B. Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension. BMC Genomics 2012 May 4;13(1):167.
  • 8. Melis JPM, Hoogervorst EM, van Oostrom CThM, Zwart E, Breit TM, Pennings JLA, de Vries A, van Steeg H Strong selection for the truncated ΔN-p53 isoform in murine urinary bladder tumors. Oncogene 2011 Apr 14;30(15):1764-72
  • 9. Smits NJP, Pronk TE, Bruning O, Wittink FRA, Breit TM, van Strijp JAG, Fluit AC, Boel CHE Operon structure of Staphylococcus aureus. Nucleic Acids Res. 2010 Jun; 38(10):3263-74.
  • 10. Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Brüning JC, Niessen CM, Hoeijmakers JH, Schumacher B. Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol. 2009 May;11(5):604-15.

We are part of the existing Dutch or international technology network(s) and/or sector programme(s);
Netherlands Bioinformatics Centre (NBIC): bioinformatics research projects and bioinformatics support projects from the start of NBIC;
Netherlands e-Science Centre (NLeSC): development within an e-infrastructure project in Green Genetics;
Virtual Lab for Plant Breeding: development of e-infrastructure for green genetics academic research groups and industry.
Green Life Sciences Hub: multi-focus initiative to create a green life sciences research campus in Amsterdam.

Hotel Characteristics

  • 3 FTE Dedicated Postdoc
  • 2 FTE Dedicated Technicians
  • 1 FTE Lab Manager
  • 6 FTE Bioinformaticians
  • 3 FTE ICT-sepcialists

90%

  • IonProton/IonChef system (Life Technologies); Genechip & GeneTitan array systems (Affymetrix); SurePrint microarray platform (Agilent); BioAnalyzer & Tape-Station (Agilent), QPCR platform (Perkin Elmer).

Surfsara Cloud; international gene-expression databases such as GEO