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Robotics and Screening Center

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The NRSC provides comprehensive stock reagent collections including siRNA, shRNA, ORF and compound libraries.  We have advanced liquid handling robotics platforms capable of aliquoting these libraries to assay plates. These platforms are coupled to, or complemented by automated incubators, plate stackers, heaters, coolers, shakers, robotic arms, sealers, labelers and barcode readers for advanced screening applications.  Depending on the assay we utilize our multilabel reader or automated high content microscopes to obtain single well readings for each screen.  Data obtained from each screen is stored and analyzed in our Screensaver application. Ultimately a gene or compound giving a desired effect in a screen is designated a 'hit', and used for further study.

A screening project is initiated by the submission of an application form to the NRSC. The NRSC then collaborates with each researcher through each stage of the screening process, including assay development, optimization, automation, screening, data acquisition and analysis.  Researchers are trained to use the robotics and assay equipment, whereas the NRSC staff is on hand for programming, maintaining and troubleshooting the equipment.

Further information

Libraries
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Libraries


The NRSC has several large collections of functional genomic tools (e.g. RNAi reagents and ORF collections) and small compound libraries available for researchers to use in high throughput screens.  For functional genomic screens, these include the Thermo Scientific Dharmacon full genome siRNA library (human and mouse), the NKI shRNA collections (human and mouse), the Mission TRC shRNA collection (TRC 1.0, 1,5 and 2.0, human and TRC 1.0 mouse) and the CCSB-Broad lentiviral expression library. For these collection we also  have customized gene subsets available e.g human kinome, DNA damage collection and epigenetic modifiers.  For drug screens, our compound collections include the LOPAC library, a pharmacologically active compound set, kinase and phosphatase inhibitor sets and several targeted sets for oncology research. 

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Equipment
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Equipment


The Netherlands Cancer Institute Robotics and Screening Center (NRSC) uses al kinds of smart equipment such as robotics liquid handling workstations, platforms, handlera and analysers.

Click here for more detailed information about the equipment of the NRSC.

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Data Analysis
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Data Analysis


Pooled shRNA screen analysis
We provide analysis of large scale pooled shRNA screens for which deep sequencing data is generated. We have developed a pipeline in which  quality control plots, correlation between replicates and a hierarchical clustering of the samples are generated. Based on this quality control information a decision is made for the inclusion and exclusion of replicate samples from further analysis. After normalization and statistical analysis, a scoring for each individual shRNA is produced. Using different analysis methods and criteria, genes are selected as hits for further validation and follow-up.

Synergy screen analysis
At the NRSC we have generated an assay and an analysis tool to calculate synergy for two compounds. The assay is performed in 384 well plate format and allows for up to six separate synergy experiments at once. Per synergy experiment a compound in 5 concentrations is done against the second compound in 5 concentrations, resulting in a 5 * 5 matrix. Synergy is calculated by subtracting  measured data from expected data, based on the dose response curves and the Loewe formula. The output of the synergy analysis provides a synergy score based on all 25 cells in an experiment.

Compound screen analysis
Data from compound screens performed at the NRSC is stored in the Screensaver database. The database provides a web-interface for the user to view their screens. In the screen view the library information is automatically linked via plate-well position. In Screensaver plate normalization can be done via the integrated R package - cellHTS2.  CellHTS2 produces quality control images and calculates a Z'factor value as quality score for the screen.  CellHTS2 also calculates  a z-score which can be used for hit selection.

The NRSC has developed a pipeline for the calculation of IC50 values. Data in screensaver are converted via an R-script into data-files which can be used in Graphpad Prism to calculate IC50, and to generate an image of the fitted curve.  

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Publications
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Publications


Sun C, Wang L, Huang S, Heynen G, Prahallad A, Robert C, Haanen J, Blank C, Wesseling J, Willems S, Zecchin D, Hober S, Bapje P, Lieftink C, Mateus C, Vagner S, Grernrum W, Hofland I, Schlicker A, Wessels L, Beijersbergen R, Bardelli A, Nicolantonio F, Eggermont A, Bernards R. (2014) Reversible and adaptive resistance to BRAF (V600E) inhibition in melanoma.Nature. ;508(7494):118-122.

Sun C, Hober S, Bertotti A, Zecchin D, Huang S, Galimi F, Cottino F, Prahallad A, Grernrum W, Tzani A, Schlicker A, Wessels LF, Smit EF, Thunnissen E, Halonen P, Lieftink C, Beijersbergen RL, Di Nicolantonio F, Bardelli A, Trusolino L, Bernards R (2014) Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon cancer through transcriptional induction of ERBB3.Cell Rep. Apr 10;7(1):86-93.

Bajpe PK, Heynen GJ, Mittempergher L, Grernrum W, de Rink IA, Nijkamp W, Beijersbergen RL, Bernards R, Huang S (2013) The corepressor CTBP2 is a coactivator of retinoic acid receptor / retinoid X receptor in retinoic acid signaling.Mol Cell Biol. Aug;33(16):3343-53.

Huang S, Hölzel M, Knijnenburg T, Schlicker A, Roepman P, McDermott U, Garnett M, Grernrum W, Sun C, Prahallad A, Groenendijk FH, Mittempergher L, Nijkamp W, Neefjes J, Salazar R, Ten Dijke P, Uramoto H, Tanaka F, Beijersbergen RL, Wessels LF, Bernards R (2012) MED12 controls the response to multiple cancer drugs through regulation of TGF-B receptor signaling.Cell. Nov 21;151(5):937-50.

Prahallad A, Sun C, Huang S, Di Nicolantonio F, Salazar R, Zecchin D, Beijersbergen RL, Bardelli A, Bernards R. (2012) Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR.Nature. 26;483(7387):100-3.

Kuiken HJ, Egan DA, Laman H, Bernards R, Beijersbergen RL, Dirac AM. (2012) Identification of F-box only protein 7 as a negative regulator of NF-kappaB signaling.J Cell Mol Med. 10.1111/j.1582-4934.2012.01524.x.  

Westerman BA, Braat AK, Taub N, Potman M, Vissers JH, Blom M, Verhoeven E, Stoop H, Gillis A, Velds A, Nijkamp W, Beijersbergen R, Huber LA, Looijenga LH, van Lohuizen M. (2011) A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation. J Exp Med. 19;208(13):2675-89.

Nijwening JH, Geutjes EJ, Bernards R, Beijersbergen RL. (2011) The histone demethylase Jarid1b (Kdm5b) is a novel component of the Rb pathway and associates with E2f-target genes in MEFs during senescence. PLoS One. ;6(9):e25235. Epub 2011 Sep 27. PubMed PMID: 21980403; PubMed Central PMCID: PMC3181323.

Paul P, van den Hoorn T, Jongsma ML, Bakker MJ, Hengeveld R, Janssen L, Cresswell P, Egan DA, van Ham M, Ten Brinke A, Ovaa H, Beijersbergen RL, Kuijl C, Neefjes J. (2011) A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation. Cell. 15;145(2):268-83.

Nijwening JH, Kuiken HJ, Beijersbergen RL. (2011) Screening for modulators of cisplatin sensitivity: unbiased screens reveal common themes.Cell Cycle. 1;10(3):380-6.

Evers B, Schut E, van der Burg E, Braumuller TM, Egan DA, Holstege H, Edser P, Adams DJ, Wade-Martins R, Bouwman P, Jonkers J. (2010) A high-throughput pharmaceutical screen identifies compounds with specific toxicity against BRCA2-deficient tumors. Clin Cancer Res. 1;16(1):99-108.

Hölzel M, Huang S, Koster J, Ora I, Lakeman A, Caron H, Nijkamp W, Xie J, Callens T, Asgharzadeh S, Seeger RC, Messiaen L, Versteeg R, Bernards R. (2010) NF1 is a tumor suppressor in neuroblastoma that determines retinoic acid response and disease outcome. Cell. 23;142(2):218-29.

Mullenders J, Fabius AW, van Dongen MM, Kuiken HJ, Beijersbergen RL, Bernards R. (2010) Interleukin-1R-associated kinase 2 is a novel modulator of the transforming growth factor beta signaling cascade. Mol Cancer Res. Apr;8(4):592-603.

Albers HM, van Meeteren LA, Egan DA, van Tilburg EW, Moolenaar WH, Ovaa H. (2010) Discovery and optimization of boronic acid based inhibitors of autotaxin.J Med Chem.  8;53(13):4958-67.

Albers HM, Dong A, van Meeteren LA, Egan DA, Sunkara M, van Tilburg EW, Schuurman K, van Tellingen O, Morris AJ, Smyth SS, Moolenaar WH, Ovaa H. (2010) Boronic acid-based inhibitor of autotaxin reveals rapid turnover of LPA in the circulation.Proc Natl Acad Sci U S A.  20;107(16):7257-62.

Drost J, Mantovani F, Tocco F, Elkon R, Comel A, Holstege H, Kerkhoven R, Jonkers J, Voorhoeve PM, Agami R, Del Sal G. (2010) BRD7 is a candidate tumour suppressor gene required for p53 function.Nat Cell Biol. Apr;12(4):380-9.

Mullenders J, Bernards R. (2009) Loss-of-function genetic screens as a tool to improve the diagnosis and treatment of cancer.Oncogene. 17;28(50):4409-20.

Mullenders J, von der Saal W, van Dongen MM, Reiff U, van Willigen R, Beijersbergen RL, Tiefenthaler G, Klein C, Bernards R. (2009) Candidate biomarkers of response to an experimental cancer drug identified through a large-scale RNA interference genetic screen.Clin Cancer Res. Sep 15;15(18):5811-9.

Hadrup SR, Toebes M, Rodenko B, Bakker AH, Egan DA, Ovaa H, Schumacher TN. (2009). High-throughput T-cell epitope discovery through MHC peptide exchange. Methods Mol Biol. 524:383-405.

Mullenders J, Fabius AW, Madiredjo M, Bernards R, Beijersbergen RL. (2009) A large scale shRNA barcode screen identifies the circadian clock component ARNTL as putative regulator of the p53 tumor suppressor pathway. PLoS One. 2009;4(3):e4798.

Otto T, Horn S, Brockmann M, Eilers U, Schüttrumpf L, Popov N, Kenney AM, Schulte JH, Beijersbergen R, Christiansen H, Berwanger B, Eilers M. (2009) Stabilization of N-Myc is a critical function of Aurora A in human neuroblastoma. Cancer Cell. 6;15(1):67-78.

Fotheringham S, Epping MT, Stimson L, Khan O, Wood V, Pezzella F, Bernards R, La Thangue NB. (2009) Genome-wide loss-of-function screen reveals an important role for the proteasome in HDAC inhibitor-induced apoptosis.Cancer Cell. 6;15(1):57-66.

Eichhorn PJ, Gili M, Scaltriti M, Serra V, Guzman M, Nijkamp W, Beijersbergen RL, Valero V, Seoane J, Bernards R, Baselga J. (2008) Phosphatidylinositol 3-kinase hyperactivation results in lapatinib resistance that is reversed by the mTOR/phosphatidylinositol 3-kinase inhibitor NVP-BEZ235. Cancer Res. 15;68(22):9221-30.

Herold S, Hock A, Herkert B, Berns K, Mullenders J, Beijersbergen R, Bernards R, Eilers M. (2008) Miz1 and HectH9 regulate the stability of the checkpoint protein, TopBP1.EMBO J. 5;27(21):2851-61.

Huang Q, Gumireddy K, Schrier M, le Sage C, Nagel R, Nair S, Egan DA, Li A, Huang G, Klein-Szanto AJ, Gimotty PA, Katsaros D, Coukos G,Zhang L, Puré E, Agami R. (2008) The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat Cell Biol.  Feb;10(2):202-10.

Kuijl C, Savage ND, Marsman M, Tuin AW, Janssen L, Egan DA, Ketema M, van den Nieuwendijk R, van den Eeden SJ, Geluk A, Poot A, van der Marel G, Beijersbergen RL, Overkleeft H, Ottenhoff TH, Neefjes J. (2007) Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1.Nature. 29;450(7170):725-30.

Le Sage C, Nagel R, Egan DA, Schrier M, Mesman E, Mangiola A, Anile C, Maira G, Mercatelli N, Ciafrè SA, Farace MG, Agami R.(2007)Regulation of the p27(Kip1) tumor suppressor by miR-221 and miR-222 promotes cancer cell proliferation.EMBO J.  8;26(15):3699-708.

Berns K, Horlings HM, Hennessy BT, Madiredjo M, Hijmans EM, Beelen K, Linn SC, Gonzalez-Angulo AM, Stemke-Hale K, Hauptmann M, Beijersbergen RL, Mills GB, van de Vijver MJ, Bernards R. (2007) A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer.Cancer Cell. Oct;12(4):395-402.

Popov N, Wanzel M, Madiredjo M, Zhang D, Beijersbergen R, Bernards R, Moll R, Elledge SJ, Eilers M. (2007) The ubiquitin-specific protease USP28 is required for MYC stability.Nat Cell Biol. Jul;9(7):765-74.

Bernards R, Brummelkamp TR, Beijersbergen RL. (2006) shRNA libraries and their use in cancer genetics.Nat Methods. Sep;3(9):701-6. Review.

Brummelkamp TR, Fabius AW, Mullenders J, Madiredjo M, Velds A, Kerkhoven RM, Bernards R, Beijersbergen RL. (2006) An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors.Nat Chem Biol. Apr;2(4):202-6.

Nicke B, Bastien J, Khanna SJ, Warne PH, Cowling V, Cook SJ, Peters G, Delpuech O, Schulze A, Berns K, Mullenders J, Beijersbergen RL, Bernards R, Ganesan TS, Downward J, Hancock DC. (2005) Involvement of MINK, a Ste20 family kinase, in Ras oncogene-induced growth arrest in human ovarian surface epithelial cells.Mol Cell. 9;20(5):673-85.

Kolfschoten IG, van Leeuwen B, Berns K, Mullenders J, Beijersbergen RL, Bernards R, Voorhoeve PM, Agami R. (2005) A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity.Cell. 17;121(6):849-58.

Brummelkamp TR, Berns K, Hijmans EM, Mullenders J, Fabius A, Heimerikx M, Velds A, Kerkhoven RM, Madiredjo M, Bernards R, Beijersbergen RL. (2004) Functional identification of cancer-relevant genes through large-scale RNA interference screens in mammalian cells.Cold Spring Harb Symp Quant Biol. 69:439-45.

Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway.Nature. 25;428(6981):431-7.

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NRSC Staff
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NRSC Staff


Roderick Beijersbergen
-  group leader and head facility

Cor Lieftink - Bioinformaticus

Ben Morris -  Technician

Hier de link naar de carroussel

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