Overview of current services

DNA-seqRNA-seqChIP-seq3C-MethodsProteo(geno)micsArray technologiesData IntegrationProject proposal
consultancy
ITMiscellaneous
Alignment to reference genome(s)Alignment to reference genome(s)Alignment to reference genome(s)Alignment to reference genome(s)Protein/Peptide identificationGene Expression Array analysis (Affymetrix, Illumina)DNA, RNA and protein data integrationPower calculationWeb-designUni/multivariate analysis
Clustering analysis along with projects supportQuality controlQuality controlQuality controlQuantitative proteomicsSNP-arraysExternal data ( TCGA or Encode data) integration and consultancyExperimental designDatabases design and implementationsSurvival analysis (Kaplan-Meier, Log-rank test)
Somatic SNV detectionCalculating expression levels for known/annotated genes (TPM)Allele-specific ChIP-seq analysisVisualization of resultsDifferential protein expression analysisMethylation ArraysData analysisSoftware developmentCLC-Bio Server available for data analysis
Somatic small Indel detectionClustering analysis along with project supportPeak detectionAllele-specific 4C-seq analysisDetection of mutated proteinsHigh-throughput qPCR analysisData IntegrationWeb-based data sharing and deliveryWork flow and pipeline building
Functional annotation genetic variantsMutation detection; SNP/SNV and small IndelsPeak annotation(such as motif detection)Differential enrichment 4C-seq peaksDetection of fusion gene productsData Management PlanCloud ComputingHigh-throughput primer design
Germline SNV/Indel detectionDifferential expression analysis between sample(s) and controlsDifferential Peak analysisShort term storagePanel design
Copy Number Variation analysisAlternative splicing detectionLong term storage (back-up)Clustering analysis along with project support
SV, large Indels and tandem duplications analysisGO and pathway enrichment analysisArchiving on Tape (via Anton Koning)
GO and Pathway analysis of genetic variantsAllele-specific Expression analysis
Mutational signature detectionGene set enrichment analysis (GSEA)
Clonality assessmentFusion gene detection
DNA-seq
Alignment to reference genome(s)
Clustering analysis along with projects support
Somatic SNV detection
Somatic small Indel detection
Functional annotation genetic variants
Germline SNV/Indel detection
Copy Number Variation analysis
SV, large Indels and tandem duplications analysis
GO and Pathway analysis of genetic variants
Mutational signature detection
Clonality assessment
RNA-seq
Alignment to reference genome(s)
Quality control
Calculating expression levels for known/annotated genes (TPM)
Clustering analysis along with project support
Mutation detection; SNP/SNV and small Indels
Differential expression analysis between sample(s) and controls
Alternative splicing detection
GO and pathway enrichment analysis
Allele-specific Expression analysis
Gene set enrichment analysis (GSEA)
Fusion gene detection
ChIP-seq
Alignment to reference genome(s)
Quality control
Allele-specific ChIP-seq analysis
Peak detection
Peak annotation(such as motif detection)
Differential Peak analysis
3C-Methods
Alignment to reference genome(s)
Quality control
Visualization of results
Allele-specific 4C-seq analysis
Differential enrichment 4C-seq peaks
Proteo(geno)mics
Protein/Peptide identification
Quantitative proteomics
Differential protein expression analysis
Detection of mutated proteins
Detection of fusion gene products
Array technologies
Gene Expression Array analysis (Affymetrix, Illumina)
SNP-arrays
Methylation Arrays
High-throughput qPCR analysis
Data Integration
DNA, RNA and protein data integration
External data ( TCGA or Encode data) integration and consultancy
Project proposal
consultancy
Power calculation
Experimental design
Data analysis
Data Integration
Data Management Plan
IT
Web-design
Databases design and implementations
Software development
Web-based data sharing and delivery
Cloud Computing
Short term storage
Long term storage (back-up)
Archiving on Tape (via Anton Koning)
Miscellaneous
Uni/multivariate analysis
Survival analysis (Kaplan-Meier, Log-rank test)
CLC-Bio Server available for data analysis
Work flow and pipeline building
High-throughput primer design
Panel design
Clustering analysis along with project support

DNA-seq

References:

  1. Jansen, M. P., Martens, J. W., Helmijr, J. C., Beaufort, C. M., van Marion, R., Krol, N. M., Berns, E. M. (2016).
    Cell-free DNA mutations as biomarkers in breast cancer patients receiving tamoxifen.
    Oncotarget. http://doi.org/10.18632/oncotarget.9727
  2. Yavuzyigitoglu submitted.

RNA-seq

References:

  1. Meinders, M., Kulu, D. I., van de Werken, H. J. G., Hoogenboezem, M., Janssen, H., Brouwer, R. W. W., Philipsen, S. (2015).
    Sp1 / Sp3 transcription factors regulate hallmarks of megakaryocyte maturation , and platelet.
    Blood, 125(12), 1957–1968. http://doi.org/10.1182/blood-2014-08-593343
  2. Papadopoulos P, Gutiérrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, Karkoulia E, Strouboulis J, van de Werken HJ, van der Linden R, Vandenberghe P, Dekkers DH, Philipsen S, Grosveld F, Tora L.(2015)
    TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis.
    Mol Cell Biol., Jun;35(12):2103-18. http://dx.doi.org/10.1128/MCB.01370-14

ChIP-seq

References:

  1. Meinders, M., Kulu, D. I., van de Werken, H. J. G., Hoogenboezem, M., Janssen, H., Brouwer, R. W. W., Philipsen, S. (2015).
    Sp1 / Sp3 transcription factors regulate hallmarks of megakaryocyte maturation , and platelet.
    Blood, 125(12), 1957–1968. http://doi.org/10.1182/blood-2014-08-593343

3C-Methods

References:

  1. Montes, M., Nielsen, M. M., Maglieri, G., Jacobsen, A., Højfeldt, J., Agrawal-Singh, S., … Lund, A. H. (2015).
    The lncRNA MIR31HG regulates p16INK4A expression to modulate senescence.
    Nature Communications, 6, 6967.http://doi.org/10.1038/ncomms7967
  2. Kolovos, P., van de Werken, H. J. G., Kepper, N., Zuin, J., Brouwer, R. W., Kockx, C. E., … Knoch, T. A. (2014).
    Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.
    Epigenetics & Chromatin, 7(1), 10.http://doi.org/10.1186/1756-8935-7-10
  3. van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., … de Laat, W. (2012).
    Robust 4C-seq data analysis to screen for regulatory DNA interactions.
    Nature Methods, 9(10), 969–972. article.http://doi.org/10.1038/nmeth.2173
  4. Holwerda, S. J. B., van de Werken, H. J. G., Ribeiro de Almeida, C., Bergen, I. M., de Bruijn, M. J. W., Verstegen, M. J. a. M., … De Laat, W. (2013).
    Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.
    Nucleic Acids Research, 41(14), 1–12. http://doi.org/10.1093/nar/gkt491

Proteo(geno)mics

References:

  1. Meinders, M., Kulu, D. I., van de Werken, H. J. G., Hoogenboezem, M., Janssen, H., Brouwer, R. W. W., Philipsen, S. (2015).
    Sp1 / Sp3 transcription factors regulate hallmarks of megakaryocyte maturation , and platelet.
    Blood, 125(12), 1957–1968. http://doi.org/10.1182/blood-2014-08-593343

Array technologies

References:

  1. Kurek, D., Neagu, A., Tastemel, M., Tüysüz, N., Lehmann, J., van de Werken, H. J. G., … Ten Berge, D. (2015).
    Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells.
    Stem Cell Reports, 4(1), 114–128.http://doi.org/10.1016/j.stemcr.2014.11.007
  2. Holwerda, S. J. B., van de Werken, H. J. G., Ribeiro de Almeida, C., Bergen, I. M., de Bruijn, M. J. W., Verstegen, M. J. a. M., … De Laat, W. (2013).
    Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.
    Nucleic Acids Research, 41(14), 1–12. http://doi.org/10.1093/nar/gkt491

Data Integration

References:

  1. Meinders, M., Kulu, D. I., van de Werken, H. J. G., Hoogenboezem, M., Janssen, H., Brouwer, R. W. W., Philipsen, S. (2015).
    Sp1 / Sp3 transcription factors regulate hallmarks of megakaryocyte maturation , and platelet.
    Blood, 125(12), 1957–1968. http://doi.org/10.1182/blood-2014-08-593343
  2. Kurek, D., Neagu, A., Tastemel, M., Tüysüz, N., Lehmann, J., van de Werken, H. J. G., … Ten Berge, D. (2015).
    Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells.
    Stem Cell Reports, 4(1), 114–128.http://doi.org/10.1016/j.stemcr.2014.11.007

Project proposal
consultancy

References:

  1. Philipsen, S. (2014).
    RESEARCH PROTOCOL NL47963.078.14 "Assessing fetal hemoglobin in patients on Tranylcypromine."

IT

References:

  1. CCBC Website
  2. Cancer portals
  3. EMC-OmicsDB
  4. SNPitty
  5. Mouse Xenograft Database

Miscellaneous

References:

  1. van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., … de Laat, W. (2012).
    Robust 4C-seq data analysis to screen for regulatory DNA interactions.
    Nature Methods, 9(10), 969–972. article.http://doi.org/10.1038/nmeth.2173
  2. Kolovos, P., van de Werken, H. J. G., Kepper, N., Zuin, J., Brouwer, R. W., Kockx, C. E., … Knoch, T. A. (2014).
    Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.
    Epigenetics & Chromatin, 7(1), 10.http://doi.org/10.1186/1756-8935-7-10
  3. Gilmour, J., Assi, S. a, Jaegle, U., Kulu, D., van de Werken, H., Clarke, D., … Bonifer, C. (2014).
    A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification.
    Development (Cambridge, England), 141(May), 2391–2401.http://doi.org/10.1242/dev.106054
  4. E Korpershoek. KWF Grant application.

*Status of services by the CCBC: Up and running, Under development, Will be developed upon request

Submit project proposal to CCBC

The CCBC has access to high-performance servers and has experience in processing and analyzing high-throughput omics data, see above for current services.
For CCBC assistance or computational resources, please submit your project proposal or e-mail us directly.