CDT Research Cores

The Center for Developmental Therapeutics is developing resources to support the greater research community. Our research cores include training, technical and intellectual assistance on projects, and access to potential collaborators.

All members of Seattle Children’s research community are encouraged to make use of these resources.  Comments or suggestions are welcome. 

We currently have two cores available to the community.

Luminex Core

Our Luminex Core provides access to a Luminex 200 instrument and expertise in bioassays development and analysis.  The primary users are Seattle Children’s investigators, but we welcome inquiries from external non-profit and for-profit groups.

The Luminex System is a flexible analyzer based on the principles of flow cytometry. The system capabilities include:

  • Ability to multiplex (simultaneously measure) up to 100 analytes in a single microplate well, using very small sample volumes.
  • Delivering fast and cost-effective bioassay results on many assay formats, such as nucleic acid assays, receptor-ligand assays, immunoassays and enzymatic assays.

The instrument runs MasterPlex QT v3.0 and MasterPlex CT v1.0 software, which is also convenient for data transfer and customized assay and data protocols.

User fees have been established for use of the facility. To learn more and gain access, please visit the CDT Luminex Core SharePoint or send an inquiry. Please note that this CDT Core SharePoint currently is accessible only via Seattle Children's intranet, but will soon be available externally.

Core Personnel
Faculty Oversight: Christian Roth, MD  
Facility Personnel: Kathleen Bongiovanni
Melissa Ralston
Financial Inquiries: Andrew Lowe, MPA

High-Throughput Data Analysis Core

Our High-Throughput Data Analysis Core provides state-of-the-art, specialized analyses for high-throughput data sets, including data generated by proteomic, genomic, microarray/transcriptomic, and metabolomics studies. Services include matching users to new analytical approaches, data analysis, proteomics data generation and analysis, and software development, to create data analysis tools, and to add value to biomedical research. In addition, the Core will provide consultation on experimental design for high-throughput experiments and resources for software and tools for analysis.

Core personnel can perform or assist with raw data analyses, data abstraction, and data integration. If algorithms and software are required for a project, we can provide software development and engineering. We also can guide and assist with use of existing software packages. The Core manages data structures, data flow, and databases for data-intensive projects. We also can assist with data mining and use of Web-based bioinformatics resources, including sequence analysis.

User fees have been established, but we encourage you to contact us for free consultations and to initiate collaborative work.  Inquiries should be sent to Director Eugene Kolker, PhD.

List of services

Bioinformatics

  • Sequence analysis
    • Similarity searches
    • Phylogenetic analyses
    • Functional annotation
  • EST assembly
  • Genome annotation
    • Gene prediction
    • Repeat Detection
  • Promoter analyses
    • Data visualization
  • Biomedical databases
    • Life Sciences databases
    • Disease databases

Microarray/Transcriptomics

  • Image analysis
  • QA/QC
  • Normalization
  • Statistical analysis
  • Functional analysis

Computational Analyses

  • Analysis of preliminary data
  • Experimental design for HT experiments
  • Data mining of proteomics, molecular and gene expression data
  • Computational proteomic analysis resources

Metabolomics/Lipidomics

  • Mass spectrometry (GC-MS and LC-MS)
  • Metabolites
  • Lipids
  • Differential metabolite expression profiling

Proteomics

  • Proteomics data generation
  • Mass spectrometry
    • Complex protein mixture analysis
      • 2D-LC mass spectrometry
      • Tandem mass spectrometry
    • Differential protein expression profiling

Specialized Software Development

  • Data standards, abstraction, and normalization
  • Modeling of data flows
  • Collaborative data sharing tools
  • Computational analysis pipelines