Stanford Core Services

Proteomics, Genomics and Imaging Resources for Translational Research @ Stanford

Protein and Nucleic Acid (PAN) Facility


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Director: Michael Eckart, PhD  (meckart@stanford.edu)
Beckman Center, B065
650.723.1907

  • Gene Expression Analysis:  Microarrays (Affymetrix), Real-time PCR, Pyrosequencing (Quantification and CpG methylation and genetic alterations), Nucleic Acid QC (Bioanalyzer).
  • DNA Sequencing
  • Oligonucleotide sequencing
  • Next-Generation Sequencing
  • Biomolecular Interaction Analysis (Surface Plasmon Resonance – Biacore)
  • Protein Sequencing
  • Peptide Synthesis
  • Protein Identification
  • Mass Spectrometry

Human Immune Monitoring Center (HIMC)


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Director: Holden T. Maecker, PhD   (maecker@stanford.edu)
Fairchild Science Building, Room D039
650.723.1671

  • Multiplex Luminex assays for cytokines
  • Immunophenotyping by flow cytometry
  • Phosho-epitope flow cytometry
  • RNA/DNA extraction and genomic assays
  • Serum and PBMC preparations and banking
  • CyTOF mass cytometry phenotyping assay

Stanford Functional Genomics Facility (SFGF)


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Director: John Coller, PhD     (John.coller@stanford.edu)
650.736.2434

  • High-throughput sequencing and library preparation for Illumina MiSeq, MiSeq, GAIIx, and HiSeq2000
  • Microarrays processing utilizing Illumina, Affymetrix, Agilent, Nimblegen, Stanford and other commercial and custom microarrays
  • Antibody phenotyping microarrays
  • Microarray production for any type of biological material (cDNA, oligonucleotides, antibodies, peptides, cells, lysates)
  • 24/7 access to equipment in the lab
  • Reagents: Antibodies, Open Biosystem products, and doping controls

Stanford University Mass Spectrometry Laboratory (SUMS)


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Director: Allis Chien, PhD
(Allis@stanford.edu)
Mudd 167A
650.723.0710

  • Proteomics: Protein identification, post-translational and synthetic modification, global proteome analysis, differential analysis and quantitative proteomics – labeled and label-free.
  • Quantitative applications and assays: Quantitation of analytes in biological matcies, pharmacokinetic studies and PK assessment, protein and peptide quantification and biomarker verification.
  • Metabolomics and drug metabolism: Primary metabolite profiling, metabolite identification, small molecule biomarker discovery and identification, lipid profiling and structural analysis.
  • General analysis: Mass determination, MS/MS, MSn, analytical scale LC-UV-MS, high resolution accurate mass MS (molecular formula confirmation)
  • Open access lab: LC-MS, GC-MS
  • Consulation, experimental design, education and informatics support for data analysis.
  • Custom projects: Method development, protein folding, non-covalent interactions.

Cell Sciences Imaging Facility (CSIF)


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Director: Jonathan Mulholland, MA (jwm@stanford.edu)
650.725.7532

  • Fluorescence microscopy services: Training and consultation in the use of confocal, deconvolution, and multi-photon for multidimentional (3D, 4D) imaging of fixed and live cell tissue samples
  • Electron microscopy services: Full service laboratory with sample preparation and training for both transmission and scanning electron microscopy technologies
  • Data management includes server storage and tape data archiving.

Stanford Center for Innovation and In-vivo Imaging (SCI3)


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Director: Tim Doyle, PhD
(tim.doyle@stanford.edu)
650.724.8250

  • Small animal imaging instrumentation for both structural and functional analyses with the capability of in vivo optical bioluminescence and fluorescence imaging, MRI, MicroCT, MicroPET, MicroSPECT, Ultrasound and Photo-acoustic imaging
  • Training and education in imaging of cellular and molecular processes for high quality image data
  • Reagents and support services for optimal in vivo analysis.
  • Data handling: 14-terabyte storage system with both RAID and tape backup.

Related Links

Calendar of Events

Med221 Course

TRAM Core Resources

Computational Resources for Translational Research @ Stanford

Philip W. Lavori PhD

Professor of Biostatistics and Statistics, and Chair, Dept. of Health Research and Policy, School of Medicine
Redwood Bldg T152a
Lavori@Stanford.edu

Area of expertise:  Clinical research (especially trials)

Nigam Shah, MBBS, PhD

Assistant Professor of Medicine (biomedical informatics
Center for Biomedical Informatics Research
MSOB, X-229
nigam@stanford.edu

Area of expertise:  Methods to analyze large unstructured data sets for data-driven medicine: medical informatics, knowledge representation, unstructured data-mining, ontologies.

Useful Websites

SPECTRUM: Bioinformatics
http://spectrum.stanford.edu/accordions/translational-informatics

Stanford Center for Biomedical Informatics Research
http://bmir.stanford.edu/

Quantitative Sciences Unit, Dept. of Medicine
http://medicine.stanford.edu/research/quantitive_welcome.html

Other Core Resources for Translational Research