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Bruce D. Koch, PhD

These are selected core resources that are relevant to clinical and translational researchers.


Analysis of Gene/Protein Function

Identification and characterization of functional perturbants (antibody, siRNA, peptide, small molecule).

Click here for selected references.

Facility Description Contact/Location
Gene Virus Vector Core (GVVC)
Provides virus production (e.g., AAV, lentiviruses, retroviruses, and others) and associated molecular biology (e.g., plasmid construction, plasmid production, PCR, Q-PCR, mutagenesis, and others) services. contact info
Lorry I. Lokey Stem Cell Research Building, Room G1027 
High Throughput Bioscience Center (HTBC) Fully automated high-throughput screening (HTS) and high content screening of compound, genomic cDNA, and genomic siRNA libraries. Consultation and assistance for assay development, design, and analysis and for instrumentation training. Access to microplate based liquid handling equipment (SciClone ALH3000, Agilent Bravo and VPrep, Plate Washers, Reagent/Cells Dispensers), for plate replication, reformatting, reagent/cell dispensing and washing. Access to multi-mode microplate based detection equipment (AnalystGT, Flexstation and Tecan Infinite M1000 96-384-well plate readers) for fluorescence (FP, HTRF, FI, FLIPR, FRET), luminescence, and absorbance reads. Access to automated microplate imaging equipment with the ImageXpress Micro (epi-fluorescence, brightfield/phase contrast, environmental control options). contact/loc
Protein & Nucleic Acid (PAN) The Protein and Nucleic Acid (PAN) Facility is a multifaceted biotechnology fee-for-service laboratory. In Molecular Genetics the services include Gene Expression and Genotypring (Affymetrix microarray), quantitative methylation and mutation analysis (PyroMark), qPCR, DNA sequencing and fragment analysis, Nucleic Acid QC (Agilent Bioanalyzer) and Oligonucleotide synthesis. For protein characterization the laboratory offers Protein Sequencing, Peptide Synthesis, Protein Identification (MALDI) and Biomolecular interaction analysis using Surface Plasmon Resonance (Biacore). contact/loc
Stanford Functional Genomics Facility (SFGF) The Stanford Functional Genomics Facility (SFGF) provides gene expression analysis using nextgen sequencing (including single-cell analysis) or microarrays  for researchers within the Stanford community and beyond. Instrumentation includes an Illumina Hiseq 4000, Miseq500s, Miseqs, as well as a 10X Genomics Chromium.   The facility provides 24/7 access to many instruments for genomics research. We support all arrays based on a microscope slide format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, the facility can also print arrays of your material in a high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc. contact/loc
Stanford University Mass Spectrometry (SUMS) Capabilities include routine analyses such as nanoLC-MS/MS protein identification; LC-MS based amino acid analysis; mass determination of small molecules, peptides, and proteins; accurate mass determinations; LC-MS, MSn, and high-resolution MS. Custom projects encompass diverse areas of proteomics, metabolomics, metabolite identification, non-covalent interactions, and targeted quantitation; examples include characterization of post-translational modifications, identification of protein binding partners, proteomic and metabolomic profiling, and biomarker verification. contact/loc
Transgenic, Knockout and Tumor Model Center (TKTC) Mouse models for gene of interest: transgenic mouse production; targeted ES cell clone production; chimeric mouse production; sperm/embryo cryopreservation; strain rederivation; xenograft tumor models; drug dosing; toxicity studies. contact/loc

Databases

Model organism sequence data. Extensive collection of gene expression data. Genetic markers of drug metabolism and efficacy.

Click here for selected references.

Facility Description Contact/Location
Aspergillus Genome Database (AspGD) The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. contact info

location
Candida Genome Database (CGD) The Candida Genome Database provides free online access to data, including genomic sequence and manually curated functional information, about genes and proteins of the human pathogen Candida albicans and related species. contact info

location
The Pharmacogenomics Knowledgebase (PharmaGKB) PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. contact/loc
Saccharomyces Genome Database (SGD) SGD is an organized collection of genetic and molecular biological information about Saccharomyces cerevisiae, bakers' and brewers' yeast. It contains the sequences of yeast genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; links to literature information; links to functional genomics datasets; and tools for analysis and comparison of sequences. contact/loc

FACS

Single cell analysis and sorting of cells in suspension.

Click here for selected references.

Facility Description Contact/Location
Fluorescence Activated Cell Sorting Facility (FACS) There are 9 sorters (plus the 4 analyzers) in the main lab, with an additional sorter and analyzer (two machines) out the satellite facility at 1651 Page Mill Road.  In the main lab, there is also a CyTOF for very high dimensional cell analysis.

contact info

location

Gene Expression Profiling, Genotyping & Genomic Analysis

DNA sequencing (standard long reads: 500-750bp or Nextgen: 18-150bp), microarrays, qPCR)

Click here for selected references.

Facility Description Contact/Location
Protein and Nucleic Acid Facility (PAN) The Protein and Nucleic Acid (PAN) Facility is a multifaceted biotechnology fee-for-service laboratory. In Molecular Genetics the services include Gene Expression and Genotypring (Affymetrix microarray), quantitative methylation and mutation analysis (PyroMark), qPCR, DNA sequencing and fragment analysis, Nucleic Acid QC (Agilent Bioanalyzer) and Oligonucleotide synthesis. For protein characterization the laboratory offers Protein Sequencing, Peptide Synthesis, Protein Identification (MALDI) and Biomolecular interaction analysis using Surface Plasmon Resonance (Biacore).  contact/loc
Genome Sequencing Service Center The Sequencing Service Center (SSC) allows the Stanford community to access cost-effective high throughput sequencing, performed at the Stanford Center for Genomics and Personalized Medicine. Our goal is to facilitate small to medium-sized projects that are best served by modest numbers of sample submissions from individual users, and that are billed on a per-lane basis.  contact/loc
Stanford Functional Genomics Facility (SFGF) The Stanford Functional Genomics Facility (SFGF) provides gene expression analysis using nextgen sequencing (including single-cell analysis) or microarrays  for researchers within the Stanford community and beyond. Instrumentation includes an Illumina Hiseq 4000, Miseq500s, Miseqs, as well as a 10X Genomics Chromium.   The facility provides 24/7 access to many instruments for genomics research. We support all arrays based on a microscope slide format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, the facility can also print arrays of your material in a high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.  contact/loc

Genomics Services Overview

Enabling Technology Cores Supporting Genomics at Stanford.

Sequencing

There are three steps in a sequencing-based experiment:

1.  Nucleic acid extraction and library preparation- This list assumes that you are starting with cells, tissues, or paraffin sections. The centers listed may not be able to perform the entire workflow in-house, but they are able to perform the initial steps and will guide you through the rest of the workflow. 

See list of Library Prep Services.

2. Sequencing

Instrumentation Reads
(Millions)
Protein & Nucleic Acid (PAN) Genome Sequencing Service (GSSC) Stanford Functional Genomics Facility (SFGF)
Illumina Miseq 25 X X X
Illumina GAIIx 50     X
Illumina Hiseq 2000 200   X  
Illumina Hiseq 4000 600   X X
Illumina Nextseq 400     X
Qiagen PyroMark Q24 96 parallel
single
clones
X    
Sanger sequencing Single
clone
X    

3. Data Analysis - (See also Illumina Basespace).

See list of tools.

Other Genomics Technologies

Service Protein & Nucleic Acid (PAN) Stanford Functional Genomics Facility (SFGF)
Human Whole Genome Gene Copy Number (Microarray)   X
Gene Expression Analysis: Microarray X X
Focused Gene Expression Analysis: qPCR X X
Highly Mulitiplexed Gene Expression Analysis: NanoString   X
Quantitation of SNPs (Qiagen PyroMark Q24) X  
Quantitation of SNPs (OpenArray RT-PCR)   X
Oligonucleotide synthesis X  

Informatics

From site-licensed software for basic research to massively-parallel computing power to handling clinical research data.

Click here for selected references.

Facility Description Contact/Location
Computational Service and Bioinformatics Facility (CSBF)

Computer resources for biomedical research at Stanford. Membership access to computer hardware; Mac, PC, and UNIX software; consulting; and workshops.

contact/loc
Data Coordinating Center (DCC) The Data Coordinating Center (DCC) provides services to members of the School of Medicine related to managing data of ongoing or new research projects. We specialize in the planning, development, management, and secure implementation of systems to achieve project goals in a technologically modern environment. In particular, we have expertise in integrating advanced statistical and bioinformatics tools in a technologically modern environment.  contact/loc
Parallel Computing (Sherlock) The Bio-X Parallel Computing Cluster is currently closed to new users.  However, high performance computing is available on the Sherlock Cluster.  contact info

Stanford Center for Clinical Informatics The Stanford Center for Clinical Informatics is a resource center for researchers’ data needs. In addition to being the official conduit of clinical data for research purposes, we offer expert advice on best practices in data management, hands-on assistance with our recommended data management framework REDCap, a suite of self-service tools for cohort identification and chart review, and a variety of other software and clinical research data related services, including real time clinical research alerting and HIPAA compliance advice and guidance. For informatics help with your clinical research, schedule a free consultation at https://clinicalinformatics.stanford.edu/ contact info/loc
HANA Immersive Visualization Environment (HIVE) The HIVE is a scientific visualization wall that is 10 feet tall and 24 feet wide with 13440X5400 resolution.

contact info

Huang Building, Suite B050

Genetics Bioinformatics Service Center Stanford Genetics Bioinformatics Service Center was set up in summer of 2013 to provide for the growing needs of Big Data genetics research at Stanford. GBSC provides best-in-class computational infrastructure for ultra high throughput high performance workload for genomics and related research. The current infrastructure has over 1000 cores, 2 petabytes of storage and offers over 50 software tools, several of which are commercially licensed. This infrastructure serves over 300 researchers and covers a wide range of research including non-mammalian and microbial genomes, basic science research like ENCODE, human variant analysis, cancer research and personalized medicine, integrative omics profiling, evolutional biology and population genetics. GBSC team comprise of BS/MS/PhDs in variety of computational fields including Computer Science, BioMedical Engineering, Computational Physics and Bioinformatics and represent over 50 years of professional experience in solving complex scientific and software problems. The team brings a suite of expertise in Next Generation Sequencing bioinformatics data analysis and software development. The team has successfully delivered on a variety of projects including large scale sequencing center data analysis, laboratory management systems, and development of cutting edge variant and cancer genomics analysis pipelines.

contact info

The computational cluster: Forsythe Hall Data Center, 275 Panama Street, Stanford, CA. Bioinformatics team: SoM Technology and Innovation Park, 3165 Porter Drive, Palo Alto, CA.

Imaging

MRI, CT, PET, SPECT, luminescence and fluorescence whole animal imaging, ultrasound, live animal and tissue-slice two-photon confocal microscopy, inverted microscope confocal imaging, deconvolution widefield microscopy, SEM, TEM.

Click here for selected references.

Facility Description Contact/Location
Animal Histology Services The Department of Comparative Medicine's Animal Histology Services (AHS) provides a broad range of histological techniques that include standard processing and embedding methods as well as processing of larger specimens, serial and step sectioning, sectioning of frozen specimens, and a variety of staining techniques. contact/loc
Cell Sciences Imaging Facility (CSIF) Microscopy: advanced, high resolution light and electron microscopy services. Confocal, multi-photon, and deconvolution wide-field microscopy for live cell/tissue and fixed samples. Transmission (TEM) and scanning electron microscopy (SEM) imaging and EM sample preparation.

contact info

Beckman B050, B051, B001 
&
SOE Shriram Center CSIF, B023

Human Pathology Histology Service Center Provides routine paraffin embedding, sectioning, staining (including special stains), cryosectioning, tissue microarrays, immunohistochemistry, and digital slide imaging for human tissue specimens. contact/loc
Lucas Center for Imaging Apply medical imaging technology to fundamental physiologic and patho-physiologic studies involving humans and animal models. Advance medical imaging technology to improve health and patient care. Provide educational opportunities to researchers, clinicians, and students. Serve the academic and industrial community. Whole Body Imaging for humans and animal models. Equipment includes: Two 3.0 Tesla MRI systems, 7.0 Tesla MRI system and Fluoro Suite.

contact info

location

Neuroscience Microscopy Service 2-photon microscopy: both in vivo and tissue slice imaging and photoactivation. Confocal microscopy: time-lapse confocal imaging with environmental control, spectral imaging, and standard fixed-tissue imaging. Fluorescence microscopy: array tomography data acquisition and analysis. Image analysis: high-end, dual quad-core image analysis workstations with 24 GB memory and 3D graphics cards, Imaris (3D visualization and rendering), NeuroLucida (process tracing and quantification), Matlab (general number-crunching, image analysis) and ImageJ (general biological image analysis) software packages. contact info/loc
PET/MRI Metabolic Service Center (PMMSC) The PET/MRI Metabolic Service Center (PMMSC) houses a state of the art simultaneous whole-body PET/MRI scanner and a carbon-13 hyperpolarizer device. contact info
Stanford Center for Cognitive and Neurobiological Imaging (CNI) The Stanford Center for Cognitive and Neurobiological Imaging (CNI) is a shared facility, dedicated to research and teaching. The Center provides resources for researchers and students used in cognitive and neurobiological sciences.
Discoveries about the brain have implications for fields ranging from Business, Law, Psychology, and Education. The Stanford Center for Cognitive and Neurobiological Imaging (CNI) supports scientific investigations into the brain that make rigorous connections between neuroscience and society.
 contact info

location
Stanford Center for Innovation and In Vivo Imaging (SCi3) The Stanford Center for Innovation in In Vivo Imaging (Sci^3) is a small animal imaging facility that allows non-invasive studies on animals such as mice and rats. In addition to instruments routinely used in the clinic, such as ultrasound, microCT, microPET, microSPECT/CT and MRI (each optimized for animal research), the facility also has instruments to investigate bio-distribution of molecular imaging probes such as GFP, fluorescent markers and bioluminescent proteins in these animals. Access to surgical benches and supplies is available. Instrument training is provided for free during regular sessions, which are posted through an email service. In addition, full computer support and data archiving is provided to investigators.  contact info

Clark Center S040
&
2nd location

Nanotechnology

Including nanofabrication of reagents and devices for biomedical research.

Click here for selected references.

Facility Description Contact/Location
Stanford Nano Center (SNC) The Stanford Nano Center (SNC) shared facilities include some of the most advanced nanoscale patterning and characterization equipment available, complementing the nearby Stanford Nanocharacterization Lab (SNL) and Stanford Nanofabrication Facility (SNF). Much of the space is specifically designed to provide for the stringent requirements on the control of vibration, acoustics, and electromagnetic interference that are essential for the manipulation of matter down to the molecular and atomic scale. The instruments are available to internal Stanford users as well as external users from industry and academia.
contact info

location
Stanford Nanocharacterization Laboratory (SNL) The Stanford Nanocharacterization Laboratory (SNL) provides modern facilities for the characterization of materials. Instruments include high-resolution electron microscopes, X-ray diffractometers, and surface science analytical instruments. The instruments are available to internal Stanford users as well as external users from industry and academia.

contact info

location

Stanford Nanofabrication Facility (SNF) Equipped with a broad spectrum of fabrication and process tools, SNF is designed to be a "sand-box" for nano- science and engineering researchers.  contact/loc

Neurobehavior

Animal models of human behavior, including disease models, and human behavioral testing.

Click here for selected references.

Facility Description Contact/Location
Stanford Behavioral and Functional Neuroscience Lab (SBFNL) Stanford behavioral and functional neuroscience laboratory (SBFNL) will provide expertise in all aspects related to the design and implementation of behavioral experiments as well as data analysis and interpretation. The core is fully equipped to accommodate a full battery of behavioral tests relevant to learning and memory, sensory gating, place/fear conditioning, motor function, nociception, and anxiety-related behaviors. We are specialized in genetic and pharmacological phenotyping in both mouse and rat. In addition the center provides expertise in an array of acute and chronic experimental models of neurodegenerative disorders such as stroke and ischemic brain injury.  contact/loc
Stanford Cognitive and Systems Neuroscience Laboratory The main goals of our research are to (1) discover fundamental principles underlying normal brain and cognitive development, (2) develop brain-based evidence and interventions to improve cognitive skills in children with learning disabilities, and (3) investigate atypical development of cognitive, affective and social information processing systems in children with autism. We use advanced brain imaging techniques (fMRI, sMRI, DTI and EEG) as well as behavioral, genetic and computational methods in our research. Populations currently under investigation include normal healthy children, adolescents and adults, children with learning disabilities and children with autism.  contact/loc

Patient Sample Analysis

Resources for supplying and analyzing anonymized patient samples.

Click here for selected references.

Facility Description Contact/Location
Fluorescence Activated Cell Sorting Facility (FACS) There are 9 sorters (plus the 4 analyzers) in the main lab, with an additional sorter and analyzer (two machines) out the satellite facility at 1651 Page Mill Road.  In the main lab, there is also a CyTOF for very high dimensional cell analysis. contact info

location
Human Immune Monitoring Core (HIMC) Analysis of clinical samples by: multiplexed immunoassays (Luminex and MesoScale Discovery); flow cytometry immunophenotyping, phosphoepitope analysis, and intracellular cytokine staining, by fluorescence and mass cytometry (CyTOF); capillary nanoimmunoassay (NanoPro); and genomic assays including microfluidic qPCR (Fluidigm BioMark). contact info

Fairchild D033 (Immunoassays and Flow Cytometry) and CCSR 0128 (Genomics and NanoPro) 
Stanford Blood Center (Part of the Stanford University School of Medicine) The Stanford Blood Center provides de-identified blood components and blood byproducts from healthy donors for in vitro investigational use, as well as phlebotomy services. The Stanford Administrative Panel for Human Research has approved these activities.

Depending on your needs, we can collect tubes or whole units of blood from individuals selected by the researcher or recruited by the Stanford Blood Center based on special criteria (e.g. HLA type, CMVsero status, red cell antigen, etc.).

We can provide anything from leukocytes (buffy coat from whole blood, residual leukocytes), plasma (frozen or liquid), platelets, red blood cells, to whole blood. We can also customize your products with irradiation, leukoreduction, or other product manipulation, or by modifying the collection procedure to fit your needs.
contact/loc
Stanford Functional Genomics Facility (SFGF) The Stanford Functional Genomics Facility (SFGF) provides gene expression analysis using nextgen sequencing (including single-cell analysis) or microarrays  for researchers within the Stanford community and beyond. Instrumentation includes an Illumina Hiseq 4000, Miseq500s, Miseqs, as well as a 10X Genomics Chromium.   The facility provides 24/7 access to many instruments for genomics research. We support all arrays based on a microscope slide format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, the facility can also print arrays of your material in a high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.  contact/loc
Tissue Bank (Pathology Tissue Bank) Activities and services include collecting and banking freshly-frozen tissue specimens for viable cell studies, processing and banking blood components, maintaining a tissue database and coordinating patient consent and assuring regulatory compliance. contact/loc
Translational Applications Service Center (TASC)

The Translational Applications Service Center (TASC) Program is designed to focus on removing barriers and communication gaps between scientists and the clinicians. Our initiatives include research facilities and pilot grants that support translational projects of faculty, clinical fellows and students. The program also fosters education by organizing a series of seminars, symposia and an annual retreat.

Our program is interested in all phases of translational research, as well as both directions of translation (from bench to bedside and from bedside to bench) and also in the extension to the population level. TASC provides:
      –  Clinical Specimen Processing
      –  Sample Preparation
      –  Tissue Banking and Clinical Sample Storage
      –  Cell Culture Facility
      –  Laboratory Bench Space Use
      –  Methods and Assay Development
      –  Data Analysis and Consulting
      –  very small scale analysis of protein expression and modification using
          Nanoimmunoassay

 contact/loc

Preclinical Translational Services

High throughput screening, compound formulation, and pharmacokinetic analysis.

Click here for selected references.

Facility Description Contact/Location
High Throughput Bioscience Center (HTBC) Fully automated high-throughput screening (HTS) and high content screening of compound, genomic cDNA, and genomic siRNA libraries. Consultation and assistance for assay development, design, and analysis and for instrumentation training. Access to microplate based liquid handling equipment (SciClone ALH3000, Agilent Bravo and VPrep, Plate Washers, Reagent/Cells Dispensers), for plate replication, reformatting, reagent/cell dispensing and washing. Access to multi-mode microplate based detection equipment (AnalystGT, Flexstation and Tecan Infinite M1000 96-384-well plate readers) for fluorescence (FP, HTRF, FI, FLIPR, FRET), luminescence, and absorbance reads. Access to automated microplate imaging equipment with the ImageXpress Micro (epi-fluorescence, brightfield/phase contrast, environmental control options).  contact/loc
Medicinal Chemistry Core The Director, Dr. Mark Smith, is Medicinal Chemist with industry experience in Drug Discovery. Mark can help biologists and clinicians at Stanford incorporate medicinal chemistry into ongoing and/or future research endeavors including: the design and execution of small molecule syntheses relevant to a research project; co-mentoring an undergraduate, predoctoral, or postdoctoral researcher in a faculty member’s lab who aspires to use medicinal chemistry approaches in their research; and collaborating with faculty toward the development of one or more specific aim(s) in their grant proposals where medicinal chemical expertise is required.

 In the near future, the Institute will help Mark set up a rudimentary chemical laboratory, where he will be able to pursue hands-on research on behalf of his collaborators.  Currently the most effective way for faculty to make use of Mark’s expertise in furthering their research may be through co-mentoring of a student or postdoc. Alternatively, Mark can design and have custom-synthesized small molecules which can become tools for better understanding of biological systems.

contact info

location

Stanford Behavioral and Functional Neuroscience Lab (SBFNL) Stanford behavioral and functional neuroscience laboratory (SBFNL) will provide expertise in all aspects related to the design and implementation of behavioral experiments as well as data analysis and interpretation. The core is fully equipped to accommodate a full battery of behavioral tests relevant to learning and memory, sensory gating, place/fear conditioning, motor function, nociception, and anxiety-related behaviors. We are specialized in genetic and pharmacological phenotyping in both mouse and rat. In addition the center provides expertise in an array of acute and chronic experimental models of neurodegenerative disorders such as stroke and ischemic brain injury. contact info
Stanford Biomaterials and Advanced Drug Delivery Laboratory (BioADD) Stanford Biomaterials and Advanced Drug Delivery Laboratory (bioADD) is a cutting edge research facility located at Stanford University . Today’s problems in drug design require complex answers to achieve effective delivery and treatment. The Stanford BioADD Laboratory helps to solve these problems with advanced modern technology and innovative solutions. Specializing in the creation of biomaterials and drug delivery agents, the laboratory lends its expertise toward designing drug formulations and developing smart materials for biomedical applications. contact/loc
Stanford University Mass Spectrometry (SUMS) Capabilities include routine analyses such as nanoLC-MS/MS protein identification; LC-MS based amino acid analysis; mass determination of small molecules, peptides, and proteins; accurate mass determinations; LC-MS, MSn, and high-resolution MS. Custom projects encompass diverse areas of proteomics, metabolomics, metabolite identification, non-covalent interactions, and targeted quantitation; examples include characterization of post-translational modifications, identification of protein binding partners, proteomic and metabolomic profiling, and biomarker verification.
contact/loc

Proteomics

Analysis of tissue samples, QC of purified proteins.

Click here for selected references.

Facility Description Contact/Location
Protein & Nucleic Acid Facility (PAN) The Protein and Nucleic Acid (PAN) Facility is a multifaceted biotechnology fee-for-service laboratory. In Molecular Genetics the services include Gene Expression and Genotypring (Affymetrix microarray), quantitative methylation and mutation analysis (PyroMark), qPCR, DNA sequencing and fragment analysis, Nucleic Acid QC (Agilent Bioanalyzer) and Oligonucleotide synthesis. For protein characterization the laboratory offers Protein Sequencing, Peptide Synthesis, Protein Identification (MALDI) and Biomolecular interaction analysis using Surface Plasmon Resonance (Biacore). contact/loc
Stanford University Mass Spectrometry (SUMS) Capabilities include routine analyses such as nanoLC-MS/MS protein identification; LC-MS based amino acid analysis; mass determination of small molecules, peptides, and proteins; accurate mass determinations; LC-MS, MSn, and high-resolution MS. Custom projects encompass diverse areas of proteomics, metabolomics, metabolite identification, non-covalent interactions, and targeted quantitation; examples include characterization of post-translational modifications, identification of protein binding partners, proteomic and metabolomic profiling, and biomarker verification. contact/loc

Structural Biology

Resources for the determination of three dimensional protein structure.

Click here for selected references.

Facility Description Contact/Location
ChEM-H Macromolecular Structure Knowledge Center The Macromolecular Structure Knowledge Center (MSKC) aims to provide scientific expertise and state-of-the-art equipment for the production, purification, and characterization of biological macromolecules.

contact info

location

Stanford Synchrotron Radiation Lightsource (SSRL) SSRL is a Department of Energy Office of Science user facility that provides synchrotron radiation facilities used to study our world at the atomic and molecular level, leading to advances in drug discovery, medicine, energy production, environmental remediation, nanotechnology and new materials. The facility supports (with instrumentation and staff) researchers using macromolecular crystallography, small-angle x-ray scattering, x-ray imaging and microscopy, x-ray absorption spectroscopy, and scattering techniques, among others. Access is obtained by submitting a proposal and is provided at no charge for scientists who conduct non-proprietary research, with the understanding that significant results are to be publicly disseminated.  contact/loc

Veterinary Services & Animal Models

Animal husbandry and veterinary care. Generation of animal models. Testing the effect of perturbants and/or genetic changes in behavioral, disease, and pharmacological models.

Click here for selected references.

Facility Description Contact/Location
Animal Histology Services The Department of Comparative Medicine's Animal Histology Services (AHS) provides a broad range of histological techniques that include standard processing and embedding methods as well as processing of larger specimens, serial and step sectioning, sectioning of frozen specimens, and a variety of staining techniques.
contact/loc
Fly Facility Fly food and media for various School of Medicine labs: fly bottle; dextrose rack; molasses rack; fly cage; small, medium, large, and xl caps; fly house collection; seeded bottles.  contact/loc
Stanford Behavioral and Functional Neuroscience Lab (SBFNL) Stanford behavioral and functional neuroscience laboratory (SBFNL) will provide expertise in all aspects related to the design and implementation of behavioral experiments as well as data analysis and interpretation. The core is fully equipped to accommodate a full battery of behavioral tests relevant to learning and memory, sensory gating, place/fear conditioning, motor function, nociception, and anxiety-related behaviors. We are specialized in genetic and pharmacological phenotyping in both mouse and rat. In addition the center provides expertise in an array of acute and chronic experimental models of neurodegenerative disorders such as stroke and ischemic brain injury.  contact/loc
Transgenic, Knockout and Tumor Model Center (TKTC) Mouse models for gene of interest: transgenic mouse production; targeted ES cell clone production; chimeric mouse production; sperm/embryo cryopreservation; strain rederivation; xenograft tuomr models; drug dosing; toxicity studies.  contact/loc
Veterinary Service Center (VSC)

The Veterinary Service Center assures that the use of animals is humane and complies with all relevant policies and legal requirements. The functions of the VSC include:

  • provision of animal husbandry services
  • provision of veterinary care
  • Animal Diagnostic Lab
  • Animal Pathology/Histology Services
  • oversight of animal holding areas including laboratories where animal procedures are performed
  • procurement, acquisition, and exportation of animals for research and teaching
  • provision of technical services, training, and specialized facilities and equipment to facilitate animal research
contact info

location

Other

Biomedical research supplies, photography and graphic arts, and a machine shop.

Click here for selected references.

Facility Description Contact/Location
Chemistry NMR Facility The NMR Facility for the Stanford University Chemistry Department houses 5 Varian NMR Spectrometers: Inova 300, Varian 400, Mercury 400, Inova 500, Inova 600.

contact info

Stauffer Chemistry Building 

Chemistry Optics Facility The Optics Facility for the Stanford University Chemistry Department houses 4 Optical Spectroscopy Instruments: Cary 6000i UV/Vis/NIR Spectrometer, Vertex 70 FTIR with RAM II Raman accessory, and two Fluorolog 3 Fluorimeters.

contact info

Stauffer Chemistry Building

MCP-SINTN Engineering Shop This shop is dedicated to assisting researchers in the Medical School with their custom instrumentation and equipment needs at an affordable price contact/loc
Stanford Microfluidics Foundry This facility assists in the design and fabrication of Silicon replica molds and PDMS microfluidic chips. contact info