NERTRN Core Facility Survey August 2008

The New England Regional Translational Research Network
Core Laboratory Survey


The New England Regional Translational Research Network (NERTRN) is a voluntary cooperative organization comprised of the University of Vermont (Richard Galbraith, MD, PhD), Dartmouth Medical School (Murray Korc, MD, PhD), the University of Massachusetts (John Sullivan, MD), the University of Connecticut (Judith Fifield, PhD), Brown University (Timothy Flanigan, MD), the Maine Medical Center Research Institute (Ken Ault, MD), and The Jackson Laboratory (Rick Woychik, PhD). The Network was formed to facilitate and enable clinical and translational research across the region. Examples of initiatives underway are attempts to build IRB reciprocity, interoperability of information services, educational and training programs, standardization of data reporting and adverse event reporting, co-recruitment of subjects for studies, and sharing of core facilities.

The attached survey specifically addresses the issues of core facilities. Please help us by taking the time to fill in this form and submitting it after which it will be routed automatically to Valerie Scott, Senior Director of Scientific Services at The Jackson Laboratory, who is coordinating our efforts to collate and publicize the core laboratories available throughout the region. When the data have been collated and analyzed, they will be distributed to each of the institutional representatives for feedback to you.

Many thanks for your help.

Richard Galbraith, MD, PhD
Chair, NERTRN
*
1. Please give us your contact information:
2. Would you be interested in accessing the following core facilities if they were accessible to NERTRN participating institutions? (Yes or No) (NERTRN CORE GROUP: note this would be the working groups recommended list)
Yes/No
Deep Sequencing Core/UMass Medical School (http://www.umassmed.edu/nemo/index.aspx) Library Services, Genomics, Bioinformatics
shRNA Library Core/UMass Medical School (http://www.umassmed.edu/shrna/index.aspx) Provides Clones
Reproductive Sciences (murine)/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Cell Culture, Stem Cell Procurement & Derivation, Tissue Culture, Transgenics, Gamete Cryopreservation
Molecular Phenotyping Sciences/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Western Blot, SDS-PAGE, RNA Integrity, RNA analysis, Real-time PCR, Proteomics, Protein Extraction, Nucleic Acid Extraction, Microarray (Affy expression & SNP-Chip), Mass Spectrometry, Flow Cytometric Analysis, DNA Analysis, Data Analysis, Cell Sorting, Cell Culture, Biochemical Analysis, 2D-PAGE
Stem Cell Core/Univ. of Connecticut Health Center (http://genetics.uchc.edu/stemcell/index.htm) Stem Cell Procurement, Cell Culture
Viral Vector Core Facility/Maine Medical Center Research Institute (http://www.mmcri.org/facility/vector.html) Recombinant viral vector
Center for X-Ray Crystallography/Univ. of Vermont (http://www.uvm.edu/sbb/cxx/cxx.html) Molecular Imaging; Single Crystal X-ray Pattern Analysis; X-Ray Crystallography
Molecular Pathology CoreCOBRE - Center for Cancer Res. Dev./Rhode Island Hospital (http://www.rih-cobre-cares.org/moleoverview.html) RNA Integrity; RNA analysis; Real-time PCR; PCR Arrays; Optical Imaging; Microscopy; Laser Capture Microdissection; Immunohistochemistry; Tissue microarray, Human tumor bank
3. Which of following Core Facilities would you be interested in accessing? (NERTRN CORE GROUP: note I would remove redundant cores based on overlap in the description of deliverables)
Yes/No
Advanced MRI Center/UMass Medical School - Functional Brain Imaging, MRI Imaging Center
Biochemical Analysis and Biorepository Core/Univ. of Vermont - Biochemical Analysis
Biochemistry Core/Univ. of Vermont (http://www.uvm.edu/~gcrc/) Assays and Measurements
Bioinformatics/U Mass Medical School (http://www.umassmed.edu/derc/bioinfo.aspx) Bioinformatics, Data Analysis, Microarray, Proteomics
Bioinformatics Core/Univ. of Vermont (http://bioinformatics.uvm.edu/) Bioinformatics
Biostatistics/Univ. of Vermont (http://vermontcancer.org/index.php?page=research-sr-biostatistics) Biostatistics
BSL-3/U Mass Medical School - Self-contained laboratory with space and equipment to handle hazardous pathogens with BL3 containment as described in the CDC/NIH publication "Biosafety in Microbiological and Biomedical Laboratories." USDA and CDC approved for research airborne viruses such as the Hong Kong chicken flu, and for select agent research.
Cell Imaging/Univ. of Vermont (http://vermontcancer.org/index.php?page=research-sr-cell-imaging) Cell Imaging
Center for X-Ray Crystallography/Univ. of Vermont (http://www.uvm.edu/sbb/cxx/cxx.html) Molecular Imaging; Single Crystal X-ray Pattern Analysis; X-Ray Crystallography
Clinical & Translational Research Support Core/U Mass Medical School (http://www.umassmed.edu/shriver/research/mrddrc/psc.aspx) participant recruitment, characterization of participants (e.g., psychological testing), participant tracking & assistance with IRB interactions (applications, amendments, progress reports, renewals, etc.)
Clinical Research Management/Univ. of Vermont (http://vermontcancer.org/index.php?page=trials-doctors) Protocol Development/Clinical Trial Coordination
Clinical Trials Unit/U Mass Medical School (http://www.umassmed.edu/ocr/ctu/index.aspx?linkidentifier=id&itemid=8890) Clinical Study Support and Resources
COBRE for Perinatal Biology - Mol bio and histology core/Women and Infants Hospital of Rhode Island (http://bms.brown.edu/COBRE/) Cell Imaging, Cell Sorting, Flow Cytometric Analysis, Immunohistochemistry, Instrumentation, Microscopy, Molecular Imaging, Optical Imaging, Real-time PCR
Computational Sciences/The Jackson Laboratory - Data Analysis, Biostatistics, Bioinformatics, Scientific Software Development
Cryo-Electron Microscopy Facility/Univ. of Vermont (http://physiology.med.uvm.edu/radermacher/) Electron Microscopy; Cryo-Electron Microscopy
Crystallography Core Facility/U Mass Medical School (http://xrayweb.umassmed.edu/) Data Collection
Cytogenetics Service (murine)/The Jackson Laboratory - F.I.S.H.
Deep Sequencing Core/U Mass Medical School (http://www.umassmed.edu/nemo/index.aspx) Library Services, Genomics, Bioinformatics
Digital Imaging Core/U Mass Medical School (http://www.umassmed.edu/digitalimages/index.aspx) Provides high resolution multi-mode, digital microscopic imaging and image analysis
DNA Analysis/Univ. of Vermont (http://vermontcancer.org/index.php?page=research-sr-dna) Molecular Imaging, DNA Analysis
Electron Microscopy Core Facility/U Mass Medical School (http://www.umassmed.edu/cemf/index.aspx) Cell Imaging, Cryo-Electron Microscopy, Molecular Imaging, Spectroscopy, Electron Microscopy
Electron Microscopy Service/The Jackson Laboratory - SEM (Scanning electron microscopy), TEM (Transmission electron microscopy), x-ray microanalysis, sample preparation
Engineering and Mathematical Sciences Research Facilities/Univ. of Vermont (http://www.uvm.edu/~cems/soe/?Page=grad/matsci/facilities.php&SM=grad/_gradmenu.html) Light Scattering, Microscopy, Rheology, Small-Angle Neutron Scattering, Spectroscopy, Thermal Analysis, Ultrasonic Imaging, X-ray Diffraction and Scattering
Experimental Pathology Translational Research Core/Univ. of Vermont (http://www.med.uvm.edu/pathology/TB1+BL.asp?SiteAreaID=560) Nucleic Acid Extraction, Microscopy, In Situ Hybridization, Immunohistochemistry, F.I.S.H.
Flow Cytometry/U Mass Medical School (http://www.umassmed.edu/facslab/index.aspx) Cell Imaging, Cell Sorting, Data Analysis, Flow Cytometric Analysis, Microscopy, Optical Imaging
Flow Cytometry/Univ. of CT Health Center - Cell Sorting, Flow Cytometric Analysis
Flow Cytometry Center/Univ. of Vermont (http://www.med.uvm.edu/research/TB1+BL.asp?SiteAreaID=566) Cell Sorting, Flow Cytometric Analysis
Flow Cytometry Facility/Univ. of Vermont (http://vermontcancer.org/index.php?page=research-sr-flow-personnel) Flow Cytometric Analysis
Flow Cytometry-Confocal Microscopy Facility/Univ. of CT (www.biotech.uconn.edu/fccmf/) Cell Imaging, Cell Sorting, Molecular Imaging, Optical Imaging
Fly Kitchen/U Mass Medical School - Media Preparation
Functional Brain Imaging Core/Univ. of Vermont (http://www.uvm.edu/~cnru/?Page=fbip.html&SM=subtrials.html) Functional Brain Imaging
General Clinical Research Center/Univ. of Vermont (http://www.uvm.edu/~gcrc) Biostatistics, Mass Spectrometry, Optical Imaging, Bioinformatics, Functional Brain Imaging, Protocol Development/Clinical Trial Coordination
Genome Sciences/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Genomics, DNA Analysis, Data Analysis Genotyping, Nucleic Acid Extraction
Genomics and Proteomics Core Facility/Brown Univ. (http://www.brown.edu/Research/CGP/index.php) Data Analysis, Flow Cytometric Analysis, Genomics, Microarray, Real-time PCR, RNA analysis, RNA Integrity, Sequencing
Genomics Core Facility/U Mass Medical School (http://www.umassmed.edu/gcf/index.aspx) Microarray, Genomics
Glass Blowing Shop/Univ. of Vermont - Glass Washing/Autoclaving; Glassblowing
Histology Core/Maine Medical Center Research Institute (http://www.mmcri.org/facility/histology.html) Immunohistochemistry, Microscopy
Histology Service/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Immunohistochemistry, Tissue Processing, Embeding, Sectioning and Staining
Human Embryonic Stem Cell Core Facility/U Mass Medical School (http://www.umassmed.edu/content.aspx?id=39860) Stem Cell Procurement, Undifferentiated stem cells; two NIH approved cell lines, H1 (male) and H9 (female), on mouse feeder layers.
Informatics Core/Univ. of Vermont (http://www.uvm.edu/~gcrc/) Data Analysis
Instrumentation and Modeling Facility/Univ. of Vermont (http://its.uvm.edu/IMF1/IMF_Home.htm) Fabrication, Instrumentation
Library (Dana Medical Library)/Univ. of Vermont (http://library.uvm.edu/dana/about/) Library Services
Library Facilities/Univ. of Vermont (http://library.uvm.edu/services/cook/) Library Services
Light and Confocal Microscopy Service/The Jackson Laboratory - Sample preparation, imaging/data capture, image analysis. Leica SP2 Multiphoton; Leica SP5 Spectral Confocal Imaging Workstations; Arcturus XT LCM
Machine Shop/U Mass Medical School (http://www.umassmed.edu/machineshop/index.aspx) Design, manufacture and repair of biomedical lab equipment
Mass Spectrometry/Univ. of Vermont (http://www.uvm.edu/~vgn/proteomics/) Single Crystal X-ray Pattern Analysis
Microarray/Univ. of Vermont (http://vermontcancer.org/index.php?page=research-sr-microarray) Microarray, Genotyping, RNA Integrity
Microscopy Imaging Center/Univ. of Vermont (http://www.med.uvm.edu/microscopyimaging/HP-DEPT.ASP?SiteAreaID=513) Cell Imaging, Immunohistochemistry; Instrumentation, Laser Capture Microdissection, Microscopy
Molecular Biology Core Lab (MBCL)/U Mass Medical School (http://www.umassmed.edu/cfar/ResourcesFacilities/Molecular_Biology_Core/index.aspx?linkidentifier=id&itemid=3204) DNA fragment analysis, Genotyping, and SPR services. UMass Oligonucleotide program.
Molecular Pathology CoreCOBRE - Center for Cancer Res. Dev./Rhode Island Hospital (http://www.rih-cobre-cares.org/moleoverview.html) RNA Integrity; RNA analysis; Real-time PCR; PCR Arrays; Optical Imaging; Microscopy; Laser Capture Microdissection; Immunohistochemistry; Tissue microarray, Human tumor bank
Molecular Phenotyping Sciences/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Western Blot, SDS-PAGE, RNA Integrity, RNA analysis, Real-time PCR, Proteomics, Protein Extraction, Nucleic Acid Extraction, Microarray (Affy expression & SNP-Chip), Mass Spectrometry, Flow Cytometric Analysis, DNA Analysis, Data Analysis, Cell Sorting, Cell Culture, Biochemical Analysis, 2D-PAGE
Morphology/U Mass Medical School (http://www.umassmed.edu/morphology/index.aspx) F.I.S.H., Immunohistochemistry, In Situ Hybridization, Microscopy
Mouse Transgenic Facility/Maine Medical Center Research Institute (http://www.mmcri.org/facility/transgenics.html) Animal Husbandry, Genotyping, Stem Cell Procurement, Transgenics mouse embryo cryopreservation and re-derivation
Necropsy Service/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Necropsy
Neuroscience COBRE - Cellular and Molecular Biology Core/Univ. of Vermont (http://www.uvm.edu/~cbmrexne/?Page=corecellularmolecular.html&SM=submenucore.html)2D-PAGE, Assays and Measurements, Cell Culture, Data Analysis, Immunohistochemistry, In Situ Hybridization, Laser Capture Microdissection, Library Services, Mass Spectrometry, Microscopy, Nucleic Acid Extraction, PCR Arrays, Protein Extraction, Proteomics, Real-time PCR, RNA analysis, SDS-PAGE, Spectroscopy, Tissue Culture, Western Blot
Neuroscience COBRE - Imaging and Physiology Core/Univ. of Vermont (http://www.uvm.edu/~cbmrexne/?Page=coreimagingphysiology.html&SM=submenucore.html) Optical Imaging
New England Center for Stroke Research (NecSTR)/U Mass Medical School - Fabrication, 3D Printer, X-ray guided surgery and vascular intervention
NMR Facility/Univ. of Vermont - 2d Spectra Acquisition and Interpretation. Spectroscopy
Nursing/Univ. of Vermont (http://www.uvm.edu/~gcrc/) Bioinformatics; Mass Spectrometry
Office of Animal Care Management/Univ. of Vermont (http://www.uvm.edu/~oacm/) Animal Husbandry; Veterinary Services
Peptide-HPLC/U Mass Medical School (http://www.umassmed.edu/peptide/contacts.aspx?linkidentifier=id&itemid=10228)Gel chromatography, HPLC, Assay Development, Amino acid analysis, Peptide-protein conjugation
Physiology Core/Univ. of Vermont (http://www.uvm.edu/~gcrc/ ) Protocol Development/Clinical Trial Coordination
Protein Core Facility/Univ. of Vermont (http://proteins.uvm.edu/) Mass Spectrometry
Proteomic Fractionation Group/U Mass Medical School (http://www.umassmed.edu/proteomic/fractionation/index.aspx?linkidentifier=id&itemid=10570) 2D-PAGE, Assays and Measurements, Biochemical Analysis, Microarray, SDS-PAGE, Western Blot
Proteomics & Mass Spectrometry Facility/U Mass Medical School (http://www.umassmed.edu/proteomic/Evans/index.aspx?linkidentifier=id&itemid=10556)Assays and Measurements, Mass Spectrometry, Protein Sequencing, Proteomics, Fatty acid analysis, Lipidomics, Metabolomics,Small molecule analysis
Proteomics Facility/Univ. of Vermont (http://www.uvm.edu/~vgn/proteomics/) Proteomics
Reproductive Sciences (murine)/The Jackson Laboratory (http://jaxservices.jax.org/index.html) Cell Culture, Stem Cell Procurement & Derivation, Tissue Culture, Transgenics, Gamete Cryopreservation
shRNA Library Core/U Mass Medical School (http://www.umassmed.edu/shrna/index.aspx) Provides Clones
Small Animal Imaging Core/U Mass Medical School - Small animal SPECT, CT and Pet Imaging
Small Molecule Screening Facility/U Mass Medical School (http://www.umassmed.edu/smsf/index.aspx) Assays and Measurements, Library Services
Stem Cell Core/Univ. of CT Health Center (http://genetics.uchc.edu/stemcell/index.htm) Stem Cell Procurement, Cell Culture
Tissue Bank Core/U Mass Medical School (http://www.umassmed.edu/cancercenter/tissuebank/index.aspx) Laser Capture Microdissection; Human tissue samples, Frozen Sections, Formalin-fixed tissue sections
Tissue Procurement Core/Univ. of Vermont
Transgenic Animal Modeling Core/U Mass Medical School (http://www.umassmed.edu/tkomouse/index.aspx) Cell Culture, Nucleic Acid Extraction, Tissue Culture, Transgenics
Transgenic Core/Brown Univ. (http://www.brown.edu/Departments/Molecular_Biology/transgenic.html ) Transgenics
Viral Vector Core Facility/Maine Medical Center Research Institute (http://www.mmcri.org/facility/vector.html) Recombinant viral vector
Votey Inhalation Facility/Univ. of Vermont - Optical Imaging, Animal exposure to particulate and soluble aerosol antigens
4. Please identify core facilities which do not appear on the list above to which you would like access.
5. What core facilities would you like to see developed across NERTRN sites?
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