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| DNA Analysis Facility on Science Hill Yale University 21 Sachem Street ESC Room 150 New Haven, CT 06511 (203) 432-7394 dnanalysis@yale.edu View Website Primary Contact: Carol Mariani (203) 432-7394 carol.mariani@yale.edu | Services offered: DNA Analysis DNA Sequencing Genotyping Sequencing | Medium Throughput Facility offering DNA Sequencing and Fragment Analysis for AFLP's, microsatellites. Our staff is especially knowledgable in the fields of Conservation & Population Genetics, therefore we can offer troubleshooting help to our customers from the lab bench through data analysis. |
| Flow Cytometry University of Connecticut Health Center CT (860) 679-3463 pizzo@nso1.uchc.edu | Services offered: Cell Sorting Flow Cytometric Analysis Associations: NERTRN |
Fully equipped flow cytometry facility housing a FACSVantage SE, FACSAria, 2-BD LSR II, 3- FACSCaliburs http://flowcytometry.uchc.edu |
| Flow Cytometry/Confocal Microscopy Facility University of Connecticut Unit 3149 91 N. Eagleville Road Storrs, CT 06269-3149 (860) 486-3080 carol.norris@uconn.edu View Website Primary Contact: Carol Norris carol.norris@uconn.edu | Services offered: Cell Imaging Cell Sorting Molecular Imaging Optical Imaging Associations: NERTRN | The FCCM Facility was developed to assist investigators with the use of several different sophisticated instruments designed to detect and measure fluorescent light emission. A BD FACSCalibur flow cytometer is available for analysis of cells and particles from each other based on size, internal complexity, and/or up to four different fluorescent signals. Cells labeled either internally or externally with fluorescent antibodies, calcium or pH specific probes, fluorescent proteins, or with DNA specific probes and dyes. Cells or particles can also be aseptically sorted to obtain pure populations for either further analysis or subsequent culture. A Leica SP2 laser scanning confocal microscope and an automated Zeiss Axiovert 200M driven by OpenLab software are available for imaging of live or fixed cells or other fluorescent materials. A spinning disk confocal and TIRF microscopy system will be added to the facility in 2008. |
| University of Connecticut Stem Cell Core University of Connecticut Health Center 263 Farmington Ave. MC-3301 Farmington, CT 06030-3301 (860) 679-8380 ucscicore@uchc.edu View Website | Services offered: Cell Culture Stem Cell Procurement Associations: NERTRN |
The mission of the UConn Stem Cell Core (UCSCC) is to support human embryonic stem cell (HESC) research, with special attention to Connecticut and the neighboring region. These are our primary services: 1. Culture and bank HESCs 2. Provide HESC culture training and technical support 3. Provide HESCs to UCSCC users 4. Track and quality control HESCs 5. Validate reagents for HESC culture 6. Derive new HESCs and make them available to UCSCC users |
| Biomolecular Core Laboratory Nemours Center for Pediatric Research Alfred I duPont Hospital for Children 1600 Rockland Rd Wilmington, DE 19899 (302) 651-6712 mbcore@nemours.org View Website Primary Contact: Dr. Katia Sol-Church (302) 651-6705 ksolchur@nemours.org | Services offered: DNA Sequencing Genomics Genotyping Instrumentation PCR Arrays Real-time PCR Pyrosequencing, Forensics Associations: NERTRN | Statement of purpose: A resource for the staff of the Alfred I. duPont Hospital for Children, Nemours affiliates, COBRE / INBRE investigators and outside customers, the Biomolecular Core Laboratory is a centralized, state-of-the-art facility that offers expertise in molecular genetics and genomics. The service lab is run according to the policies set forth by the federal CLIA standards to provide high data integrity and to maintain appropriate safeguards for patient confidentiality. |
| Delaware Biotechnology Institute University of Delaware 15 Innovation Way Newark, DE 19711 (302) 831-3456 oneal@dbi.udel.edu View Website Primary Contact: Douglas O'Neal | Services offered: Bioinformatics Associations: NERTRN | The DBI Bioinformatics Core provides computational resources to the research institutions in Delaware. Facilities include a 270-core linux compute cluster, a relational database cluster, and an immersive visualization environment. Staff are available to consult with usage of the installed software, web site design, data storage infrastructure, and scientific programming. |
| Sequencing and Genotyping - Allen Laboratory University of Delaware Townsend Hall 045, 531 S. College Ave. Newark, DE 19716 (302) 831-0823 brucek@udel.edu View Website Primary Contact: Bruce Kingham brucek@udel.edu | Services offered: DNA Analysis DNA Sequencing Genotyping Nucleic Acid Extraction Real-time PCR RNA Integrity Sequencing Associations: NERTRN |
The DNA Sequencing & Genotyping Center provides state of the art genetic analysis for University of Delaware research groups and outside users on a fee-for-service basis. The Applied Biosystems 3130XL Genetic Analyzer housed in the center is a state-of-the-art capillary-based instrument capable of moderate- to high-throughput DNA sequencing and fragment analysis (up to 656 samples/day). The center is currently operating the Genome Analyzer II from Illumina. This platform is massively parallel genome sequencer capable of 6 GB of output for a single run. |
| Advanced MRI Center UMass Medical School 55 Lake Ave North SA 107F Worcester, MA 01655 (508) 856-1096 mitchell.albert@umassmed.edu Primary Contact: Mitchell Albert (508) 856-1096 mitchell.albert@umassmed.edu | Services offered: Functional Brain Imaging MRI Imaging Center Associations: NERTRN | The new research dedicated MRI center includes a 3T Philip’s human whole body MRI system for human and animal research, clinical support space, as well as laboratory and office space. Specific areas of research include, but are not limited to, fMRI, cardiac MRI, interventional MRI, and Hyperpolarized Gas MRI. |
| Bioinformatics UMass Medical School 373 Plantation Street Worcester, MA 01605 (508) 856-1302 juerg.straubhaar@umassmed.edu View Website Primary Contact: Juerg Straubhaar (508) 856-1302 juerg.straubhaar@umassmed.edu | Services offered: Bioinformatics Data Analysis Microarray Proteomics Associations: NERTRN |
Purpose Bioinformatics is at the interface between biology, informatics, and mathematics. Using methods from computer science, we analyze and interpret biological data in the form of gene sequences and cellular proteins, contributing new knowledge about the functioning of cells and living organisms. To DERC investigators, the Bioinformatics Core provides help and support in storing, visualizing, and analyzing biological data. Services Microarray and proteomics experimental design, data acquisition, management and analysis Analysis of microarray experiments Data mining and integration with public data resources Statistical genetics and SNP analysis Analysis pipeline scripting Analysis of promoter sequences for transcription factor binding sites Comparative genomics Life science focused web-based database development |
| Biopolymers Facility Harvard Medical School NRB088 77 Avenue Louis Pasteur Boston, MA 02115 (617) 432-7480 director@genome.med.harvard.edu View Website Primary Contact: Robert Steen director@genome.med.harvard.edu | Services offered: DNA Analysis DNA Sequencing Genomics Genotyping Microarray Nucleic Acid Extraction oligo synthesis Real-time PCR RNA analysis Sequencing Next Generation DNA Sequencing Associations: NERTRN |
About the BPF The Biopolymers Facility is a non-profit technology service center in the Department of Genetics at Harvard Medical School. The investigators at Harvard Medical School make up the primary client base of the BPF. Through the University's partnerships with surrounding Hospitals and research organizations we also serve labs throughout the entire Longwood Medical Area (LMA). While the majority of our users are from the LMA we also serve labs at schools, universities and biotechnology companies from all across the country. Our mission is to provide investigators with access to technology services that will help them speed along their research programs while conserving both time and money by not having to conduct the experiments within their own labs. In addition, we provide a wide variety of the most popular reagents and supplies for immediate pick up from our facility, in an effort to decrease the amount of time it takes to go from an idea to an experiment while simultaneously saving research funds through bulk pricing agreements and no shipping charges. We strive to provide high quality data and a rapid turn around time for all samples. Services offered include DNA Sequencing, Next-Generation DNA Sequencing (Illumina Genome Analyzer), Genotyping, Affymetrix Gene Chips, DNA Prep, Oligonucleotide Ordering and Reagents and Supplies Ordering. We have a comprehensive web based Laboratory Information Management System (LIMS) which provides our users with access to order services and supplies as well as retrieve data and review and pay invoices. ---- Reagents and Supplies Stock Room Program.PCR services. |
| BSL-3 UMass Medical School 55 Lake Ave North LRB 303 Worcester, MA 01655 (508) 856-2646 hardy.kornfeld@umassmed.edu Primary Contact: Hardy Kornfeld | Services offered: Secure enviorment to work in Associations: NERTRN | The BL3 Core Lab is a campus-wide facility for safe or moderate risk pathogens in vitro. It is a 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”. The lab has been specifically approved by the USDA and CDC for research airborne viruses such as the Hong Kong chicken flu, and for select agent research. The laboratory has a dedicated ventilation system that maintains a negative pressure with respect to the adjacent corridor and rooms, and which provides HEPA filtration of exhaust air at a remote location on the roof. |
| BT Wyeth 87 Cambridgepark Drive Cambridge, MA 02140 (617) 665-8318 jkieleczawa@wyeth.com View Website Primary Contact: Jan Kieleczawa jkieleczawa@wyeth.com | Services offered: Bioinformatics Data Analysis DNA Analysis DNA Sequencing Nucleic Acid Extraction oligo synthesis Associations: NERTRN | DNA Sequencing group |
| Clinical & Translational Research Support Core UMass Medical School 200 Trapleo Road Waltham, MA 02452 (781) 642-0256 carol.curtin@umassmed.edu View Website Primary Contact: Carol Curtin | Services offered: participant recruitment, characterization of participants (e.g., psychological testing), participant tracking & assistance with IRB interactions (applications, amendments, progress reports, renewals, etc.) Associations: NERTRN |
The Clinical and Translational Research Support (CTRS) Core provides assistance to funded research projects involving human participants to ensure that they have sufficient numbers of well-characterized individuals to fulfill the projects' primary aims. The CTRS Core also provides access and information resources that will support investigators of all types who have clinical and/or translational research interests. Our Core currently provides the following services: 1.Recruitment of participants; 2.Assessment/characterization of participants; 3.Tracking of recruited participants across multiple projects and maintenance of a database of specialized populations; 4.Coordination of interactions with the UMMS IRB, which includes assisting investigators to submit clear and complete applications and follow-up IRB communications. |
| Clinical Trials Unit UMass Medical School 55 Lake Ave North Worcester, MA 01655 (508) 856-2800 sheila.noone@umassmed.edu View Website Primary Contact: Sheila Noone (508) 856-2800 | Services offered: Clinical Study Support and Resources Associations: NERTRN |
The Clinical Trials Unit (CTU), a dedicated ambulatory service unit for clinical study support and resources, is under the direction of the Director of Clinical Research in the Office of Research. The CTU works collaboratively with clinical investigators to ensure high quality and efficient study initiation and can provide support throughout the life cycle of a study. This includes: 1. Provision of dedicated space: includes 4 exam rooms, an infusion room with 2 recliners, open workstations for CTU users, a small laboratory for spinning, freezing, packaging, and shipping of study specimens; 2. Study coordination: four (4) fulltime, experienced research nurse coordinators who are able to recruit, screen, enroll and manage study conduct over the life cycle of the study or clinical trial Regulatory Support for study initiation through the services of one regulatory coordinator who can assist investigators with IRB submissions and FDA communications for IND and IDE |
| Crystallography Core Facility UMass Medical School 55 Lake Ave North LRB 921 Worcester, MA 01655 (508) 856-6912 william.royer@umassmed.edu View Website | Services offered: Data Collection Associations: NERTRN |
The X-ray Crystallography Lab is a core facility with operations at UMASS Medical School's Lazare Research and Biotech II buildings. The laboratory provides facilities and resources for conducting research, advanced teaching, and comprehensive data processing. The facility is jointly funded by user fees, departmental contributions and the Office of Research. Facilities include two detectors (R-AXIS IV, MAR 180) and generators (RU-300 and RU-300HR). The in-house UNIX computing environment supports data processing, 3-D visualization and design. To allocate time on one of the detectors, see the online scheduler. There are six faculty members associated with the facility. Course work includes graduate classes and professional training. ---- Data and Information Processing,Hardware and software training, Graphics and visualization resources, Consultation on structure analysis. |
| Deep Sequencing Core UMass Medical School Biotech II 373 Plantation Street Room 207 Worcester, MA 01605 (508) 856-6137 Ellen.Kittler@umassmed.edu View Website Primary Contact: Ellie Kittler | Services offered: Bioinformatics Genomics Library Services Associations: NERTRN | The Deep Sequencing Core provides a next-generation sequencing platform for investigators using Massively Parallel Signature Sequencing (MPSS), also known as Parallel Sequencing by Synthesis, or "Deep Sequencing". The core analyzes genomic DNA, DNA fractions (e.g. Chromatin Immunoprecipitation), cDNA and RNA samples by generating libraries of small tagged fragments which are simultaneously sequenced in parallel using a Solexa (Illumina) 1G Genome Analyzer. Deep Sequencing generates a large number of short overlapping sequences as well as quantifying the occurrence of each individual sequence within the library. The Deep Sequencing Core also provides assistance with sample preparation and bioinformatics analysis |
| Digital Light Microscopy Core UMass Medical School Biotech II 373 Plantation Street Room 114 Worcester, MA 01605 (508) 856-0045 paul.furcinitti@umassmed.edu View Website Primary Contact: Paul Furcinitti (508) 856-0045 paul.furcinitti@umassmed.edu | Services offered: Cell Imaging Microscopy Optical Imaging Deconvolution of Images Associations: NERTRN | The Core Digital Imaging Facility provides high-resolution multi-mode light microscopy services to UMass Medical School researchers and investigators at other academic and commercial institutions. Services include wide-field and spinning disk confocal microscopy, fluorescence recovery after photobleaching measurements, live cell imaging, digital deconvolution of microscopy images and image analysis. Training and technical assistance are provided in a user friendly environment. |
| Electron Microscopy Core Facility UMass Medical School 55 Lake Ave North SA-114 Worcester, MA 01605 (508) 856-2602 gregory.hendricks@umassmed.edu View Website | Services offered: Cell Imaging Cryo-Electron Microscopy Electron Microscopy Molecular Imaging Spectroscopy Associations: NERTRN | The Core Electron Microscopy Facility provides state-of-the-art methodologies and instrumentation for researchers at UMass Medical School and the surrounding research community. It is located in the lower level of the Medical School (SA-114). The facility is equipped with one scanning and three transmission electron microscopes together with the ancillary equipment required to carry out all key ultrastructural procedures from the tissue to the molecular level. |
| Flow Cytometry UMass Medical School 55 Lake Ave North S5-322 Worcester, MA 01655 (508) 856-3276 Richard.Konz@umassmed.edu View Website | Services offered: Cell Imaging Cell Sorting Data Analysis Flow Cytometric Analysis Microscopy Optical Imaging Associations: NERTRN | The Flow Cytometry Facility provides a wide variety of cytometry services for internal and external investigators with state-of-the-art cell sorting and analyzing capabilities. We currently have three FACSCailburs, two 4 laser LSRIIs, a 3 laser FACSVantage SE DiVa cell sorter, a 3 laser Digital Dako MoFlo XDP hi-speed cell sorter, an all digital 3 laser 11 color FACSVantage SE DiVa cell sorter and a 14 color, 4 laser FACSAria dedicated to BSL3 cell sorting. One LSR II and one Calibur are dedicated for customer use, after training, which we can provide. |
| Fly Kitchen UMass Medical School Biotech 4 377 Plantation Street Room 312D Worcester, MA 01605 (508) 856-6812 Birgit.Koppetsch@umassmed.edu | Services offered: Media Preparation Associations: NERTRN | Droposphila Media Core Facility |
| Genomics Core Facility UMass Medical School 55 Lake Ave North S5-116 Worcester, MA 01453 (508) 856-4076 Phyllis.Spatrick@umassmed.edu View Website Primary Contact: Phylis Spatrick | Services offered: Genomics Microarray Associations: NERTRN |
The Genomics Core Facility at UMass Medical School is an excellent resource for the UMass and Worcester area research community featuring high-density microarray technology for both GeneChip and glass slide array processing. • Sample preparation and Affymetrix instrumentation for Expression, Gene ST, Exon, and Tiling Arrays, as well as SNP chip and CustomSeq array hybridization and scanning. • Glass slide array scanning using the Agilent G6525BA Scanner. Expression, ChIP-chip, miRNA and DNA microarray. • Glass slide hybridization capabilities with the BioMicro MAUI Hybridization System • Genespring GX Analysis Software available Genomics Core Facility University of Massachusetts Medical School Department of Molecular Genetics and Microbiology S5-116, S5-125, S5-129 55 Lake Avenue, North |
| Hematologic Neoplasia Flow Cytometry Core Facility Dana-Farber Cancer Institute Mayer 584 44 Binney St Boston, MA 02115 (617) 632-4571 hemneo_flow@dfci.harvard.edu View Website Primary Contact: John Daley john_daley@dfci.harvard.edu | Services offered: Cell Sorting Associations: NERTRN | Two High Speed cell sorters, 3 Analyzers. |
| Human Embryonic Stem Cell Core Facility UMass Medical School 55 Lake Ave North S3-308 Worcester, MA 01655 (508) 856-3269 stemcell.corefacility@umassmed.edu View Website Primary Contact: Gary Stein and Jane Lian | Services offered: Stem Cell Procurement Bone MicroCT Imaging Associations: NERTRN |
The HESC Core facility will provide, to UMASS investigators on all campuses, undifferentiated stem cells; two NIH approved cell lines, H1 (male) and H9 (female), on mouse feeder layers. Our support services include: •Quality controlled undifferentiated stem cells plated •Protocols for monitoring HESCs during studies •Advice on experimental design |
| Machine Shop UMass Medical School 222 Maple Ave Shrewsbury, MA 01545 (508) 856-3716 MachineShop@umassmed.edu View Website Primary Contact: Art Allard Art.Allard@umassmed.edu | Services offered: Design, manufacture and repair of biomedical lab equipment Associations: NERTRN | The UMMS Machine Shop is a support service dedicated to assisting research in a technical/mechanical manner. Although all types of basic laboratory apparatus are manufactured and repaired on a regular basis, we specialize in design and fabrication of equipment that is not commercially available. No job too big or too small, too simple or too complex. |
| Molecular Biology Core Facilities Dana-Farber Cancer Institute Dana-Farber Cancer Institute 21-27 Burlington Ave Boston, MA 02215 (617) 632-3082 paul_morrison@dfci.harvard.edu View Website Primary Contact: Paul Morrison james_lee@dfci.harvard.edu | Services offered: Data Analysis DNA Analysis Genomics Genotyping Mass Spectrometry oligo synthesis Peptide Synthesis Protein Sequencing Proteomics Associations: NERTRN |
DNA Sequencing Mass Spectrometry Peptide Synthesis etc. |
| Molecular Biology Core Lab (MBCL) UMass Medical School 373 Plantation Street Lab 207 Worcester, MA 01605 (508) 856-3645 CFAR@umassmed.edu View Website | Services offered: DNA Fragment Analysis, Associations: NERTRN | The MOLECULAR BIOLOGY CORE LABS provide DNA fragment analysis, Genotyping, and SPR services. The MBCL is also home to the UMass Oligonucleotide program which provides discounted oligos to researchers. |
| Morphology UMass Medical School 55 Lake Ave North S2-315 Worcester, MA 01655 (508) 856-5639 yu.liu@umassmed.edu View Website Primary Contact: Yu Liu | Services offered: F.I.S.H. Immunohistochemistry In Situ Hybridization Microscopy Associations: NERTRN |
Established in 1981, the Morphology Core Facility is a DERC (Diabetes and Endocrinology Research Center) Research Core Laboratory. Major funding for the Morphology Core is provided by a Diabetes and Endocrinology Research Center grant from the National Institutes of Health. Dr. Bruce Woda, MD , Professor of Pathology Department is the core director. The Morphology Core Facility is a state-of-the-art, fully equipped histology lab that provides histology services in support of investigators at UMass Medical School, including • routine histological preparations. • special stains, • immunohistochemistry. • frozen sections. The core provides advice on techniques that are appropriate in submitting and evaluating morphologic preparations. |
| New England Center for Stroke Research (NecSTR) UMass Medical School 55 Lake Ave North SA-107R Worcester, MA 01655 (508) 856-1844 matt.gounis@umassmed.edu Primary Contact: Matt Gounis (508) 856-1844 | Services offered: Fabrication 3D Printer, X-ray guided surgery and vascular intervention Associations: NERTRN |
This facility is imaging and image guided therapeautic intervention. Services include: 1.Fully equipped sterile angiosurgical suite to support fluoroscopy guided intervention 2.Hemodynamics laboratory for in vitro investigation into the efficacy cardiovascular devices. 3.Xper CT for 3-D reconstruction of vascular tree and soft-tissue imaging. |
| Optical Imaging Immune Disease Institute 200 Longwood Ave Boston, MA 02115 (617) 278-3181 leung@idi.harvard.edu View Website Primary Contact: Harry Leung leung@idi.harvard.edu | Services offered: Cell Imaging Microscopy Optical Imaging in vivo/in vitro imaging Associations: NERTRN | confocal/multiphoton microscopy, image analysis |
| Peptide-HPLC UMass Medical School 55 Lake Ave North S4-224 Worcester, MA 01655 (508) 856-2397 Robert.Carraway@umassmed.edu View Website Primary Contact: Robert Carraway (508) 856-2397 | Services offered: Gel chromatography, HPLC, Assay Development, Amino acid analysis, Peptide-protein conjugation Associations: NERTRN | This facility provides large-scale (preparative) and small-scale analytical gel chromatography and HPLC (reverse-phase, ion exchange and sizing). Peptide hydrolysis and automated amino acid anyalysis are also performed using state of the art instruments with high sensitivity and accuracy. We also devise extraction procedures and HPCL-based assay prodecures for the quantitation of any substance that can be detected by spectrophotmetric methods. For antibody production, we prepare peptide-protein conjugates using methods shown to yield the highest immunogenicity. |
| Proteomic Fractionation Group UMass Medical School 222 Maple Ave Shrewsbury, MA 01545 (508) 856-5716 Sunny.Tam@umassmed.edu View Website | Services offered: 2D-PAGE Assays and Measurements Biochemical Analysis Microarray SDS-PAGE Western Blot Associations: NERTRN | The Proteomic Fractionation Group (PFG) at UMass Medical School is a state-of-the-art proteomics laboratory that serves both UMass and external investigators in their proteomic fractionation needs. The focus of the lab is the reproducible and quantitative analysis of complex protein mixtures derived from whole organisms, tissues, cells, sub-cellular fractions or partially purified mixtures. |
| Proteomics & Mass Spectrometry Facility UMass Medical School 365 Plantation Street Suite 190 Worcester, MA 01605 (508) 856-8917 James.Evans@umassmed.edu View Website | Services offered: Assays and Measurements Mass Spectrometry Protein Sequencing Proteomics Fatty acid analysis, Lipidomics, Metabolomics, Small molecule analysis Associations: NERTRN |
A dynamic resource for state of the art proteomic and mass spectrometric analyses that support the research, educational and clinical programs at UMMS. It also provides services to academic and industrial researchers at other institutions. Proteomics is a major focus in the facility with a comprehensive range of techniques utilized for protein identification, characterization and quantification. The facility has expertise and instrumentation for small molecule analysis by mass spectrometric techniques. |
| Proteomics Mass Spec Shrewsbury UMass Medical School 222 Maple Ave Fuller Bldg Shrewsbury, MA 01545 (508) 856-7533 john.leszyk@umassmed.edu View Website Primary Contact: John Leszyk (508) 856-7533 John Leszyk | Services offered: Protein Sequencing Proteomics Associations: NERTRN | The lab is equipped with the latest instrumentation for protein/peptide mass spectral analysis. Our equipment includes a Shimadzu Biotech Axima TOF2 (Matrix Assisted Laser Desorption tandemTime -of-Flight (MALDI-TOF-TOF) mass spectrometer, and Axima QIT ( Quadrupole Ion Trap Matrix Assisted Laser Desorption Time-of-Flight (MALDI-QIT-TOF) mass spectrometer. In addition to these we have a Finnigan Electrospray LCQ Deca Ion Trap mass spectrometer (ESI LC/MS/MS). The lab provides highly sensitive protein identifications from 1D and 2D gels as well the identities of site-specific modifications for both academic and corporate clientele. |
| shRNA Library Core UMass Medical School 55 Lake Ave North Worcester, MA 01655 (508) 856-4252 shrnaclone@umassmed.edu View Website | Services offered: Provides Clones Associations: NERTRN | UMMS has purchased the complete collections of human and mouse retroviral and lentiviral short hairpin RNA (shRNAmir) libraries from Open Biosystems, and has negotiated with them to distribute individual clones to UMMS researchers (ONLY) at a reduced price. |
| Small Animal Imaging Core UMass Medical School 55 Lake Ave North SA-107A Worcester, MA 01655 (508) 856-4256 Donald.Hnatowich@umassmed.edu Primary Contact: Mary Rusckowski (508) 856-6972 Mary.Rusckowski@umassmed.edu | Services offered: Small animal SPECT, CT and Pet Imaging Associations: NERTRN |
With the installation of both cameras, the Bioscan NanoSPECT/CT and the Philip Mosaic PET small animal cameras, UMMS and extramural investigators now have the opportunity of using radioactive agents labeled with SPECT radionuclides such as 99mTc, 111In ,123I 125I and PET radionuclides such as 18F, 64Cu, 68Ga, to follow the pharmacokinetics and biodistributions in mice, rats, rabbits, cats and marmoset monkeys and other small animals of proteins, peptides, oligomers, nanoparticles, and other biomarkers of interest. The CT component of the NanoSPECT camera will provide registration for both cameras and, in addition, can be used without radioactivity for high resolution anatomical imaging. ---- Small animal SPECT, CT and Pet Imaging |
| Small Molecule Screening Facility UMass Medical School 55 Lake Ave North LRB-827 Worcester, MA 01655 (508) 856-6696 hong.cao@umassmed.edu. View Website Primary Contact: Hong Cao (508) 856-8874 | Services offered: Assays and Measurements Library Services Associations: NERTRN |
The facility headed by Dr. Hong Cao has allowed UMMS scientists a unique opportunity to apply the tools and principles of chemistry to understand the processes of living cells. The screening facility assists researchers in developing high-throughput (HT) screening assays, performs HT screens of chemical libraries to identify new small molecules that can be used to probe biological processes of interest. The facility coordinates the screening efforts of UMMS researchers, providing access to diverse chemical libraries and state-of-the art instruments including robotic compound transfer, liquid-handling equipment, imagers and plate readers. The information from all screens performed at the facility is collected and stored in a central database. The Cheminformatics database allows researchers to rapidly evaluate and compare results of their screens and can also be used in the future to classify the function of lead structures and biological targets. |
| Transgenic Animal Modeling Core UMass Medical School 55 Lake Ave North S3-216 MA 01655 (508) 856-7500 stephen.jones@umassmed.edu View Website Primary Contact: Stephen Jones | Services offered: Cell Culture Nucleic Acid Extraction Tissue Culture Transgenics Associations: NERTRN | The Transgenic Animal Modeling Core produces genetically altered mice and rats in a timely and cost-efficient manner. Services include gene targeting in embryonic stem cells, blastocysts microinjections to generate chimeric mice, pronuclear DNA injections and lentiviral injections into oocytes to generate transgenic mice and rats, rederivation of rodents to pathogen-free status, cryopreservation of sperm and embryos, IVF assistance, modified speed congenics, and more. The Transgenic Animal Modeling Core has generated over 100 gene-targeted mice and 300 different types of transgenic mice for UMMS investigators in the past 8 years. |
| UMass Tissue Bank Core UMass Medical School 55 Lake Ave North LRB 426 Worcester, MA 01655 (508) 856-3476 stephen.lyle@umassmed.edu View Website Primary Contact: Elizabeth Hamir | Services offered: Laser Capture Microdissection Human tissue samples, Frozen Sections, Formalin-fixed tissue sections Associations: NERTRN |
The UMass Memorial Cancer Center's Tissue Bank is an institutional Core facility aimed at improving the research endeavors of the basic, clinical, and translational cancer scientists. The overarching goal of the facility is help facilitate the science underway to improve the understanding of the underlying causes of the different types of cancer through the use of human tissue. One vital component of the Tissue Bank is the archival collection of formalin-fixed, paraffin embedded tissue samples that can be connected to clinical information dating back to 1993. The second major component of the Tissue Bank is a dynamic tissue collection, annotation, storage and distribution service, which collects fresh tissue samples for rapid processing/snap freezing immediately after surgery. When possible, surrounding healthy normal tissue samples are also processed and stored for reference purposes. Looking to meet the complex needs of the research community, tissue micro arrays will be available from the bank in the near future. |
| Laboratory of Molecular Technology National Cancer Institute at Frederick 915 Tollhouse Avenue Suite 211 Frederick, MD 21702 (301) 846-5676 seqmail@ncifcrf.gov View Website Primary Contact: Claudia Stewart stewart@ncifcrf.gov | Services offered: Bioinformatics DNA Sequencing Genomics Genotyping Microarray oligo synthesis PCR Arrays Proteomics Real-time PCR RNA analysis Sequencing Western Blot Associations: NERTRN |
Government core for NCI/NIAID and others ---- offer custom viral array including all known mammalian and avial viruses (affy platform) custom cancer sequencing chip on affy platform with all oncogens and tumor supressor genes |
| Bioinformatics Mount Desert Island Biological Laboratory PO Box 35, Old Bar Harbor Rd. Salisbury Cove, ME 04672 (207) 288-3605 cmattin@mdibl.org View Website Primary Contact: Carolyn Mattingly cmattin@mdibl.org | Services offered: Bioinformatics Associations: NERTRN |
The Maine INBRE Bioinformatics Core facilitates data management and analysis for comparative functional genomics research by providing: * Sequence Analysis Software * Access to biological databases * Biomedical journals * Capabilities for data storage * Training opportunities The Core also supports communication networks for INBRE institutions to facilitate multi-center research and resource sharing and the confidential exchange of data. |
| Confocal Imaging Core Mount Desert Island Biological Laboratory Mount Desert Island Biological Laboratory PO Box 35 Salisbury Cove, ME 04672 (207) 288-3605 achristie@mdibl.org Primary Contact: Andrew Christie | Services offered: Cell Imaging Optical Imaging Associations: NERTRN | MDIBL provides access to two single photon confocal microscopes: a Zeiss 510 Meta and a Olympus FV1000. Technicians provide training services to new users. Reservations can be made via an online sign up system. |
| Cytogenetics Service The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6000 james.denegre@jax.org View Website Primary Contact: Lesley Bechtold lesley.bechtold@jax.org | Services offered: F.I.S.H. Associations: NERTRN | The Cytogenetics Service offers preparation of metaphase chromosomes and karyotyping (by G-band analysis), labeling probes by Nick Translation, and performing fluorescent in situ hybridization (FISH) to map genes, identify transgene integration sites, and detect chromosomal rearrangements. In addition, spectral karyotyping (SKY) services are also available. |
| DNA and Protein Analysis and Cell Imaging Core Maine Medical Center Research Institute 81 Research Drive Scarborough, ME 04074 (207) 885-8148 varyc@mmc.org View Website Primary Contact: Calvin Vary | Services offered: Cell Imaging DNA Sequencing Mass Spectrometry Proteomics Associations: NERTRN | DNA sequence analysis, quantitative protein analysis via tandem msms using ICAT and related technologies; Confocal microscopy, four lasers, of living and fixe specimens. |
| Electron Microscopy Service The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6000 pete.finger@jax.org View Website Primary Contact: Lesley Bechtold lesley.bechtold@jax.org | Services offered: Electron Microscopy Protocol Development/Clinical Trial Coordination Immunogold Labeling Associations: NERTRN |
The EM Service offers both SEM (Scanning electron microscopy) and TEM (Transmission electron microscopy) as well as sample preparation for both types of EM. The EM Service is equipped with a Hitachi S3000N Variable pressure Scanning electron Microscope and a JEOL 1230 Transmission electron Microscope, both with digital image capture capability. |
| Equipment Repair Service The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 (207) 288-6275 jeff.forthofer@jax.org Primary Contact: Jeff Forthofer | Services offered: Instrumentation Associations: NERTRN | The Equipment Repair Service provides technical support and maintenance of the wide variety of shared scientific equipment and common equipment rooms. In-house repair of PI instrumentation is also available. Custom fabrication of new fixtures and devices, or modification of existing instrumentation is also offered as part of the service. |
| Genome Sciences, Scientific Services Department The Jackson Laboratory The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 (207) 288-6219 lucy.rowe@jax.org View Website Primary Contact: Lucy Rowe lucy.rowe@jax.org | Services offered: Data Analysis DNA Analysis Genomics Genotyping Nucleic Acid Extraction Associations: NERTRN | DNA Sequencing (ABI3730), genotyping with SNP or SSLP technology, genome scans for genetic mapping and breeder selection, genetic map building, custom genotyping projects, high quality genomic DNA available from inbred mouse strains, custom high throughput DNA prepapration for in-house genotyping applications, consultation and data alaysis. Some services are limited to in-house clients, others available to outside - see http://jaxmice.jax.org/services/index.html model development and other research services. |
| Glassware Service The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 (207) 288-6275 jeff.forthofer@jax.org Primary Contact: Jeff Forthofer | Services offered: Glass Washing/Autoclaving Associations: NERTRN | The Glassware Service provides for cleaning and sterilizing of laboratory glassware and associated instruments. The central facility has 2 Steris Century Pre-vac Autoclaves, 2 Steris Reliance 400 Washers, several ovens, an acid-wash station, and a pipette plugger. Personnel also support the several autoclaves in shared equipment rooms throughout the laboratory complex. |
| Histology Core Maine Medical Center Research Institute 81 Research Dr. Scarborough, ME 04074 (207) 885-8151 lindnv@mmc.org View Website Primary Contact: Kathleen Carrier carrik@mmc.org | Services offered: Immunohistochemistry Microscopy Associations: NERTRN | Tissue processing, sectioning (frozen, paraffin, plastic), routine stains, specialty stains, immunohistochemistry |
| Histology Service The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6000 lesley.bechtold@jax.org View Website Primary Contact: Lesley Bechtold lesley.bechtold@jax.org | Services offered: Immunohistochemistry Tissue Processing, Sectioning and Staining Associations: NERTRN | The Elizabeth Fekete Histology Laboratory provides a centralized service for the preparation of murine tissues for light and fluorescent microscopy. Routine and specialized histological methods are available. |
| Light and Confocal Microscopy Service The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6000 james.denegre@jax.org View Website Primary Contact: Lesley Bechtold lesley.bechtold@jax.org | Services offered: Cell Imaging Electron Microscopy Laser Capture Microdissection Associations: NERTRN |
The Microscopy Service is open twenty-four hours per day. Instruments may be used under supervision of the Staff, or trained users may work independently. The Service has a full wet bench, cell biology and molecular biology, and complete tissue culture facilities. The Light Microscopy Staff is prepared to help you design and analyze your experiment. The following instrumentation is available for use: 2 Fluorescent Stereomicroscopes; 2 Upright microscopes capable of brightfield, darkfield, fluorescence, DIC; Leica SP2 Multiphoton microscope; Leica SP5 Spectral Confocal Microscope; Imaging Workstations; Arcturus XT LCM; Zeiss Inverted Microscope |
| Mount Desert Island Biological Laboratory Mount Desert Island Biological Laboratory PO Box 35 Old Bar Harbor Rd. Salisbury Cove, ME 04672 (207) 288-9880 mdibl_info@mdibl.org View Website Primary Contact: David Towle dtowle@mdibl.org | Services offered: Microarray oligo synthesis Real-time PCR RNA analysis Sequencing Associations: NERTRN | The Mount Desert Island Biological Laboratory is an independent, not-for-profit marine and biomedical research facility and an international center for comparative physiology, toxicology and marine functional genomic studies. |
| Mouse Transgenic Facility Maine Medical Center Research Institute 81 Research Drive Scarborough, ME 04074 (207) 885-8142 harria@mmc.org View Website Primary Contact: Anne Harrington harria@mmc.org | Services offered: Animal Husbandry Genotyping Stem Cell Procurement Transgenics mouse embryo cryopreservation and re-derivation Associations: NERTRN | The Mouse Transgenic Core Facility provides a series of high quality services related to mouse genetics, manipulation of mouse embryos, re-derivation and cryopreservation, and the stocking and distribution of shared mouse strains. Transgenic mouse lines are generated by microinjection, and chimeric mice are made by blastocyst injection of embryonic stem cells. |
| Phenotyping Sciences The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6703 douglas.hinerfeld@jax.org View Website Primary Contact: Doug Hinerfeld douglas.hinerfeld@jax.org | Services offered: 2D-PAGE Biochemical Analysis Cell Culture Cell Sorting Data Analysis DNA Analysis Flow Cytometric Analysis Mass Spectrometry Microarray Nucleic Acid Extraction Protein Extraction Proteomics Real-time PCR RNA analysis RNA Integrity SDS-PAGE Western Blot Associations: NERTRN |
The Phenotyping Sciences is composed of four core labs including Protein Chemistry, Gene Expression, Flow Cytometry and Molecular Biology. The Molecular Biology Service engineers constructs for the generation of KO and transgenic mice. |
| Reproductive Sciences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 (207) 288-6000 rob.taft@jax.org View Website Primary Contact: Rob Taft (207) 288-6727 rob.taft@jax.org | Services offered: Cell Culture Stem Cell Procurement Tissue Culture Transgenics Gamete Cryopreservation Associations: NERTRN | Reproductive Sciences is composed of Importation, Cryopreservation, Cell Biology and Microinjection groups. These groups provide a variety of services including creation of genetically modified mice, cryopreservation, recovery of cryopreserved mouse strains, rapid expansion of lines using in vitro fertilization, rederivation of imported mouse lines and maintenance of a repository of publicly distributed cryopreserved embryos, sperm and ovaries. In addition to providing these services, the Reproductive Sciences group maintains an active research program focused on the development, refinement and implementation of assisted reproductive technologies that can be used to manage strains more effectively and an education program designed to facilitate the transfer of these technologies to the scientific community. |
| The Jackson Laboratory - Computational Sciences The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6339 cjd@jax.org View Website Primary Contact: Chuck Donnelly cjd@jax.org | Services offered: Bioinformatics Biostatistics Data Analysis Scientific Software Development Associations: NERTRN |
The Computational Sciences core is an interdisciplinary group of bioinformatics software engineers, biologists, and mathematicians providing statistical consulting, data analysis, method development, algorithm design, software engineering, LIMS development, high performance computing, regional compute grid development, data resources, analysis tools and tool integration, and experimental design services to biomedical research investigators at The Jackson Laboratory. The CS core also manages the TJL liaison office to the NCI caBIG program. ---- Regional Compute Resources, Scientific Software DevelopmentHigh Performance Computing Laboratory Information Management Systems (development/support) |
| The Jackson Laboratory - Necropsy Service The Jackson Laboratory 600 Main St. Bar Harbor, ME 04609 (207) 288-6000 lesley.bechtold@jax.org View Website Primary Contact: Lesley Bechtold | Services offered: Necropsy Associations: NERTRN |
Necropsy Service The Necropsy Service performs necropsies on mice from both production and research animal facilities for diagnostic pathology purposes as part of TJL’s routine monitoring to ensure the health status of its mice. Mice may also be sent to us from research colonies for either surveillance purposes or as part of a research project in which specific tissues need to be harvested. Training is provided to Researchers and their staff who wish to learn to perform their own necropsies. In addition to necropsies and tissue collection for histological processing, we can collect blood smears for staining and do fluid collection for PCR, hematology analysis and microbiology culturing. We also collect tumors for inclusion in the Tumor Database, photograph mice prior to necropsy and take X-rays as needed. |
| Viral Vector Core Facility Maine Medical Center Research Institute 81 Research Drive Scarborough, ME 04074 (207) 885-8269 chandn@mmc.org View Website Primary Contact: Nancy Chandler-Conrey, MS chandn@mmc.org | Services offered: Recombinant viral vector Associations: NERTRN |
The Viral Vector Core was established at MMCRI in 2004. The objective of the core is to provide high quality viral vector services to support research performed at MMCRI. Viral vectors are produced in a dedicated BL2 facility within the MMCRI building. Vector systems currently being used include adenovirus, retrovirus and lentivirus. The Core operates on a fee-for-service basis for both MMCRI and external investigators. |
| Core Biology Facility North Dakota State University Dept. 2710 PO Box 6050 1320 Albrecht Blvd. Fargo, ND 58108 (701) 231-5334 Jodie.Haring@ndsu.edu View Website Primary Contact: Jodie Haring (701) 231-5334 Jodie.Haring@ndsu.edu | Services offered: Assays and Measurements Cell Culture Cell Imaging Data Analysis DNA Analysis Flow Cytometric Analysis Instrumentation Microarray Microscopy Nucleic Acid Extraction Real-time PCR RNA analysis RNA Integrity Tissue Culture Associations: NERTRN | The Center for Protease Research Core Biology Facility (CBF) was established to provide access to equipment and specialized training in the areas of molecular biology and tissue culture in order to enhance the biomedical research environment at NDSU. We provide student training and consultation on experimental design and data interpretation. |
| Core Synthesis Facility North Dakota State University 156 Dunbar Hall NDSU Dept-2735, PO Box 6050 Fargo, ND 58108 (701) 231-8322 Rajesh.Murthy@ndsu.edu Primary Contact: Rajesh S. Murthy, Ph.D. (701) 231-8322 Rajesh.Murthy@ndsu.edu | Services offered: Spectroscopy Organic Synthesis Associations: NERTRN | The Core Synthesis Facility (CSF) at the Center for Protease Research (CPR) was established in April 2008 with funding from an NCRR-NIH-COBRE grant. The CSF is aimed towards assisting principal investigators in the COBRE program, by providing synthetic and analytical services. We are equipped with modern synthetic technologies and state-of-art instrumentation. We specialize in the synthesis of small molecules for biological applications. We also offer quantitative and qualitative analysis of substrates using HPLC and LC-MS. |
| Dartmouth Molecular Biology Core Facilty Dartmouth Medical School HB 7650 Dartmouth Medical School Hanover, NH 03755 (603) 650-6546 mbcore@dartmouth.edu View Website Primary Contact: Christian Lytle (603) 650-6546 Christian.H.Lytle@Dartmouth.edu | Services offered: DNA Analysis DNA Sequencing Genotyping Instrumentation Real-time PCR Associations: NERTRN | The Dartmouth Molecular Biology Core Facility offers DNA sequencing, DNA fragment analysis and a shared instrument service for DNA applications. |
| Dartmouth Proteomics Core Facility Dartmouth Medical School HB 7937 Dartmouth Medical School Hanover, NH 03755 (603) 653-6188 pcore.dartmouth.edu View Website Primary Contact: Steve Bobin (603) 653-6189 sbobin@dartmouth.edu | Services offered: Assays and Measurements Biochemical Analysis Instrumentation Mass Spectrometry Protein Extraction Protein Sequencing Proteomics Associations: NERTRN | The Dartmouth College proteomic Core Facility offers LC MS/MS protein identification, Edman sequencing, MALDI MS, LC and general analytical biochemistry services. |
| Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Gregg Hall Durham, NH 03824 (603) 862-2474 jobriaha@unh.edu View Website Primary Contact: Dr Kelley Thomas (603) 862-2470 kelley.thomas@unh.edu | Services offered: DNA Analysis DNA Sequencing Genomics RNA analysis Sequencing Associations: NERTRN | We provide DNA sequencing using ABI 3130. We also have a Agilent 2100 Bioanalyzer to analyze DNA and RNA samples. |
| Immune Monitoring Laboratory Dartmouth Medical School 710 Rubin 1 Medical Center Drive Lebanon, NH 03756 (603) 653-9913 jacqueline.smith@dartmouth.edu View Website Primary Contact: Jacqueline Smith jacqueline.smith@dartmouth.edu | Services offered: Cell Culture Flow Cytometric Analysis Tissue Culture ELISPOT, Treg analysis; Treg function Associations: NERTRN |
Immune Monitoring Laboratory Mission The Immune Monitoring Laboratory provides (i) state-of-the-art immunoassays to allow NCCC clinicians to monitor the immune responses of patients enrolled in clinical trials; (ii) expert guidance in the choice and interpretation of immunoassays most relevant to a particular clinical trial; (iii) quality control by rigorous analysis of a reference population to define baseline responses as well as validation of the reproducibility of the result; and (iv) a resource for all NCCC Investigators and Dartmouth community to use various dedicated instruments not normally available in individual laboratories, e.g. ELISPOT reader, autoMACS, Luminex. Overview of Services Provided ELISPOT assays autoMACS magnetic bead cell separation Cell proliferation assays Cytokine assays including Luminex multiplex assays Leukocyte subset analysis T regulatory cell assays: inhibition assay FoxP3+ phenotype ---- Immunoassayse.g. ELISPOT, Luminex cytokine multiplexing, CFSE lymphoproliferation, cell counting/viability assay Peripheral blood mononuclear cell separation, plasma/serum isolation cell subset enrichment using magnetic beads |
| The Bioinformatics Shared Resource Dartmouth Medical School One Medical Center Dr. Lebanon, NH 03756 (603) 653-0367 The Bioinformatics Shared Resource View Website Primary Contact: David Jewell (603) 653-3674 | Services offered: Bioinformatics Biostatistics Data Analysis DNA Analysis Mass Spectrometry Microarray Proteomics QSAR Associations: NERTRN |
Genome, Transcriptome and Proteome analysis ---- Data mining research and software development |
| Coriell Genotyping and Microarray Center Coriell Institute for Medical Research 403 Haddon Ave Camden, NJ 08103 (856) 580-6244 ngerry@coriell.org View Website Primary Contact: Norman Gerry ngerry@coriell.org | Services offered: Data Analysis Genotyping Microarray Associations: NERTRN | The Coriell Institute Genotyping and Microarray Center is a high capacity facility, consisting of 12 FS450 Affymetrix fluidics stations and 3 state of the art GCS3000 scanners. Each scanner is equipped with an autoloader. The facility can process up to 2,000 DNA or RNA samples per month. Optional help with data interpretation, both statistical and bioinformatics, is also available. |
| RWJMS DNA Core Facility UMDNJ-RWJMS Research Annex 663 Hoes Lane Piscataway, NJ 08854 (732) 235-4934 dnalbweb@umdnj.edu View Website Primary Contact: Lee Ann Schein scheinla@umdnj.edu | Services offered: DNA Analysis DNA Sequencing Genomics Genotyping oligo synthesis Real-time PCR Sequencing Associations: NERTRN |
The UMDNJ-RWJMS DNA Sequencing and Synthesis Core Facility, a core facility of the Cancer Institute of New Jersey, is committed to provide quality, inexpensive services to scientists at UMDNJ, Rutgers University, and other scientific institutions and companies. Services are provided for automated DNA sequencing, DNA/RNA oligonucleotide synthesis, DNA fragment analysis, SNP analysis, and quantitative Real-Time PCR. |
| New Mexico Genome Sequencing Center (NMGSC) National Center for Genome Resources (NCGR) 2935 Rodeo Park Drive East Santa Fe, NM 87505 (505) 995-4449 fds@ncgr.org View Website Primary Contact: Faye Schilkey (505) 995-4449 fds@ncgr.org | Services offered: Bioinformatics Data Analysis DNA Analysis DNA Sequencing Genomics Genotyping RNA analysis Sequencing mRNA/Transcriptomic sequencing Associations: NERTRN |
The NMGSC at NCGR hosts Generation 2 Sequencing and Analysis Technologies for the IDeA network to leverage - 4 Illumina GA II sequencers for mRNA and DNA sequencing - Alpheus web-based sequence analysis, visualization & discovery for gigabase-scale projects (currently only software system of its kind) - JMP-Genomics expertise and interface for downstream statistical analysis The Illumina platform is based on massively parallel shotgun clonal sequence acquisition in which nucleic acid samples are fragmented and the resultant fragments sequenced using Illumina’s proprietary Clonal Single Molecule Array technology. Supporting the DNA and mRNA sequencing efforts are two cluster stations for flow cell construction, as well as an Agilent bioanalyzer and a NanoDrop device for sequencing library QA/QC. The wet lab at the NMGSC boasts a full compliment of molecular laboratory equipment (e.g. ultra-low , -20 and 4 oC temperature freezers, centrifuges, agarose gel electrophoresis and gel documentation equipment) to support up to four workstations/researchers. IT Infrastructure: Data Storage Sun X4500 - Dual Processor, Dual Core 24 TB file Server Image processing/Basecalling Sun X4150 – 2 x 4-core processors, 8GB RAM, 4 x 146GB Hard drives Variant detection 4 Sun Blade 6000 chassis with 10 x 6220 Blades (160 Cores, 160G of RAM and 11.6 TB disk) DB storage Sun V490 DB Servers, 6140 SAN with 10 TB for DB disk space, 4 Gb/s Switch fabric Access to the New Mexico Computing Applications Center Encanto: #7 fastest public supercomputer in the world 14,000+ core compute engine 125 TB RAM Very fast network fabric ---- Next Generation Sequence Data Analysis: Analyzing high-throughput, low-cost next generation sequencing data (Illumina-Solexa, Roche-454, ABI-SOLiD) with characteristically short reads is problematic for conventional assembly and analysis pipelines. The Alpheus software system identifies variants (i.e. SNPs or indels) in these short reads and filters them based on consistency, allele frequency, quality, coverage, and variant type to reduce false positives. Alpheus can also analyze gene expression, comparing values across groups of samples. AlpheusTM features automated data handling, a computational analysis pipeline, a relational database and a web-based query and visualization interface allowing researchers secure access via any web browser. |
| Advanced Light Microscopy & Image Analysis Core New York State Dept. of Health PO Box 509 Empire State Plaza Albany, NY 12201 (518) 474-7048 rcole@wadsworth.org View Website Primary Contact: Richard Cole rcole@wadsworth.org | Services offered: Assays and Measurements Cell Culture Cell Imaging Immunohistochemistry Optical Imaging Tissue Culture Associations: NERTRN |
Adherent cells or tissue fragments can be imaged in a variety of methods depending on the question being asked. If drug delivery is required, a perfusion style chamber is used; if gas exchange for the growth media is needed glass bottom Petri dishes can be used; if long term (> 3 days) sterility is needed, there are sealed Rose chambers for imaging. Regardless of what the experimental design, the specimen can be maintained from RT to 50 ºC. Non-destructive image modes i.e. phase contrast, differential interference contrast or polarized light coupled with shutter and filtered illumination provide as close to homeostatic conditions as possible. Once the images are collected there is an extensive array of image processing & analysis software to assist in data analysis/interpretation. These “tools” range from the simple, contrast manipulation to complex tracing and counting algorithms. There are also different forms of deconvolution available for "removing" the blur from fluorescent specimens, or transmitted light images. If multiple molecules are labeled, co-localization can be determined for either a static image or an image sequence. There are both automatic and semi-automatic 2 and 3-D tracking/montaging algorithms available. ---- Fluorescence imaging:Multiple labeled biomolecules such as GFP etc. or fluorophore can be imaged in four-dimensions. This can be done over time (5th dimension) for live specimens as well as statically for fixed specimens. Specimens can be as thin as a single cell or as thick as a whole organism (i.e. drosphilia) or anything in between. Conventional two-dimensional imaging can be done at high sensitivity, i.e. low bleaching rates. Three-dimensional imaging can be done in wide-field for relatively thin specimens or by confocal microscopy for thick specimens. |
| Analytical Imaging Facility Albert Einstein College of Medicine 1300 Morris Park Avenue Jack & Pearl Resnick Campus Bronx, NY 10461 (718) 430-3547 macaluso@aecom.yu.edu View Website Primary Contact: Frank Macaluso macaluso@aecom.yu.edu | Services offered: Cell Imaging Data Analysis Immunohistochemistry Molecular Imaging Optical Imaging Associations: NERTRN |
The Analytical Imaging Facility provides a comprehensive light and electron microscope imaging facility dedicated to bringing state of the art methods in modern imaging to biomedical scientists with all levels of expertise. The AIF staff has been cross-trained to offer a seamless transition from classical histology, to high resolution light microscope imaging in 3D, to state of the art electron microscopy. This unified approach facilitates the efficient and appropriate complementary use of these methods in research. For the infrequent user, the AIF provides a completely assisted technical support service. For the trained microscopist, the AIF is an available equipment resource. A significant effort is devoted to training investigators who require microscopy techniques to advance their projects. |
| Applied Genomic Technologies Core Wadsworth Center -- New York State Department of Health 120 New Scotland Ave Albany, NY 12208 (518) 408-2137 gcfac@health.state.ny.us View Website Primary Contact: Nick Cirino (518) 474-1838 nmc02@notes.health.state.ny.us | Services offered: DNA Analysis DNA Sequencing Genomics Genotyping Microarray Nucleic Acid Extraction gene copy number analysis Associations: NERTRN | Core Facility providing genotyping (e.g., SNP, STR), DNA sequencing, and microarray services. |
| Biochemistry Shared Instrumentation Core Wadsworth Center -- New York State Department of Health Empire State Plaza PO Box 509 Albany, NY 12201-0509 (518) 486-4908 eisele@wadsworth.org View Website Primary Contact: Leslie Eisele eisele@wadsworth.org | Services offered: Biochemical Analysis Instrumentation Spectroscopy Associations: NERTRN |
Biochemistry Core Facility includes instrumentation for protein purification, analysis and physical measurments. The Biochemistry Core contains a selection of shared instrumentation available to researchers at the Wadsworth Center as well as scientists from neighboring institutes. The purpose of the Core is to provide easy access to highly technical instrumentation and highly specialized methods not other wise readily accessible. The Core was designed to study biological molecules by means of purification, analysis and the study of their physical properties. The methods employed for purification and analysis include liquid chromatography and isoelectric focussing. Physical measurements can be achieved by a variety of spectrophotometric techniques (circular dichroism, ultra-violet, visible, and fluorescence spectroscopy), dynamic light scattering, and analytical ultracentrifugation. A Jasco circular dichroism spectrometer is one of many insturments in the Biochemistry Core Facility which investigators use to perform biophysical analyses of proteins and other molecules. Staff provide initial training in concepts and use of the instruments, primarily through one to one tutorial instruction, with the overall objective that researchers will be able to perform their own experiments and run the instrumentation independently. A course on theoretical and specific instrumentation is periodically presented. The Core's mission is to continually seek out new methods and technologies which will support public health studies and make them available to the scientific community. Protein purification equipment (HPLCs, FPLC) Isoelectric Focusing Analytical Ultracentrifuge Fluorescence Spectroscopy UV/Vis spectroscopy Circular Dichroism Spectroscopy Dynamic Light Scattering For further information contact: David LeMaster at lemaster@wadsworth.org - Biggs Laboratory, Empire State Plaza ---- Instrumentation includes: Circular Dichroism, Analytical Ultracentrifugation, Protein Purification, HPLC analysis (including UPLC), SEC-MALLS (Size Exclusion Chromatography-Multiangle Laser Light Scattering, Dynamic Light Scattering,Fluorescence, Luminometer, Capillary Electrophoresis |
| Biomolecular Interaction University of Rochester 601 Elmwood Ave Box 611 Rochester, NY 14642 (585) 273-1629 mark_sullivan@urmc.rochester.edu Primary Contact: Mark Sullivan | Services offered: Monoclonal Antibody Associations: NERTRN |
Antibody isolation using phage display, recombinant antibody technology, affinity measurement. ---- Automated colony picking, surface plasmon resonance. |
| Biopolymer Facility Rosewell Park Cancer Institute Elm and Carlton Buffalo, NY 14052 (716) 845-8032 biopolymer@roswell.park.org View Website Primary Contact: Michelle Detwiler michelle.detwiler@roswellpark.org | Services offered: DNA Analysis Genomics Genotyping Mass Spectrometry Sequencing Associations: NERTRN | DNA sequencing and mass spectrometry |
| Cell Screening Core Weill Cornell Medical College 1300 York Avenue, Rm E-00.05 New York, NY 10065 (212) 746-6480 har2001@med.cornell.edu View Website Primary Contact: Harold "Skip" Ralph har2001@med.cornell.edu | Services offered: Cell Imaging Data Analysis Optical Imaging Associations: NERTRN | The cell screening core provides equipment and expertise to assist investigators in screening chemical compound libraries for drug discovery and siRNA libraries for gene knockdown using cell-based assays, automated fluorescence microscopy, digital image processing and data mining software. |
| Center for Functional Genomics, Flow Cytometry Core University at Albany, SUNY One Discovery drive, CRC319A Rensselaer, NY 12144 (518) 591-7200 genomics@albany.edu View Website Primary Contact: Sridar Chittur schittur@albany.edu | Services offered: Assays and Measurements Cell Culture Cell Sorting Data Analysis Flow Cytometric Analysis Microarray Proteomics RNA analysis RNA Integrity Associations: NERTRN |
Cell Culture/ Staining/FACS analysis/Cell Sorting Beckman-coulter ALTRA, BD FACS Aria BD- LSRII ---- The Flow Cytometry Core is co-located with other core facilities including Molecular Biology & Sequencing, Proteomics, Tissue culture & LCM, Transgenics and Microarray. The Center for Functional Genomics offers a comprehensive portfolio with seamless integration of any of these technologies for a given project. |
| Center for Functional Genomics, Microarray Core University at Albany, SUNY One Discovery Dr, CRC328 Rensselaer, NY 12144 (518) 591-7219 genomics@albany.edu View Website Primary Contact: Sridar Chittur schittur@albany.edu | Services offered: Assays and Measurements Biochemical Analysis Bioinformatics Data Analysis Genomics Genotyping Laser Capture Microdissection Microarray Nucleic Acid Extraction PCR Arrays Real-time PCR RNA analysis RNA Integrity Tiling arrays Associations: NERTRN |
DNA microarrays (Affymetrix, Agilent, Nimblegen, custom, Eppendorf) ---- The Microarray Core is co-located with other core facilities including Molecular Biology & Sequencing, Proteomics, Tissue culture & LCM, Transgenics and flow cytometry. The Center for Functional Genomics offers a comprehensive portfolio with seamless integration of any of these technologies for a given project. |
| Center for Functional Genomics, Molecular Biology Laboratory University at Albany, SUNY CRC 319 I Discovery Drive Rensselaer, NY 12144 (518) 591-7217 jtine@albany.edu View Website Primary Contact: John Tine (518) 591-7212 jtine@albany.edu | Services offered: Assays and Measurements Data Analysis DNA Analysis DNA Sequencing Genomics Genotyping Nucleic Acid Extraction PCR Arrays Real-time PCR RNA analysis RNA Integrity Sequencing Associations: NERTRN |
The CFG Molecular Biology Laboratory offers comprehensive research services in molecular biology. Our facilities are equipped with state-of-the-art instrumentation and our experienced staff provides a valuable resource to help our customers, from both academic and commercial laboratories, to meet their research goals and objectives. Our services include standard core services such as DNA sequencing, genotyping, SNP analysis, nucleic acid isolation, and quantitative PCR analysis, as well as customized services. Our customized services include gene isolation and characterization; gene cloning; mutagenesis; promoter isolation, design and construction of expression plasmids, knockout plasmids, and knockdown plasmids; and gene expression studies. Major instrumentation in the laboratory includes an Applied Biosystems (AB) 3730XL DNA Analyzer, two AB 7900HT quantitative PCR systems, a Corbett CAS1200 liquid handling system, and a Qiagen QIAcube automated nucleic acid extraction system. |
| Center for Pediatric Research Flow Lab University of Rochester 601 Elmwood Ave, Box 703 MRBX 1-11314 Rochester, NY 14642 (585) 273-1361 tim_bushnell@urmc.rochester.edu View Website Primary Contact: Timothy Bushnell tim_bushnell@urmc.rochester.edu | Services offered: Cell Imaging Cell Sorting Flow Cytometric Analysis Associations: NERTRN |
The goal and mission of the Center for Pediatric Biomedical Research flow facility is to develop, validate and implement polychromatic flow cytometric protocols to support and enrich the research programs of CPBR faculty. This flow facility will focus on the development of experimental and unique protocols to breach previously unexplored avenues of experimentation with flow cytometry. Our current instrumentation includes: (1) a 3-laser (488, 633 and 355 nm) 12-color LSR-II with high throughput sampler system. (2) a 3-laser (488, 633 and 405 nm) 13-color FACSAria cell sorter with ACDU system. This system is validated for BSL-2 sorting. (3)a 3-laser (488, 653 and 405 nm) Amnis Imagestream imaging cytometer with extended depth of focus module. Training, consulting and collaboration with investigators (internal and external)is available. |
| Computational Biology Service Unit (CBSU) Cornell University 616 Rhodes Hall Ithaca, NY 14853 (607) 254-6333 cbsu@tc.cornell.edu View Website Primary Contact: Jaroslaw Pillardy jp86@cornell.edu | Services offered: Bioinformatics Associations: NERTRN |
CBSU was founded in 2001 as a computational resource for the Tri-institutional Collaboration among Cornell University, Cornell/Weill Medical College, Rockefeller University, and Memorial Sloan-Kettering Cancer Center, and later become Cornell's core facility for bioinformatics and computational biology. In February 2006 CBSU was chosen to become one of ten Microsoft High-Performance Computing Institutes worldwide. Being a Microsoft HPC Institute enables us to provide more bioinformatics and research support for Cornell community, CBSU also participates in testing and development of new Microsoft HPC software and system solutions like Windows Compute Cluster Server (CCS) . Test version of CCS running on CBSU's newest computer cluster is already linked to some of our web-based applications. Click here for more information on CBSU and Microsoft High-Performance Computing. CBSU is part of Cornell Life Sciences Core Laboratories Center and is hosted at Cornell Center for Advanced Computing. The Computational Biology Service Unit group provides research, software and hardware support for computational biology applications. Assistance in the design and implementation of computational solutions is also provided. CBSU responsibilities cover a wide variety of topics and tasks, including: · Computational Resources One of the major obstacles faced by many biologists is the difficulty of accessing and using state-of-the-art computational biology tools, especially on high performance computing platforms that are required for many tasks. We developed and maintain an extensive suite of computational biology applications on clusters (BioHPC) accessible through simple-to-use, web-based interface. It allows an easy access to our dedicated computational resources. · Research We collaborate on specific research projects that require expertise in genomics and structural biology. Our expertise in molecular modeling, databases and genomics has already been found helpful by a number of investigators. · Software Development We are developing (or modifying) software tools for customized solutions. Since many applications are computationally intensive, we also adapt selected programs to the massively parallel environment. |
| Cornell Core Transgenic Mouse Facility Cornell University T4002 VRT C1036 VMC Ithaca, NY 14853 (607) 253-4211 LSCLC_Transgenics@cornell.edu View Website Primary Contact: Ke-Yu Deng kd49@cornell.edu | Services offered: Transgenics Associations: NERTRN | Cornell Core Transgenic Mouse Facility is one of the members of Cornell University Life Sciences Core Laboratories Center (CLC). Our goal is to facilitate the production and study of gain-of-function and loss-of-function transgenic mice to the university community and to outside investigators. Cornell Core Transgenic Mouse Facility offers centralized services for pronuclear injection of DNA into fertilized oocytes, ES cell injections into blastocysts and mouse embryo cryopreservation. The Core Transgenic and Barrier Facilities are overseen by a committee consisting of campus investigators, veterinarians, and animal care personnel. |
| Cornell LSCLC DNA Sequencing and Genotyping Facility Cornell University 147 Biotech Bldg Ithaca, NY 14853 (607) 254-4857 DNA_Services@cornell.edu View Website Primary Contact: Peter Schweitzer pas48@cornell.edu | Services offered: DNA Analysis DNA Sequencing Genotyping Nucleic Acid Extraction Real-time PCR Sequencing Associations: NERTRN | Full Services DNA Sequencing and Genotyping facility. Instrumentation platforms include ABI 3730xl sequencers, an Illumina Genome Analyzer, ABI 7900 SDS, an Illumina Beadstation, and a Sequenom Compact MS. |
| Cornell LSCLC Protein Production and Characterization Facility Cornell University Cornell University 121 Baker Lab Ithaca, NY 14853 (607) 255-8844 lsclc_protein@cornell.edu View Website Primary Contact: Cynthia Kinsland clk10@cornell.edu | Services offered: Assays and Measurements Cell Culture Nucleic Acid Extraction Protein Extraction SDS-PAGE Tissue Culture Western Blot Associations: NERTRN |
The objective of the Protein Facility is to provide investigators with equipment, expertise and custom services for the production and characterization of biomolecules. The Protein Facility encompasses four major efforts: 1) molecular biology (cloning, mutagenesis, etc.) 2) prokaryotic protein production/purification (E. coli) 3) eukaryotic protein production/purification (yeast and insect cells) 4) characterization instrumentation (binding studies, kinetics) |
| DNA Sequencing Core Wadsworth Center -- New York State Department of Health 120 New Scotland Ave Albany, NY 12208 (518) 474-4200 genomics@health.state.ny.us View Website Primary Contact: Matt Shudt shudt@wadsworth.org | Services offered: DNA Sequencing Associations: NERTRN | The Genomics Core Facility provides a variety of services in the area of genomics and genetics research including DNA sequencing, microarray analysis, DNA extraction, and genotyping. Nick M. Cirino, Ph.D., Director. |
| Flow Cytometry Core Cornell University Vet Res Tower, TB-018 Tower Rd. Ithaca, NY 14853 (607) 253-4004 jls269@cornell.edu View Website Primary Contact: Jim Smith jls269@cornell.edu | Services offered: Cell Sorting Data Analysis Flow Cytometric Analysis Associations: NERTRN | Our mission is to provide research labs a service-oriented facility to meet the research communities flow cytometry and FACS needs. The lab uses a 3 laser/12color BDFACSAria and a 3 laser/ 8 color LSR II. Please contact us with any questions regarding flow cytometry, new applications or our facility. We can be reached at biomedflowcore@cornell.edu or you can give us a call to discuss how flow cytometry can complement your research. |
| Flow Cytometry Resource Center (FCRC) Rockefeller University 1230 York Avenue, Box 344 New York, NY 10065 (-21) 327-7657 mazels@rockefeller.edu View Website Primary Contact: Svetlana Mazel | Services offered: Cell Sorting DNA Analysis Flow Cytometric Analysis Associations: NERTRN |
Flow Cytometry Resource Center: FACSVantage SE with DiVa (3 lasers/8 colors) FACSAria (3 lasers/12 colors) BD LSRII-1 (4 lasers/14 colors, FACSFlow) BD LSRII-2 (4 lasers/16 colors, FACSFlow, HTS) FACSort (2 lasers/4 colors) FACSCalibur-1 (1 laser/3 colors) FACSCalibur-2 (2 lasers/4 colors) |
| Gene Targeting and Transgenic Facility Rosewell Park Cancer Institute Elm and Carlton Sts. MRC 312A Buffalo, NY 14263 (716) 845-5843 aimee.stablewski@roswellpark.org View Website Primary Contact: Aimee Stablewski aimee.stablewski@roswellpark.org | Services offered: Cell Culture Associations: NERTRN |
The Gene Targeting and Transgenic Facility at Roswell Park provides investigators in the Western New York area with genetically modified animals for their research. ---- We provide generation of transgenics via pronuclear microinjection and targeted mutants via blastocyst microinjection. |
| Human Immunology Center Core Laboratory Unoversity of Rochester David H. Smith Center for Vaccine Biology and Immunology 601 Elmwood Ave., P.O. Box 609 Rochester, NY 14642 (585) 273-4473 Sally_Quataert@urmc.rochester.edu View Website Primary Contact: Sally A. Quataert | Services offered: Assays and Measurements Cell Culture Cell Sorting Flow Cytometric Analysis Protocol Development/Clinical Trial Coordination Associations: NERTRN |
Modern immunological techniques are sophisticated and powerful, and can be applied effectively to many basic and clinical projects. However, it is difficult for any one investigator to become expert in all of these complex techniques and expertise in immunology is typically spread across different Departments. The Human Immunology Center (HIC) within the David H. Smith Center for Vaccine Biology and Immunology has been established to acquire, refine and develop expertise in cutting-edge techniques and to support applications in Human Immunology research. The HIC is designed with capabilities to enhance multi-disciplinary research initiatives catalyzing key clinical and basic immunology research in vaccines, HIV/AIDS, autoimmunity, allergy/asthma, transplantation as well as cancer immunology. ---- method validation |
| Microarray Core Cornell University T2-003 Vet Res Tower Tower Rd Ithaca, NY 14853 (607) 253-4351 microarrays@cornell.edu View Website Primary Contact: Wei Wang ww77@cornell.edu | Services offered: Data Analysis Genomics Genotyping Microarray RNA Integrity Associations: NERTRN |
Affy Agilent Combimatrix Illumina SNP array array printing RNA preparation for next-generation sequencing |
| Microscopy and Imaging Cornell University Ithaca, NY 14853 (607) 254-4860 mifbiotech@cornell.edu View Website Primary Contact: Carol mifbiotech@cornell.edu | Services offered: Cell Imaging Molecular Imaging Optical Imaging Associations: NERTRN |
Laser Scanning Confocal Microscopy Wide-field fluorescence microsocpy Live Animal Imaging Ultrasound Fluorometry |
| Monoclonal Antibody Core Facility Memorial Sloan Kettering Cancer Center 1275 York Avenue - Box 509 New York City, NY 10065 (646) 888-2354 macf@mskcc.org Primary Contact: Dr. Frances Weis-Garcia weisgarf@mkscc.org | Services offered: Monoclonal Antibody Associations: NERTRN |
The Monoclonal Antibody Core Facility at Memorial Sloan Kettering Cancer Center (MSKCC)/ Sloan Kettering Institute (SKI) serves scientists and clinicians by: 1.) Generating new MAbs/hybridomas from mice, rats and hamsters 2.) Produceing MAbs in vitro (NO Ascites)at high c |