Searchable Core Facilities Database
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NICL (Network of IDeA-funded Core Laboratories) Facilities (INBRE & COBRE)
| Basic Sciences Imaging Center University of North Dakota Anatomy and Cell Biology 501 N Columbia Rd Grand Forks, ND 58202-9037 (701) 777-2579 bgrove@medicine.nodak.edu Primary Contact: Bryon Grove (701) 777-2579 | Services offered: Cell Imaging Confocal Microscopy Microscopy Optical Imaging Associations: COBRE | Confocal and fluorescence microscopy |
| Bioinformatics Core University of Vermont 200C Farrell Hall 210 Colchester Ave Burlington, VT 05405 (802) 656-9798 James.Vincent@uvm.edu View Website Primary Contact: James Vincent | Services offered: Computational - Bioinformatics Associations: NERTRN INBRE | The goal of the Bioinformatics Core is to provide informatics and statistical support for the design and analysis of molecular biological experiments. To accomplish this goal we meet with investigators to identify consensus needs and then develop "pipelines" consisting of support services that efficiently satisfy these needs. Our current emphasis is on Affymetrix GeneChip and enzyme kinetics experiments, the latter based on analysis of protein functional characteristics in the context of information about sequence, structure, and phylogeny. We continue to work to identify emerging consensus needs, for example, in the areas of laboratory information management/exchange and proteomics. |
| Biomolecular Core Laboratory Nemours Center for Pediatric Research Alfred I duPont Hospital for Children 1600 Rockland Rd Wilmington, DE 19803 (302) 651-6712 mbcore@nemours.org View Website Primary Contact: Dr. Katia Sol-Church (302) 651-6705 ksolchur@nemours.org | Services offered: Genomics Genotyping Nucleic Acid Extraction oligo synthesis PCR Arrays Protocol Development/Clinical Trial Coordination Real-time qPCR RNA analysis Sequencing - DNA Sequencing Sequencing - Pyrosequencing Support Services - Shared Instrumentation Oversight & Maintenance Forensics Associations: INBRE COBRE | 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. |
| Cell Analysis Facility (Flow Cytometry) University of Nebraska Medical Center 68198 Nebraska Medical Center Omaha, NE 68198-5816 (402) 559-6267 ckuszyns@unmc.edu View Website Primary Contact: Dr. Charles Kuszynski (402) 559-6299 ckuszyns@unmc.edu | Services offered: Assays and Measurements Cell Sorting Data Analysis DNA Analysis Flow Cytometric Analysis Protocol Development/Clinical Trial Coordination Support Services - Shared Instrumentation Oversight & Maintenance Multiplex assays Associations: EPSCoR COBRE Cancer Center INBRE |
The UNMC Cell Analysis Facility provides flow cytometry services to investigators on and off the UNMC campus on a fee for service basis. Services include: •Immunophenotyping •cell cycle and DNA content analysis •protein expression and bead based multiplex assays for signal transductionmolecules •soluble proteins cytokines and growth factors. Instrumentation includes: 1) three B-D FACSCalibur dual-laser cytometers capable of four color, 4 fluorescent parameter analysis, 2) a B-D LSR II four-laser cytometer capable of 13 color, 15 parameter analysis, 3) a B-D FACSArray dual-laser bioanalyzer capable of four color, plate-based multiplex assays, 4) A B-D FACSAria four-laser, high speed digital cell sorter capable of 15 color, 17 parameter analysis, 5)A B-D FACSAria II four-laser, high speed digital cell sorter capable of 15 color, 17 parameter analysis,7) a Miltenyi AutoMACs automated magnetic cell separation system. Wet laboratory space for sample preparation and incubators for cell storage following sorting operations. |
| Center for Collaboration on Research Design and Analysis University of Nebraska Medical Center Omaha, NE 68502 (402) 559-6825 jmeza@unmc.edu View Website Primary Contact: Jane Meza PhD (402) 559-6825 jmeza@unmc.edu | Services offered: Computational - Biostatistics Data Analysis Associations: CTSA COBRE Cancer Center INBRE |
The vision of the CCORDA is to advance clinical, translational and public health research at UNMC and in the community and region. The mission of the CCORDA is to provide expertise in the quantitative sciences, including biostatistics, epidemiology, and health services research, and to coordinate the collaborative design, planning, conduct, analysis and interpretation of laboratory, clinical, and public health research studies. In addition, the center will provide educational training opportunities for quantitative sciences graduate students and educational opportunities for public health, clinical, and translational investigators. ---- Additional services include: Biomedical ethics, epidemiology, geospatial analysis, health services research, health promotin research and environmental and occupational health research. |
| COBRE Imaging and Physiology Core University of Vermont E015 Given 89 Beaumont Ave. Burlington, VT 05405 (802) 656-0413 tclason@uvm.edu View Website Primary Contact: Todd Clason (802) 656-0413 tclason@uvm.edu | Services offered: Cell Imaging Confocal Microscopy Data Analysis Microscopy Multiphoton Microscopy Optical Imaging Outreach Support Services - Shared Instrumentation Oversight & Maintenance Associations: NERTRN COBRE | The COBRE Imaging and Physiology Core provides a wide range of imaging techniques for fixed and live-cell immunofluorescence preparations. We maintain a Noran/Prairie Technologies LSCM (laser scanning confocal microscope), a DeltaVision RT restoration microscopy system, a Zeiss/BioRad dedicated multiphoton LSCM, a Nikon TIRF (total-internal reflection fluorescence) system, a Lamda DG-4 calcium ratiometric imaging system, an Andor iXon/Olympus widefield fluorescence microscope, and a Nikon SMZ-1500 fluorescence stereoscope. Patch-clamp electronics are available for use on most microscope systems, and each system has an integrated perfusion setup. |
| 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 View Website Primary Contact: Rajesh S. Murthy, Ph.D. (701) 231-8322 Rajesh.Murthy@ndsu.edu | Services offered: Mass Spectrometry Nuclear Magnetic Resonance (NMR) Peptide Synthesis Spectroscopy Organic Synthesis Associations: COBRE | 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 the 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. |
| Delaware Biotechnology Institute University of Delaware 15 Innovation Way Newark, DE 19711 (302) 831-3456 oneal@dbi.udel.edu View Website Primary Contact: Dr. Douglas O'Neal (302) 831-3456 oneal@dbi.udel.edu | Services offered: Computational - Bioinformatics Data Analysis Associations: INBRE EPSCoR COBRE | 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. |
| DNA Core Lab - Core Facility for Nucleic Acid Analysis University of Alaska PO Box 757000 909 N. Koyukuk Dr., 207 West Ridge Research Building Fairbanks, AK 99775 (907) 474-7336 fydna@uaf.edu View Website Primary Contact: Carrie Topp (907) 474-7336 fydna@uaf.edu | Services offered: DNA Analysis Genotyping Real-time qPCR Sequencing - DNA Sequencing Support Services - Shared Instrumentation Oversight & Maintenance Associations: INBRE EPSCoR |
History: The Core Facility for Nucleic Acid Analysis was established at the Institute of Arctic Biology in 1995 with a grant from the National Science Foundation (Instrumentation and Instrument Development Program). It is a staffed facility intended to keep UAF at the "cutting edge" of nucleic acid analysis in evolutionary biology, molecular biology, and wildlife and fisheries management. UAF was recently the beneficiary of an NSF EPSCoR grant, an NIH BRIN (INBRE) grant, and an NIH COBRE grant, part of which was designated for new genomic instrumentation. Over the last few years the Core Facility has grown from having only one ABI 373 slab gel sequencer to having two capillary sequencers ( ABI 3100, ABI 3130xl) plus several other major pieces of instrumentation and various other supporting equipment. See Equipment listing on our website for more information on instruments. Services: The Core Facility provides nucleic acid sample analysis, and maintenance and support for molecular instruments (some of which may be too expensive for individual labs to own) for both UAF and outside users. The Core Lab facilitates learning by hosting training workshops and seminars for instrumentation and techniques to help students, faculty, and staff learn to use available equipment. The Core Lab also provides tours to middle and high school students/teachers, undergraduate students, graduate students, research staff, faculty candidates, and local or out of state visitors. The Core Lab has also been involved in several undergraduate/graduate classes offered by the Biology Department and the Chemistry Department. See Services and Fees on our website for more information on lab services. Users and Research: Of all facilities at UAF, the Core Facility may have the broadest interdisciplinary focus, since it attracts users from more than twenty PI labs from seven departments at UAF and UAA, the Alaska Sea Life Center, visiting students and scholars from Sweden, Russia, the Czech Republic, and others. See Past and Present Research for more research information. |
| IBEST Bioinformatics Core University of Idaho, IBEST Dept. of Biological Sciences Moscow, ID 838443051 (208) 885-7062 foster@uidaho.edu View Website Primary Contact: James A Foster (208) 885-7062 foster@uidaho.edu | Services offered: Computational - Bioinformatics Computational - Biostatistics Data Analysis DNA Analysis Associations: COBRE EPSCoR INBRE |
IBEST Bioinformatics Core – Four compute clusters: 512 core AMD64 primary production system; 96 processor Intel Xeon secondary production system; 96 processor PowerPC G5 tertiary production system; 44 processor Intel Xeon development system. Data Storage: 70TB total storage capacity; 30TB used by the main production cluster and 20TB split between the secondary and tertiary production systems and the development system; 20TB of the total belongs to our tape backup system. Several high end stand-alone servers for non-parallel or non-array projects. All systems are housed in a data center on the University of Idaho campus specifically designed for the purpose of high performance computing. ---- Bioinformatics training, and bioinformatics workbooks for the classroom |
| 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 (603) 653-9916 jacqueline.smith@dartmouth.edu | Services offered: Cell Culture Flow Cytometric Analysis Tissue Culture ELISPOT, Treg analysis; Treg function Associations: Cancer Center COBRE |
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 |
| Laboratory for Genomics and Bioinformatics University of Oklahoma Health Sciences Center 975 NE 10th Street BRC1106 Oklahoma City, OK 73104 (405) 271-2337 microgen_support@ouhsc.edu View Website Primary Contact: Dr. Allison Gillaspy (405) 271-1201 x 2 allison-gillaspy@ouhsc.edu | Services offered: Computational - Bioinformatics Genomics Genotyping Microarray Nucleic Acid Extraction Proteomics Real-time qPCR RNA analysis Sequencing - Capillary Sequencing Sequencing - DNA Sequencing Surface Plasma Resonance (SPR) small molecule interactions using SPR Associations: INBRE COBRE | The Laboratory for Genomics and Bioinformatics is a genomics facility offering DNA sequencing (custom and genome-scale projects) via both the Applied Biosystems SOLiD sequencing platform and 3730xl capillary sequencers. Other services include high-throughput plasmid prepping, genotyping (microsatellite and SNP), microarray design, hybridization and data analysis as well as protein separation using the Beckman PF2D system and small molecule interaction studies using SPR technology. |
| Life Science Informatics University of Alaska 909 Koyukuk Drive, Room 222 PO Box 757280 Fairbanks, AK 99775 (907) 474-6384 biotech@alaska.edu View Website Primary Contact: Rebecca Koskela (907) 474-6384 rebecca.koskela@alaska.edu | Services offered: Computational - Bioinformatics Computational - Biostatistics Data Analysis Outreach Data Management Associations: INBRE EPSCoR |
The Life Science Informatics Core cyberinfrastructure includes two computing clusters, a large memory computational server, a database server, and a file server. All of the Core servers are housed in University of Alaska Butrovich Computer Data Center. The Data Center provides uninterrupted power systems (UPS), room environmental monitoring, fire alarm/suppression systems, and card access and video security systems. The 19-node (64-bit Linux) Penguin Cluster hosts the Bioinformatics Computational Portal. This cluster provides accessible computations: users without the knowledge of Unix can submit computational jobs through a web-based interface. The Portal was designed to meet the needs of researchers at University of Alaska. The Computational Portal has over 40 applications in the following categories: similarity and homology, sequence analysis, population genetics, phylogenetic analysis, and miscellaneous utilities. Although the most current applications are for genomics, we generally install and attach the web interface to any life-science software requested. The Portal software is flexible enough to create web-based data-analysis pipelines. In addition, educators can use the Portal for undergraduate training: students can experience first-hand genomic analysis through a web interface that is not intimidating. The 7-node Apple Mac G5 Clusters 7-node is used as a login cluster. Parallelized custom work flows have been created for investigators to run on the login cluster. Users who are more comfortable with a command-line interface, who write their own scripts and install or write their own analysis programs use the login cluster. An IBM system consisting of 3 nodes, each with 24 cores and 128GB of memory, was recently purchased and will be in production by 4th quarter 2009. The Core also provides an infrastructure for collaboration among researchers that enables dissemination of data and information collected by researchers. The Secure File Share (SFS) allows researchers to securely share documents and data with their collaborators, both within and outside of the United States. The SFS allows users on different architectures (PCs, Macs, and Linux computers) to seamlessly share files through an easy drag and drop interface. Users can also request a locking file share that requires that multiple users check out documents in order to facilitate editing of the documents. The Life Science Informatics Core maintains and designs web pages to share the data collected by University of Alaska investigators. |
| Marine DNA Sequencing and Analysis Center Mount Desert Island Biological Laboratory PO Box 35 Old Bar Harbor Rd. Salisbury Cove, ME 04672 (207) 288-9880 x 130 mdibl_info@mdibl.org View Website Primary Contact: Christine Smith (207) 288-9880 x 130 cmsmith@mdibl.org | Services offered: Computational - Bioinformatics Data Analysis DNA Analysis Genomics Genotyping Microarray Nucleic Acid Extraction oligo synthesis Real-time qPCR RNA analysis RNA Integrity Sequencing - Capillary Sequencing Sequencing - DNA Sequencing Associations: INBRE |
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. ---- Expressed sequence tags (ESTs) are produced for six marine species from the Gulf of Maine: dogfish shark (Squalus acanthias), little skate (Leucoraja erinacea), killifish (Fundulus heteroclitus), American lobster (Homarus americanus), green crab (Carcinus maenas), and copepod (Calanus finmarchicus). All ESTs are available in GenBank and library clones are available upon request. Oligonucleotide microarrays based on ESTs and other transcripts are available for killifish, lobster, green crab, and copepod. |
| Mass Spectrometry and Proteomics Core Facility University of Nebraska Medical Center 985819 Nebraska Medical Center Omaha, NE 68198-5819 (402) 559-4956 mspcf@unmc.edu View Website Primary Contact: Melinda Fittje (402) 559-4956 mfittje@unmc.edu | Services offered: Mass Spectrometry Proteomics Support Services - Shared Instrumentation Oversight & Maintenance Associations: INBRE |
Mission of Mass Spectrometry and Proteomics Core Facility (MSPCF) at the University of Nebraska Medical Center is to enhance the capacity for research. Our main goals are: 1. to establish an integrated proteomics program to support researchers at the UNMC in their efforts to seek extramural funding, 2. to provide high quality services, to facilitate collaborative scientific effort with other institutions of higher education within State of Nebraska, and 3. to provide state-of-the-art environment for education of researchers in techniques of mass spectrometry and proteomics. ---- MSPCF provides services for UNMC and non-UNMC affiliates. These services include: protein identification, molecular weight determination, zip tipping, consultations and training.MSPCF has the following instruments: LTQ Orbitrap XL ETD, LCQ Deca Plus System, 4800 MALDI TOF/TOF Analyzer, 4000 Q TRAP LC/MS/MS System, to provide better services. Please visit our website to learn more about us. |
| Medical University of South Carolina Proteogenomics Facility Medical University of South Carolina 173 Ashley Avenue Charleston, SC 29425 (843) 792-2418 argraves@musc.edu View Website Primary Contact: Scott Argraves (843) 792-5482 argraves@musc.edu | Services offered: Computational - Bioinformatics Data Analysis Microarray Associations: INBRE EPSCoR COBRE | The MUSC ProteoGenomics Facility offers a range of proteomic and genomics services to the MUSC research community as well as to outside academic and corporate researchers. We perform multiplex bead array analysis (i.e., phosphoprotein, cytokine and miRNA analysis), surface plasmon resonance based biomolecular interaction analysis (i.e., BIAcore), qualitative analysis of RNA (Agilent Lab-on-a-chip Bioanalyzer), DNA microarray screening (i.e., Affymetrix gene expression and SNP analysis), analysis of DNA microarray data and web-based archiving of array data |
| Microarray University of Vermont 305 Health Science Research Facility Burlington, VT 05405 (802) 656-2557 timothy.hunter@uvm.edu View Website Primary Contact: Tim Hunter (802) 656-2559 timothy.hunter@uvm.edu | Services offered: Genotyping Microarray Outreach RNA Integrity Associations: NERTRN INBRE COBRE | The UVM Microarray Core Facility was initiated by the Vermont Genetics Network and established in 2002 in collaboration with the Vermont Cancer Center and UVM College of Medicine. The facility utilizes the Affymetrix GeneChip system for microarray analysis, the NanoDrop spectrophotometer and Qubit for critical nucleic acid quantification, the Agilent 2100 Bioanalyzer for DNA and RNA analysis, and the MP Biomedicals Fast Prep-24 for extracting RNA or DNA from difficult tissues or sample types. Services offered include: RNA extraction from difficult sample types, training for proper RNA handling and extraction, global gene expression profiling for eukaryotes and prokaryotes using the standard 3’ arrays, gene and exon arrays for human and mouse, DNA mapping (SNP) studies, and custom arrays. The facility staff has developed protocols for novel sample types including formalin fixed paraffin embedded tissues for DNA mapping studies, high recovery isolation of nucleic acids from LCM and FACS sorted samples, and prokaryotic target preparation from limited quantity RNA samples. All microarray projects are reviewed using an integrated approach to experimental design, workflow, and sample collection in collaboration with the UVM Bioinformatics Core Facility to ensure high quality, statistically relevant results. The facility also sponsors user educational forums such as technology seminars, tutorials, general lectures, workshops, and an annual open house. |
| MidSouth Bioinformatics Center at UALR University of Arkansas at Little Rock Applied Science/ETAS 575 2801 S. University Ave. Little Rock, AR 72204 (501) 569-8501 bioinformatics@ualr.edu View Website Primary Contact: Roger Hall, Technical Director (501) 569-8074 rahall2@ualr.edu | Services offered: Computational - Bioinformatics Computational - Biostatistics Outreach Associations: INBRE | The MidSouth Bioinformatics Center (MBC) at UALR provides computational and consulting resources for researchers and students in Arkansas. Founded in 2002 by Dr. Steve Jennings (Executive Director), the Center has been instrumental in supporting the growth of bioinformatics within the State of Arkansas and the MidSouth region of the US. The MBC's primary clients are the graduate students in the UALR/UAMS bioinformatics graduate program, the undergraduate institutions and researchers affiliated with the Arkansas NIH NCRR INBRE program, and researchers at the medical institutions in Arkansas (the University of Arkansas for Medical Sciences, the VA Hospitals, and Arkansas Children's Hospital). Additionaly, Center staff provide outreach and workshops on bioinformatics-related technologies to a variety of audiences and provides technical support to the MidSouth Computational Biology and Bioinformatics Society (www.MCBIOS.org). |
| Molecular Bioinformatics Shared Resource University of Vermont E-315 Given Building Burlington, VT 05405 (802) 656-4608 Julie.Dragon@uvm.edu View Website | Services offered: Computational - Biostatistics Associations: NERTRN Cancer Center COBRE CTSA INBRE |
Personnel: Jeff Bond and Julie Dragon Services: Bioinformatics, almost exclusively Affymetrix GeneChip expression analysis |
| Molecular Pathology Core of the COBRE Center for Cancer Res. Dev. Rhode Island Hospital Aldrich 611, 593 Eddy St. Providence, RI 02903 (401) 444-5849 pmeitner@lifespan.org View Website Primary Contact: Trish Meitner (401) 444-5849 pmeitner@lifespan.org | Services offered: Assays and Measurements DNA Analysis Immunohistochemistry Laser Capture Microdissection Microscopy Nucleic Acid Extraction Optical Imaging PCR Arrays Real-time qPCR RNA analysis RNA Integrity Support Services - Shared Instrumentation Oversight & Maintenance Tissue microarray, Human tumor bank Associations: Cancer Center COBRE INBRE | Our core provides specialty immunohistochemical services, instrumentation, training and support personnel for the research efforts of the COBRE CCRD mentors and their junior associates as well as the academic community at large. We are located on the sixth floor of the Aldrich Building within the main campus of Rhode Island Hospital. Our equipment includes an Arcturus AutoPix automated laser capture microdissector, Stratagene MX4000 realtime PCR instrument, BioRad iCycler, Agilent Bioanalyzer, Olympus fluorescence-capable microscope with image analysis software, Ventana Discovery immunohistochemistry processor, microtome, cryostat, Beecher tissue arrayer and Aperio ScanScope. Our tissue bank has 40 cu ft of ultra-low freezer space and provides human tumor tissue samples to all interested investigators who have received IRB approval for academic testing and research. |
| Molecular Research Core Facility Idaho State University 921 S. 8th Ave. Stop 8007 Gale Life Sciences Building Room 461 Pocatello, ID 83209-8007 (208) 282-4890 mrcf@isu.edu View Website Primary Contact: Erin O'Leary-Jepsen (208) 282-4890 oleaerin@isu.edu | Services offered: Data Analysis DNA Analysis Genomics Genotyping Microarray Microscopy Nucleic Acid Extraction Optical Imaging Real-time qPCR RNA analysis Sequencing - Capillary Sequencing Sequencing - DNA Sequencing Support Services - Shared Instrumentation Oversight & Maintenance Western Blot Associations: INBRE EPSCoR | Molecular Research Core Facility |
| MSU Functional Genomics Core Facility Montana State University Dept of Microbiology 109 Lewis Hall Bozeman, MT 59717 (406) 994-5666 kmcinnerney@montana.edu View Website Primary Contact: Kate McInnerney (406) 994-5666 kmcinnerney@montana.edu | Services offered: Data Analysis Laser Capture Microdissection Microarray Real-time qPCR RNA analysis Associations: INBRE |
The Functional Genomics Core Facility provides instrumentation and support for academic investigators, primarily in Montana and the Rocky Mountain west. The Core's current instrumentation and software includes: (1) Agilent Bioanalyzer for qualitative assessment of RNA integrity; (2) Affymetrix GeneChip station: Hyb Oven 640, Fluidics Station 450, G7 Scanner and GCOS v1.4 processing software; (3) Slide-type microarray station: hyb oven with rotation, Tecan HS400 hybridization and fluidics station (accomodates four full length slide arrays), and GenePix 4000B dual wavelength scanner with GenePix Pro data extraction software; (4) qPCR station: Corbett CAS-1200 liquid handling robot, five-laser RotorGene 3000 qPCR cycler, and five-laser RotorGene 6000 with high resolution melt for qPCR and SNP detection; (5) Open-source analysis software including FlexArray, MeV, and VAMPIRE; (6) Zeiss-PALM laser-capture/catapult (UV) microdissection microscope and optical tweezers (IR) for manipulation of living or fixed cells and tissues. |
| Neuroscience COBRE - Cellular and Molecular Biology Core University of Vermont 414A Health Science research Facility Burlington, VT 05405 (802) 656-2007 Sheryl.White@uvm.edu View Website Primary Contact: Sheryl White | Services offered: 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/Purification Proteomics Real-time qPCR RNA analysis SDS-PAGE Spectroscopy Tissue Culture Western Blot Associations: NERTRN COBRE |
This facility, sponsored by the NCRR COBRE program, provides consulting expertise, training and many sophisticated pieces of equipment for performing molecular biology, proteomics, cell culture, histology and microscopy. The following major pieces of equipment are available in the core: Zeiss Palm Microlaser, Ciphergen SELDI-TOF, Microbrightfield Neuroleucida Morphometrics system, Odyssey Infrared Imager, BioRad Calligrapher microarray printer, Qiacube robot, BioRad Experion and much more. Use of the equipment is currently free for all users. ---- This core is available to all researchers at UVM, UVM affiliates and also researchers outside of UVM by prior agreement. Please contact us for further information. |
| Next Gen Sequencing Center at NCGR 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: Computational - Bioinformatics Data Analysis DNA Analysis Genomics Genotyping RNA analysis Sequencing - Capillary Sequencing Sequencing - DNA Sequencing Sequencing - Next-Gen Sequencing mRNA seq, small RNA seq, ChIP seq, DGE, JMP Genomics Associations: INBRE |
Next Generation Sequencing Center --------------------------------- CS-Pro certified Illumina Genome Analyzer Sequencing and Alpheus® (http://alpheus.ncgr.org/) Pipelining and Analysis Services - whole genome shotgun sequencing - mRNA-seq - small RNA-seq - ChIP-seq - Digital Gene Expression (tagged) - 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 sequencing efforts are cluster stations for flow cell construction, and Agilent bioanalyzer and a NanoDrop devices for sequencing library QA/QC. The wet lab at the NCGR Sequencing Center 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 ---- Alpheus® Next Generation Sequence Data Analysis: Analyzes 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 also determines gene expression, comparing values across groups of samples. Alpheus 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. |
| Pathology Laboratory For Translational Medicine West Virginia University Robert C. Byrd Health Sciences Center Mail Stop 9203 Morgantown, WV 26506 (304) 293-0287 jcoad@hsc.wvu.edu View Website Primary Contact: James Coad, MD (304) 293-1635 jcoad@hsc.wvu.edu | Services offered: Assays and Measurements F.I.S.H. Immunohistochemistry In Situ Hybridization Laser Capture Microdissection Microscopy Monoclonal Antibody Necropsy Protocol Development/Clinical Trial Coordination Thermal Analysis Associations: Cancer Center COBRE |
The Pathology Laboratory for Translational Medicine (PLTM) has been in existence since 2002 and serves the anatomic pathology (histology) needs of basic, clinical and translational researchers at WVU and other outside institutions. The PLTM mission is to provide both local and national researchers with access to high quality tissue processing and histology techniques. By providing these services, the PLTM helps fulfill WVU Health Sciences Center’s mission to strengthen basic and clinical scientific research by providing education and access to pathology services. The PLTM operates under Good Laboratory Practices (GLP) and CLIA 88 regulations. The laboratory currently provides assistance with tissue handling, fixation, processing, staining and/or interpretation on a fee for service basis. Dr. James Coad, a board certified anatomic pathologist with over 15 years of experience in human and animal translational medical research, directs the laboratory. The PLTM is staffed by an administrator, three ASCP registered histotechnicians and one laboratory assistant. These employees are also cross-trained with the WVU tissue bank to optimize work flow coverage. The most requested PLTM services are professional guidance (dissection, processing and interpretation), tissues processing (frozen and paraffin-embedding), tissue staining (routine and advanced immunostaining), frozen sectioning and unstained paraffin sectioning. Other custom services are available upon request, such as paraffin ribbon cutting for DNA/RNA/protein work or sections for laser capture microdissection. At a time when new methodologies are continuously emerging, the PLTM seeks to provide guidance and access to these techniques for basic and clinical biomedical researchers. Future technologies for the PLTM would include expansion of hybridization techniques for the confirmation and localization of protein expression, viruses, genetic translocations/changes (in situ hybridization: chromogenic or FISH) and genetic complement changes (comparative genomic hybridization). Automated immunohistochemical procedure expansion will be sought to provide more uniform and reproducible staining to complement quantitative image analysis advances. The PLTM strives to participate in multidisciplinary investigations by providing access to state-of-the-art pathology techniques, tissue handling and expert interpretive consultation. It seeks to provide pathology services that will optimize utilization of other WVU core laboratories, such as the imaging core (fostering well prepared and stained tissues) and specimens for molecular core testing (frozen or paraffin ribbons). These services are available to investigators using animal models and human tissues alike. |
| Protein Production Core Facility University of Delaware Delaware Biotechnology Institute 15 Innovation Way Newark, DE 19711 (302) 831-4687 wu@dbi.udel.edu View Website Primary Contact: Yu-Sung Wu (302) 831-3441 wu@dbi.udel.edu | Services offered: Protein Extraction/Purification SDS-PAGE Support Services - Shared Instrumentation Oversight & Maintenance Protein purification Associations: COBRE |
The Protein Production Core Facility at DBI provides fermentation and purification capabilities for large-scale protein expression and purification. We have New Brunswick BioFlo 4500 fermentor for bacterial and yeast cell growth. The facility also includes equipment for cell rupture and for protein purification and characterization. The installation was established and is operated with the support of the National Center for Research Resources of the National Institutes of Health as part of the COBRE Membrane Protein Production and Characterization at the University of Delaware. ---- fermentation |
| RI-INBRE Centralized Research Core Facility University of Rhode Island Fogarty Hall 222 41 Lower College Road Kingston, RI 02881 (401) 874-5731 inbrelab@etal.uri.edu View Website Primary Contact: Aftab Ahmed (401) 874-5731 aahmed@uri.edu | Services offered: 2D-PAGE Assays and Measurements Biochemical Analysis Cell Culture Cell Imaging Cell Sorting Computational - Bioinformatics Data Analysis Flow Cytometric Analysis Mass Spectrometry Microarray Microscopy Molecular Imaging Optical Imaging PCR Arrays Protein Extraction/Purification Proteomics Real-time qPCR RNA analysis SDS-PAGE Sequencing - Protein Sequencing Spectroscopy Support Services - Glass Washing/Autoclaving Tissue Culture SELDI-TOF Associations: INBRE |
Research Core Facility The facility is supported by the Rhode Island IDeA Network of Biomedical Research Excellence (RI-INBRE) grant and by the institutions participating in the grant. The facility provides research and training support to RI-INBRE participants and to the Rhode Island biomedical research community. It is equipped with instrumentation for biomedical, pharmaceutical, and biotechnological research. ---- Poster printingFPLC/HPLC Purification Flash Chromatography |
| SD BRIN Bioinformatics Core Facility University of South Dakota 414 E Clark St Vermillion, SD 57069 (605) 677-5388 csci@usd.edu View Website Primary Contact: Carol Lushbough (605) 677-5388 carol.lushbough@usd.edu | Services offered: Computational - Bioinformatics Computational - Biostatistics Associations: INBRE |
We are working on a variety of projects in conjunction with the USD Sanford School of Medicine. This collaboration is intended to get computer science students involved in bioinformatics research at both the graduate and undergraduate levels. Students in our department are involved in developing the infrastructure necessary to carry on research in bioinformatics by creating software solutions to fit the needs of faculty involved in this field of research. These projects are funded through external grant sources. ---- Large computing cluster, BioExtract Server, BioStream, Table Maker |
| SD BRIN Genomics Core Facility University of South Dakota 414 E Clark St Vermillion, SD 57069 (605) 677-5159 keyster@usd.edu View Website Primary Contact: Dr. Kathy Eyster (605) 677-5159 | Services offered: Data Analysis DNA Analysis Genomics Microarray Real-time qPCR Sequencing - DNA Sequencing Associations: INBRE | The Genomics Core Facility will continue to support DNA microarray analysis of differential gene expression, RNA and DNA analysis by the Agilent microfluidics chip reader, and real time PCR/RT-PCR. To maintain the relevance of the core, we believe that it is important to add new services to the core to enable examination of the functions of genes that have been shown to be differentially expressed by DNA microarray. To this end, the GCF is currently purchasing the Amaxa Nucleofector II transfection equipment. This technology allows transfection of DNA constructs, RNAi/siRNA/ shRNA, peptides, antibodies and other biomolecules into living eukaryotic cells. The Amaxa nucleofection system is optimized for transfection of cells that are otherwise difficult to transfect. |
| SD BRIN Proteomics Core Facility University of South Dakota 414 E Clark St Vermillion, SD 57069 (605) 677-5530 eduardo.callegari@usd.edu View Website Primary Contact: Eduardo Callegari (605) 677-5530 eduardo.callegari@usd.edu | Services offered: 2d Spectra Acquisition and Interpretation Computational - Bioinformatics Data Analysis Mass Spectrometry Molecular Imaging Proteomics Support Services - Shared Instrumentation Oversight & Maintenance Associations: INBRE | The SD BRIN/USD Proteomics Core Facility provides state-of-the-art proteomics services to researchers from South Dakota and the region. Since 2002, the USD PCF has been providing proteomic analyses, as well as collaborating in the training of the use of common equipment such as the scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. Our goal is to provide all South Dakota researchers with the capability to rapidly analyze and identify protein expression patterns in their experimental systems. |
| The Bioinformatics Shared Resource Dartmouth Medical School One Medical Center Dr. Lebanon, NH 03756 (603) 653-9939 jason.h.moore@dartmouth.edu View Website Primary Contact: Jason H. Moore, Ph.D. (603) 653-9939 jason.h.moore@dartmouth.edu | Services offered: Computational - Bioinformatics Computational - Biostatistics Data Analysis Visualization Associations: Cancer Center COBRE CTSA INBRE |
Cutting-edge bioinformatics analysis of genetic, genomic and proteomic data. Services include: 1) Applied bioinformatics and data mining 2) Database development and programming 3) Computer programming and software engineering 4) High-performance computing ---- Scientific visualization |
| Transgenic Animal Core Facility West Virginia University PO Box 9303 Morgantown, WV 26506 (304) 293-7271 transgenic@hsc.wvu.edu Primary Contact: Peter Mathers (304) 293-0271 pmathers@hsc.wvu.edu | Services offered: DNA Analysis Transgenics Rederivation, Cryopreservation, Chimera Production Associations: COBRE | The Transgenic Animal Core Facility (TACF) at WVU offers pronuclear DNA injection for transgenic mouse production and embryonic stem cell injection for chimera production. Cryopreservation and rederivation/resuscitation services are also available for the management of genetically modified mice. The facility is housed within an SPF barrier facility on the Health Sciences Center campus. Free consultation is also available to assist in construct design, genotyping, colony management, and special husbandry needs. |
| UAMS Proteomics Core Facility University of Arkansas for Medical Sciences 4301 West Markham St Slot 516 Little Rock, AR 72205 (501) 686-8152 ajtackett@uams.edu Primary Contact: Alan Tackett ajtackett@uams.edu | Services offered: Mass Spectrometry Associations: COBRE INBRE | proteomics |
| University of Louisville Microarray Faciltity University of Louisville Room 807A Anatomical Sciences and Neurobiology 500 S. Preston St. Louisville, KY 40292 (502) 852-3798 sjwaig01@louisville.edu View Website Primary Contact: Sabine waigel (502) 852-3798 sjwaig01@louisville.edu | Services offered: Data Analysis Microarray Sequencing - Capillary Sequencing Associations: COBRE INBRE | The facility contains both Affymetrix and Agilent platforms and provides preliminary analysis of data with the aid of GeneSpring, Partek and Ingenuity software. |
| USC DNA Microarray Facility University of South Carolina at Columbia University of South Carolina School of Medicine Building 1, Room B 47, 6439 Garners Ferry Road Columbia, SC 29208 (803) 463-6852 kim.creek@uscmed.sc.edu View Website Primary Contact: Dr. Kim E Creek (803) 463-6852 kim.creek@uscmed.sc.edu | Services offered: Computational - Bioinformatics Data Analysis Microarray RNA analysis RNA Integrity Associations: INBRE |
Services Provided: The USC DNA Microarray Facility (formerly the SCCC DNA Microarray Facility) can produce Custom Arrays, support Array Design, conduct RNA quality control, amplification and labeling; conduct array hybridization, scanning and data analysis, and assist customers in all aspects of the design and performance of microarray experiments, using Agilent (pre-made and custom) and spotted arrays. In addition, the facility provides support for quantitation and wuality assessment of DNA, RNA and protein on an Agilent 2100 Bioanalyzer. Custom Arrays The facility is equipped to provide custom microarrays for academic and industrial clients. So far we have successfully spotted cDNAs, 50 to 70 base pair oligonucleotides and 18 to 22 base pair short primers. In addition to nucleic acids, the Biochip Arrayer can spot antibodies, proteins, peptides and bacterial cells as well. We produce arrays of the highest quality but at a low density (up to about 2,000 spots per slide). Array Design We assist all clients in designing the appropriate microarray for your needs. We take the guesswork out of array alignment and maintain a high level of spatial precision throughout the printing run. Specification with regard to array design and spot placement is tightly monitored. This attention to detail results in saved scanner time and fewer auto format failures. Hybridization We provide extensive on site training and support for all HybStation, Maui, and Agilent’s Hybridization Oven users. Scanning and Data Analysis Support is provided for spotted microarray scanning and for data analysis with a variety of software packages, including GenSifter. Analysis of RNA, DNA, Proteins and Cells Quantity and quality of your RNA, DNA, proteins and cells are determined with the help of an Agilent 2100 Bioanalyzer. |
| Vermont Genetics Network Outreach Core University of Vermont 120A Marsh Life Science 109 Carrigan Drive Burlington, VT 05405 (802) 656-0028 Janet.Murray@uvm.edu View Website Primary Contact: Janet Murray (802) 656-0028 Janet.Murray@uvm.edu | Services offered: Outreach Associations: NERTRN INBRE |
The goal of the VGN Outreach Core is to expose undergraduates in the state of Vermont to scientific technology & resources using hands-on experiences. We provide all teaching materials, laboratory materials, and laboratory equipment for baccalaureate colleges within the state to run each module. All materials become the property of the recipient institution upon completion of the module. These modules will increase the skills of undergraduate science students within the state and we believe these additional skills help them in their future scientific career development. Currently we provide a Microarray Module and a Bioinformatics Module. Plans for a forthcoming Proteomics Module are in development. |
| WestCore (Western S.D. DNA Core Facility Black Hills State University 1200 University Blvd, Unit 9502 Spearfish, SD 57799-9502 (605) 642-6854 cynthia.anderson@bhsu.edu View Website Primary Contact: Dr. Cynthia Anderson (605) 642-6854 cynthia.anderson@bhsu.edu | Services offered: Genotyping Library Services Sequencing - DNA Sequencing marker development Associations: INBRE |
The Western South Dakota DNA Core Facility (WestCore) was established in 2003 as part of the South Dakota Biomedical Research Infrastructure Network (SD-BRIN). We complement the Proteomics and Genomics BRIN core facilities. Our primary services include DNA sequencing, genotyping, marker developing and library construction. Priority is given to SD-BRIN/INBRE research, but services are also provided to non-BRIN/INBRE university researchers as well as government agencies and some private organizations. Westcore is a fully staffed laboratory with automated DNA instrumentation, and has a federally approved quality management plan. |
| WVU Flow Cytometry Core Facility West Virginia University HSCN Room 2160 PO Box 9177 Morgantown, WV 26506-9177 (304) 293-6273 flowcore@hsc.wvu.edu View Website Primary Contact: Kathleen Brundage, Ph.D. (304) 293-6273 kbrundage@hsc.wvu.edu | Services offered: Cell Sorting DNA Analysis Flow Cytometric Analysis Associations: Cancer Center COBRE INBRE | The WVU Flow Cytometry Core Facility provides instrumentation and scientific support for cell analysis and sorting. The facility routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell quantitation, cytokine production, and cell sorting based on antigen expression or cell cycle. This facility is currently equipped with two cytometers. The Becton-Dickenson (BD) FACSAria is a 15 parameter (13 fluorescent markers and two scatter parameters) high-speed bench top sorter capable of sorting into 4 different populations. In addition, the FACSAria has a BD aerosol management system for aseptic sorting as well as the ability to maintain temperature during the analysis and sorting of samples. The second instrument in the facility is a BD dual laser FACSCalibur equipped with a sample autoloader and has the capability of 4 color analysis. In addition to the two cytometers, the facility has a Miltenyi Biotec AutoMACS and tissue culture hood for sterile magnetic cell sorting. The Flow Cytometry Core has several software packages including FCS Express, CellQuest Pro, ModfitLT and BD Diva software for data acquisition and analysis. |
