HSC Core Research Facilities - University of Utah

Core Facility News/Announcements

Dear Colleagues:

We wish to announce the following.

1. An Illumina BeadXpress Station is available in the DNA Sequencing and Genomics Core Facility for researchers doing medium to high throughput SNP genotyping. GoldenGate technology from Illumina allows researchers to genotype hundreds to thousands of samples using custom selected SNP assays. Illumina currently offers these SNP assays in 96 or 384 multiplex level formats allowing for flexibility in the number of SNPs that can be genotyped at one time. Users will coordinate with Illumina to develop a working list of SNPs and have assays delivered directly to the Core. All lab work and initial analysis will be performed by Core Lab technicians and the user will be provided with results tables and the opportunity to review the data generated by the BeadXpress Station. The price for GoldenGate SNP genotyping can vary from 7 cents per genotype to $1 or more depending on the number of samples and the level of multiplexing for the project. More information about using GoldenGate SNP genotyping assays along with a calculator to estimate project costs can be found at http://www.cores.utah.edu/dsgc/services/BeadXpress.html

For further information contact
Michael Klein
DNA Sequencing and Genomics Core Facility
(801) 585.2977
mklein@cores.utah.edu


2. Photon Confocal Microscope Update:
Imaging Core facility confocul users, the 2photon is ready for regular users. This instrument is specialized for live cell imaging in particular thick samples. 2photon minimizes the photobleaching that occurs with repetitive z scanning, and allows laser penetration through thick light scattering samples. The FV300 2photon runs using the older confocul software similar to the other two FV300s and is on an upright microscope. We currently have filters and excitation lines for single imaging of either CFP, GFP, YFP or mCherry. Water immersion 40x 60x dipping and 10 and 30x dry objectives are available. Schedule 2 hours for software use and laser safety training.

3. HCI recently purchased a Solexa next generation sequencer from Illumina and placed it under the management of the Microarray Core facility. The machine currently supports single end and paired end sequencing. Bioinformatic assistance with Solexa data analysis is available through the Bioinformtic Core facility.
http://bioserver.hci.utah.edu/BioInfo/index.php/Sequencing

Thank you,

Jerry Kaplan, Ph.D.
Director, HSC Core Research Facilties

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Our Mass Spectrometry and Proteomics facility recently ranked 1st in a national contest to identify proteins within a complex mixture and 4th in its identification of phosphorylation sites. This competition was held by the Association of Biomolecular Resource Facilities in January 2007; 120 facilities were sent the same complex mixture of proteins and 44 labs submitted results. Congratulations Chad, Krishna and Mike!

The DNA Sequencing and Genomics Core now offers robotic services for those wishing to automate a variety of lab protocols, from 384-well plate pipetting to DNA and plasmid preps, using the Biomek FX and Velocity 11 Vprep robotic stations.

The Microarray core facility has expanded its services to include Affymetrix and Nimblegen platforms, in addition to the Agilent platform. We thank Bob Weiss for his generosity in sharing his lab's Affymetrix chip reader.

The Cell Imaging core has a new high-throughput confocal imager with liquid handling and environmental controls (Pathway 885 from BD Biosciences; http://www.atto.com/products/pathway/). This instrument will allow users to screen small molecule and RNAi libraries for their effects on cell cycle, cytoplasmic and nuclear translocation and co-localization.

The Biostatistics facility offers Ph.D.-level consultation for grant proposals, manuscripts and other research activities requiring biostatistical input. The available services include sample size and power calculations, the development of study designs and analysis plans, interpretation of analysis results and advice

Tom Greene, Ph.D., Director
School of Medicine, 5C124
(801) 585-3812
Tom.greene@hsc.utah.edu

Greg Stoddard, M.S.
(801) 587-9250
greg.stoddard@hsc.utah.edu

The Cell Imaging/ Fluorescence Microscopy facility provides training and consultation on the use of confocal microscopy, widefield automated microscopy, and software analysis tools for the deconvolution and quantitative analysis of image data. Three Olympus confocal microscopes (one FV1000 and two FV300s) can be used with live or fixed samples. Sophisticated image acquisition and analysis regimes are possible, including time-lapse, z-series, ratiometric analysis, and deconvolution.

Chris Rodesch, Ph.D., Director Radiobiology Bldg, Room 55
801-587-7964
crodesch@cores.utah.edu

The DNA Sequencing Core lab is equipped with state-of-the-art high throughput capillary sequencers and robotics. It offers 24-hr turnaround time sequencing services at very competitive prices. It also provides individualized troubleshooting help with sequencing data.

Other custom services include primer walking, PCR services for sequencing based mutation detection, genotyping and SNP discovery, as well as custom sequence data analysis and assembly. Robotics services are also available for those wishing to automate a variety of lab tasks, from 384-well plate pipetting to DNA and plasmid preps using the Biomek FX and Velocity 11 Vprep robotic stations.

Helaman Escobar, Director
School of Medicine, 4A432
801-581-4736
DNA@cores.utah.edu

The Oligonucleotide/Peptide Synthesis facility provides synthetic peptides and oligonucleotides, with specific modifications as needed. Additionally, the facility performs Edman sequencing of proteins/peptides, including the identification of phosphorylation sites using this methodology.

Robert Schackmann, Ph.D., Director
Radiobiology Bldg, Room 12
801-581-4051
bschackmann@cores.utah.edu

The Electron Microscopy core provides investigators with a variety of electron microscopy capabilities and image analysis (quantitative morphology). Technical services offered by the core include transmission and scanning electron microscopy, histochemistry and immunohistochemistry.

Nancy Chandler, Sr. Lab Specialist
801-581-4571
nancy.chandler@hsc.utah.edu

Kurt Albertine, Ph.D., Director
Radiobiology Bldg, Room 71
801-581-4178
kurt.albertine@hsc.utah.edu

The Flow Cytometry facility offers cell sorting and quantitative fluorescent measurements. The facility has a Becton-Dickinson Vantage cell sorter, a Union Biometrica “worm sorter” to fractionate C. elegans based on developmental stage, viability and expression of fluorescent proteins, and two FACscans.

Wayne Green, Ph.D., Director
Wintrobe Bldg, Room 656
801-581-8641
wayne.green@cores.utah.edu

The Genomics Core facility provides full-service genotyping, from PCR set-up through data analysis, for genome-wide scans, fine mapping, allelic imbalance (LOH), microsatellite instability, and SNP detection using capillary electrophoresis and/or TaqMan Assays. The facility also offers researchers access to real-time quantitative PCR instruments (ABI 7900HT) for gene expression and SNP genotyping experiments. Training, consulting and software are made available free of charge to those users. There is also availability to accommodate large SNP genotyping projects using the ABI SNPlex detection system. Please contact the Core for more details.

Helaman Escobar, Director
School of Medicine, 4A432
801-581-4736
DNA@cores.utah.edu

The Microarray Core Facility provides researchers at the University of Utah with access to the Affymetrix and Agilent Technologies microarray platforms. These services are complimented by the acquisition of an Illumina Genome Analyzer which enables the facility to also perform massively parallel DNA sequencing. The combined support for these technologies offers a diverse set of tools for researchers that include measuring gene, exon, or miRNA expression, SNP and DNA copy number profiling, location analysis of DNA binding proteins, defining DNA methylation status, and the sequencing of genomic DNA or resequencing of targeted regions of DNA

Brian Dalley, Ph.D., Director
Office: Huntsman Cancer Institute, Room 3363
801-585-7192
Lab: Huntsman Cancer Institute, Room 3350
801-581-6346
brian.dalley@hci.utah.edu

The Nuclear Magnetic Resonance facility helps researchers determine the structure of proteins, nucleic acids and natural products. The instruments available in the facility include a Varian Unity 500 MHz NMR, a Varian Inova 600 MHz NMR and a Varian Mercury 400. The facility also has several Sun and

Jack Skalicky, Ph.D., Director
Skaggs Hall, Room 295E
801-585-7363
skalicky@biochem.utah.edu

The Protein Interaction (Biacore) facility provides characterization of the assembly state, affinity, and kinetics of macromolecular binding interactions. Currently, the facility has 8 SPR-based biosensors including the BIACORE 3000, 2000 and S51 optical biosensors. These instruments can be used to study interactions between proteins, oligonucleotides, oligosaccharides

David Myszka, Ph.D., Director
School of Medicine, Room 4A417
801-585-5358
dmyszka@cores.utah.edu

The Small Animal Imaging facility has a small animal computed tomography (CT) scanner for use with sacrificed or live animals. Uses include embryonic and adult specimen anatomy, bone mineral density, bone mineral content, bodyfat content, and

Osama Abdullah
A300 (basement level)
E.E. Jones Medical Science Building (EEJMRB)
oabdullah@cores.utah.edu

If there are any difficulties contacting Osama Abdullah please contact:

Edward W. Hsu, PH.D.
Assistant Professor
Bioengineering department
Warnock Engineering Building room 2857
Salt Lake City, UT. 84112-5331
(801) 585-7550

Transgenic and Gene-targeting Mouse Facility

The Core is available to make transgenic mice using both pronuclear injection of embryos and gene-targeting of ES cells and blastocyst injection. The Transgenic and Gene-targeting Core offers related procedures including sperm freezing, embryo freezing, rederivation of mouse lines, IVF, karyotyping, and has added new services such as ICSI and development of primary ES cell lines. The Core is available for technical advice regarding injection procedures, cell culture techniques, vector design and construction; and we are open to new ideas and available to try new methods that you are interested in. The Core maintains the necessary mouse colonies for basic procedures, now including a colony of flp mice.

Susan Tamowski, Director
801-581-3437
tamowski@genetics.utah.edu

Mario Capecchi, Ph.D., Co-Director
801-581-7096
capecchi@genetics.utah.edu

Phillip Clair, M.S.
801-585-7414
pclair@genetics.utah.edu

Leslie Jerominski, M.S.
801-581-3437
leslie.jerominski@genetics.utah.edu

Richard Focht
801-585-7414
rfocht@genetics.utah.edu

The CZAR Facility provides state-of-the-art systems for housing, breeding, and doing experiments with zebrafish, an emerging vertebrate model system. It comprises 6000 fish tanks and redundant circulating water systems, and houses a large number of wildtype and mutant fish strains. It allows large genetic screens carried out as collaborations between multiple laboratories, and can provide animals and training for laboratories wishing to try pilot zebrafish experiments.

Gretchen King, Ph.D., Director
Radiobiology Building, Room 10
801-585-6574
gking@cores.utah.edu

The Bioinformatics Core provides consulting, training, and analysis services for researchers using one-color or two-color microarrays. The services include consultation on experimental design (gene expression, CGH, or ChIP-chip), choice of appropriate microarray platform, selection of analysis methods or tools, and annotation of microarrays.

Bioinformatics Core Facility Wiki

Brett Milash, Co-Director
Huntsman Cancer Institute, Room 3346
brett.milash@hci.utah.edu
801-585-0567

David Nix, Co-Director
Huntsman Cancer Institute
david.nix@hci.utah.edu
801-587-4611

Update on the Worm Core: The worm core has been closed due to staffing and use issues. For those of you that still need to have worm work done there are many good, helpful laboratories on campus tha are willing to assist you in starting up your experiments. The worm sorter has been moved to the flow cytometry core and is still available for use. Other resources of the Worm Core have been distributed to members of the worm community here on campus. If you have some particular need please contact Jerry kaplan through the Core office 581-2425.

Thank you.