DILLER RETREAT TECHNOLOGY POSTERS
Core Technologies Poster Session
2015 HDFCCC Retreat @ Chaminade
Come by to see what CCSG-sponsored
Core Facilities have to offer HDFCCC
members:
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DILLER RETREAT TECHNOLOGY POSTERS
Core Technology Posters:
------------------------------------------- ------------------- ------------------------ --------------------Jennifer Bolen
Manager
Mouse Pathology Core
The Mouse Pathology Core provides histologic research support services to investigators studying the
pathogenesis and treatment of organ malignancies in mouse models of human cancer and other
diseases. To this end the Mouse Pathology Core provides both the equipment and expertise to handle
samples intended for paraffin processing, embedding, and sectioning as well as for samples intended
for frozen OCT processing, embedding, and sectioning. Researchers may submit fixed or unfixed
samples to the Mouse Pathology Core for any of the following services: processing of fixed tissues for
paraffin-embedding, paraffin-embedding, microtome sectioning of paraffin embedded blocks,
Hematoxylin & Eosin staining of paraffin-embedded tissue sections, decalcification of bony specimens
prior to processing, processing of fixed or unfixed tissue for OCT embedding, OCT embedding,
cryosectioning of OCT-embedded tissue blocks, and/ or Hematoxylin & Eosin staining of OCTembedded tissue sections. The core provides education in mouse necropsy, preparation of materials
for histologic analysis, and use of laboratory testing in mice. In addition, the core serves as a hub
through which investigators are linked with skilled pathologists with expertise in the pathologic areas
pertinent to their investigations.
------------------------------------------- ------------------- ------------------------ --------------------Ben Braun
Director
Laboratory for Cell Analysis
(Anna Celli, Sarah Elmes, Jane Gordon)
The Laboratory for Cell Analysis (LCA) supports flow cytometry, cell sorting, and advanced
microscopy. In addition to maintaining and operating instruments, we provide support such as training,
education and consultation. Our current instrument repertoire includes:
Flow cytometry analyzers
RH-512, HD-335, MZ-CRB-S171, GH-301K
Flow cytometry sorters
Fluorescent microscopes
HD-335, GH-S252
HD-355, HD-337, MZ CRB-S171
Time lapse / Spinning disc confocal / TIRF microscopy
Point scanning confocal (inverted)
HD-337
GH-N245, CVRI-559
2-photon confocal (upright) *NEW * CVRI-559
Laser capture microdissection
MZ CRB-S171
Analysis workstation HD-330. We are very pleased to now be able to offer 2-photon microscopy. Our
newly acquired Zeiss LSM 780 MP, is a high sensitivity, state of the art point scanning confocal
microscope coupled to a fully tunable Ti:Saph laser (Chameleon Ultra II, Coherent) for multi photon
excitation. Three completely spectral internal detectors and 6 visible laser lines provide high flexibility
in experimental design, allowing detection of up to 10 channels at a time. In addition, a 34 channel
GaAsP array allows spectral analysis of fluorescent samples and identification of fluorescent species
trough spectral linear unmixing. Specifically designed for in vivo imaging on small animals, this upright
setup is equipped with two external photon counting detectors that significantly increase the system
light collection efficiency thus allowing deep tissue imaging in thick specimens.
Please contact us with your questions, creative ideas, and research needs.
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DILLER RETREAT TECHNOLOGY POSTERS
Kirsten Copren, PhD
Manager
Genome Analysis Core
The UCSF Helen Diller Family Comprehensive Cancer Center Genome Analysis Core provides
services and equipment specializing in genome analysis downstream of RNA and DNA isolation. We
specialize in mid-to high-throughput quantitative PCR, SNP, and gene expression analyses using a
variety of state-of-the-art platforms. We also offer second generation sequencing on the Ion Torrent
Platform, focusing on cancer mutational panels (e.g. Cancer Hot Spot or Comprehensive Cancer
Panels), bisulfite treatment of DNA for epigenetics analysis, protocol development for custom projects,
specialized software trials, general and specific genomics training and consulting.
Instrumentation:
Available through Core services, not for individual reservation:
Ion Torrent Personal Genome Machine (Life Technologies). Semi-conductor based second generation
sequencing.
OpenArray NTCycler (Life Technologies): High throughput nanoliter QPCR with >2300 reactions per
chip.
Two MJ Research tetrad DNA engines with four independent PCR blocks
ABI 9600 PCR block with exchangeable 96- and 384-well blocks
Available for reservation via calendars in MyCores with appropriate training or available
through Core services:
AB 7900HT (Life Technologies/Applied Biosystems): QPCR instrument with exchangeable blocks (96,
384-well Fast PCR, Taqman Low Density Array (TLDA)) and high-throughput plate loading accessory
for ≥4 plates.
Nanodrop 8000 (Thermo Scientific): UV-Vis Spectrophotometer with multi-sample (1-8) micro-volume
(1ul) measurements.
Agilent 2100 Bioanalyzer (Agilent Technologies): Microfluidics-based (Lab-On-A-Chip) platform for
sizing, quantification and quality control of DNA, RNA, protein, and cells.
Synergy HT Plate Reader (BioTek): Multi-Mode Microplate Reader for fluorescence, absorbance and
luminescence measurements. 96w & 384w plates
------------------ -------------------------------- ----------------------------------------- ----------------------------Byron Hann, MD PhD
Research Scientist
Preclinical Therapeutics Core
The UCSF Preclinical Therapeutics Core (PTC), a shared resource of the UCSF Helen Diller Family
Comprehensive Cancer Center serves the preclinical needs of investigators by providing a wide range
in vivo models and animal-based methodologies. A source of expertise in animal-based translational
science, the PTC helps validate experimental agents for subsequent clinical application. The Core’s
services include: customized preclinical experimental design, generation of tumor-bearing mice,
administration of experimental agents, pharmacological evaluation (e.g, PK & PD), expertise in small
animal surgery, molecular imaging in a range of platforms, evaluation of tumor burden in response to
therapeutic intervention, and analysis and interpretation of study results.
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DILLER RETREAT TECHNOLOGY POSTERS
Sergey Magnitsky, PhD
Assistant Researcher
Small Animal MRI Facility
Preclinical Imaging Facility at China Basin. I will provide an overview of Small Animal Imaging
capabilities at China Basin. Our facility provides multi-modality radiological imaging and image
analysis for cells, tissues, and small animals. Our facility combines state-of-the-art instrumentation
and a nationally recognized staff to assist investigators with a wide range of imaging based
experimental approaches. Currently we provide a comprehensive suite of imaging modalities
including: magnetic resonance imaging (MRI) and spectroscopy (MRS), optical imaging (including
bioluminescence and fluorescence), computed tomography (CT), positron emission tomography
(PET) and single photon emission computed tomography (SPECT). In addition, dedicated housing is
available for mice and rats undergoing longitudinal imaging studies. This facility includes a
conveniently located and well-equipped animal preparation room with a wide assortment of supporting
equipment.
------------------------------------------- ------------------- ------------------------ --------------------- -------------------------
Sorena Nadav, MS MMI
Director
Translational Informatics
Assistant Director: Hannes Niedner M.D.
Translational Informatics Technology Core: providing expertise, platforms, and solutions supporting
precision oncology and clinical research operations at the HDFCCC.
The Translational Informatics Core provides experts in Informatics and Data Management for the
University of California San Francisco centralizing the operation and support for clinical and
biomedical data collection and dispersal. The Core offers a suite of services to support translational,
biomedical, clinical research and clinical care improvement by focusing on the capture, storage, and
dissemination of clinical and research information that can easily be merged, integrated, or
aggregated with other data sets.
These services include providing secure storage of large scale genomic, expression, and other
research data, as well as clinical, pathology, and imaging data, with the opportunity to link clinical and
research data. This core also implements the standardization and quality assurance of such data;
and support dataset preparation for data sharing for internal and external scientific. The TI Core is a
Core’s Core, providing Informatics support services as needed for other Core’s such as the Tissue
Core.
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DILLER RETREAT TECHNOLOGY POSTERS
Adam Olshen , PhD
Director
(Henrik Bengtsson, Saurabh Asthana, Ritu Roy, Mark Segal )
Computational Biology Core
The Computational Biology Core: High-Throughput Sequencing Analysis
The dramatic potential of high throughput sequencing is fueling demand for analysis support. We
have developed and will continue to develop both standard and specialized sequencing pipelines.
Our standard pipelines, like the copy number pipeline shown here, are built on top of the open-source
Aroma Framework (Bengtsson et al., Berkeley Statistics Tech Report, 2008) in R, which is well known
for its robustness and flexible modular architecture. These pipelines facilitate reproducible research.
We have also developed specialized pipelines, like the one shown here for ribosome profiling. These
two endeavors allow us to meet the needs of the Cancer Center community.
------------------------------------------- ------------------- ------------------------ --------------------- ------------------------Hubert Stöppler PhD
Core Manager
Tissue Resource and Immunohistochemistry Core
The primary function of the Tissue Core is to provide a useful tissue resource (tissue bank) to Center
investigators in order to support their research programs and to aid in the design, development, and
successful completion of projects that involve the use of human tissue. The Core archives/manages
more than 550,000 individual biospecimens derived from over 18,000 patients at UCSF. Services
provided by the Core include tissue procurement, storage, processing, and distribution. Tissue
processing includes histology techniques, e.g. thin sectioning and staining of fresh frozen, OCTembedded, and formalin fixed paraffin-embedded tissue, histology review, and tissue microarray
processing. Core personnel are also involved in study design and the selection of appropriate
cases/biospecimens for research projects.
The Immunohistochemistry (IHC) Core has currently IHC staining protocols developed/in use for 225
different antigens. These developed protocols can be applied immediately without further testing to
any projects. The Core additionally offers a robust and reproducible approach for efficient and reliable
IHC assay development for antigens that have not previously been analyzed by the Core. The
Immunohistochemistry Core works closely together with the Tissue Core on IHC projects in the
provision of cell line, tumor, and benign tissue control specimens and IHC project design.
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DILLER RETREAT TECHNOLOGY POSTERS
HEALTH PROMOTION and FUND RAISING:
Walker
Malinda
Administration
van 't Veer Lab
Lamorna and Malinda work within the University of California San Francisco Breast Oncology
Program. In May 2014 Lamorna and Malinda conceived a project to promote exercise and raise
awareness of diseases while supporting charitable causes and having fun. Their initial goal is to
ElliptiGO around the Bay and raise money for breast cancer research programs at UCSF. In the
process they seek to draw attention to the benefits of exercise for reducing the risk of diseases such
as breast cancer, diabetes and many others.
The 230 mile “Circle the Bay” ride is scheduled for June 4-11, 2015. The planned route for “Circle the
Bay” starts in San Francisco then goes south to San Jose, then up through Pleasanton and
Livermore, and north to Napa, then west through Sonoma to Petaluma, and finally south back to San
Francisco.
The funds raised will go to support UCSF Breast Cancer programs such as the Athena Breast Health
Network, the I-SPY2 breast cancer trial, and seed funding for developing novel breast cancer
research projects at UCSF. They have a fund raising target of $100,000.
As Lamorna and Malinda “Circle the Bay” on ElliptiGO they will be holding events at their midday and
evening stops, which will give them and opportunity share with the audience about I-SPY 2, the
Athena Breast Health Network and other breast cancer research projects at UCSF.
Here we illustrate the route, list our rest/event stops and challenge our audience to get involved and
support us along the way.
Thank you for following, or joining, us on our journey.
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