Website: 10X Connect Shared Resource
Primary Contact: Dr. Judith A. Varner
Location: CNT Building
Activity Description: The 10X Chromium Connect is a robotic system that streamlines the workflow of single-cell sequencing. This results in swift data acquisition, improved data accuracy, and decreased fluctuations. The Connect can generate 8 fresh cell libraries and 64 fixed cell/tissue libraries in 12 hours. Additionally, this service is distinctive in that the assay is entirely automated, requiring minimal hands-on time. As a result, technical variations are minimized, and the reproducibility of the assay is significantly enhanced compared to the Chromium X.
Major Equipment: 10X Connect, 10X Chromium Controller
Website: Biobehavioral Shared Resource (BBSR)
Primary Contact: Brinda Rana
Location: Moores Cancer Center, Room 2345N NN
Activity Description: The BBSR has three aims, which are addressed with three major areas of service: (1) Services that enable the measurement of biological indicators of behavior, including biospecimen collection and management, in real time in clinical cancer prevention and control studies, and laboratory services such as measurement of biomarkers; (2) Services that facilitate behavioral assessment, including assessment and analysis of dietary factors, physical activity and body composition; and (3) Services that facilitate behavioral intervention research targeted to meet the needs of study populations and behavioral outcomes.
The resource is available to all MCC members, to researchers at UCSD and SDSU interested in aspects of behavior and cancer, and to researchers at other cancer centers, including the other two members of the C3. Should demand exceed capacity, priority is given to MCC members and reviewed by the MCC Shared Resource Oversight Committee. Consistent with MCC policies, priority access is given to Cancer Center members with peer-reviewed funding, followed by members with non-peer reviewed funding and then those who are unfunded. Off-campus services might be appropriate for some of the BBSR services, so this possibility could be explored. Contributing to not running at full capacity is our limited staff. We do not have the funds to hire a full time staff person, and therefore underusing our equipment resources. Increasing our recharge income would allow hiring more staff, so we are always looking for more users of our BBSR services.
Major Equipment: Agilent 1200LC HPLC, Qiacube, MeoScale Discovery, GE/Lunar Prodigy Dual Energy X-Ray Absorptiometer (DXA), Hologic “W” Dual Energy X-Ray Absorptiometer (DXA), Three Cosmed CPET Metabolic Measurement systems (1 static, 2 portable), Quinton Q-Stress cardiac stress testing system, Lode Excalibur Sport Bicycle Ergometer and Lode Angio Arm Ergometer, NeuroCom SMART EquiTest Balance Manager System, Biodex System 4 Pro for Isokinetic/Isometric assessment of strength, GT3X+ triaxial accelerometers, ActivPal inclinometers, ActiTrainer integrated heart rate and accelerometers, Polar heart rate monitors, and Qstarz BT-1000x GPS wearables
Website: Biorepository and Tissue Technology Shared Resource (BTTSR)
Primary Contact: Sharmeela Kaushal
Location: Moores Cancer Center, Rooms 3345, 5345 & B221
Activity Description: The BTTSR is founded on a well-established model that integrates tissue procurement, processing, storage, and multimodal (histologic, immunohistochemical, and molecular) analyses with traditional epidemiologic, clinicopathologic, and outcome parameters through a highly evolved bioinformatics system.
The mission of the BTTSR is to support MCC, C3, and outside researchers’ projects by providing annotated human bio- specimens, and state-of-the-art histology processing, interpretation, and histopathological analysis of samples.
Major Equipment: 2000C Nanodrop, Gene Chip 640Hybridization Oven, Agilent Technologies TapeStation 4200, BulletBlender Homogenizer, Qiacube Connect Automated NA extraction, Excelsior ES Automated Tissue Processor, Tissue-Tek VIP 5225Tissue Processor, Histostar Embeeding System, Leica CM 1850 UV Cryostats, Microm HM 355S Microtomes, IntelliPath Automated IHC Stainer, Decloaking Chambers, Thermo Scientific PT Module, Slide Hybridization Oven, Paraffin Oven, Aperio-Leica AT2Digital Slide Scanner, Akoya PhenoCycler™-Fusion system
Primary Contact: Pablo Tamayo
Location: CNT Building, Rooms 3161, 3162 and 3176
Activity Description: This Bioinformatics Core is 100% cancer focused. This means it offers very direct and specialized cancer-oriented analysis, advise and resources which benefits from 25 years of experience in cancer genomics, cancer computational biology and precision oncology.
Most Computational and Bioinformatics cores primarily focus on upstream analysis such as those associated with running the initial processing and preparation of raw data obtained from high-throughput sequencing experiments, such as Next-Generation Sequencing (NGS). The MCC Bioinformatics core focuses on advanced downstream analysis, addressing biological questions and interpreting the processed data obtained from the upstream analysis. This stage involves higher-level analyses and statistical methods to extract meaningful insights from the data
Other Computational and Bioinformatics cores focus on general biology or medicine problems using well established tools and methodologies to offer straightforward analyses that are mostly of shorter duration. In contrast, the MCC Bioinformatics core addresses those cancer-related problems that:
- require new or significant cancer genomics and bioinformatics support
- require bioinformatics training/education to the supported lab
- are critical to obtain funding for project-oriented or career-oriented grants in cancer
- introduce novel methods or advanced computational analysis
- expand the applicability of an existing method to new types of data or problems
- require to adapt analysis methodologies to fit an specific goal (address reviewers’ comments in papers or grants)
- require interdisciplinary approaches to new problems with significant analytics component
- are strategic for next-generation cancer genomics, translational research or precision oncology paradigms
- require a more in-depth involvement with the domain or the cancer subtype
Website: Biostatistics Shared Services
Primary Contact: Emily Pittman
Location: Moores Cancer Center, Room 3037
Activity Description: The Biostatistics Resource (BSR) strengthens the research capabilities and furthers the scientific rigor of cancer-related research by collaborating in all phases of protocol and grant development, data analysis and interpretation, and manuscript preparation at Moores Cancer Center (MCC).
Compared to ACTRI, our cancer focus and expertise distinguishes us, and allows our faculty to become more deeply involved in grant submissions and protocol development for Moores Cancer Center members than might be possible otherwise. We are focused more on long-term collaboration in cancer related research although we do short term consulting as well.
Compared to a CRO, we additionally offer more academically oriented services geared to smaller investigator initiated early phase trials. We typically create more cutting edge clinical trials designs than a CRO would propose, with greater involvement from PhD level academic statisticians. We offer collabortive support from design through paper publication, which can support publication in a higher impact journal. We are highly integrated with the Moores Cancer Center Clinical Trials Office.
Website: Flow Cytometry Shared Services
Primary Contact: Thomas Kipps
Location: Moores Cancer Center, Room 4314Q QQ
Activity Description: Provides access to high-speed flow cytometry-based analysis and fluorescence activated cell sorting (FACS) of dissociated cell populations from clinical samples, animal experiments, and cell culture studies. The Symphony S6 sorter is a 5 laser/23 color sorter that can sort 6 populations and is enclosed in a biosafety cabinet. The Sanford Consortium has a 4 laser Fusion that can sort 15-16 colors and 4 populations in a not truly sterile environment.
Major Equipment: BD Symphony S6, BD Symphony A1
Primary Contacts: Fitzgerald Lao and Vince Truong
Activity Description: Provide a means to charge MCC Faculty with in-house CO2 and LN2 service.
Website: Microscopy Shared Services
Primary Contact: David J. Hall
Location: Moores Cancer Center, Room 4304
Activity Description: The Cancer Center core offers a full range of services from whole animals imaging, fixed and live cell/organoid/tissue imaging, confocal widefield and super resolution microscopy, advanced imaging modalities such as STORM, PALM, TIRF, FRET and FRAP. The core is equipped with software packages for data analysis and includes 2D and 3D deconvolution, segmentation analysis and tracking tools.
Training rates for Cancer center members are the lowest on and outside campus and include any assistance that may be needed following the training. Rates for the use of the microscopes are lower for cancer center members.
The presence of multiple imaging modalities such as confocal, TIRF, STORM and in the near future a spinning disk system enables correlative microscopy on the same sample. The STORM module enables 2D and 3D super resolution imaging in three user selectable channels simultaneously.
Major Equipment: IVIS Imager, Nikon A1R Confocal TIRF STORM, BZ-X700 fluorescent microscope, Deltavision Deconvolution Microscope
Website: Radiation Medicine Shared Services
Primary Contact: Andrew Sharabi
Location: Moores Cancer Center, B010
Activity Description: This recharge service is unique in that it provides stereotactic body radiation therapy (SBRT) services to the Moores Cancer Center and its associated investigators. It uses a cone beam computed tomography (CBCT) imaging modality in combination with a proprietary treatment planning software to generate unique X-Ray radiation treatment plans for MCC investigators and collaborators interested in amplifying their experiments with a CT-guided radiation treatment modality with millimeter precision. This Core Facility is critical to the research mission of the Cancer Center given that radiation therapy is one of the four cornerstones of cancer treatment and management for a variety of cancer types. Besides this, the Core also offers large-field radiation services for clients seeking to irradiate cells, tissues, viruses, materials, etc. under a variety of conditions. Lastly, it offers cheaper and more comprehensive services to the Moores Cancer Center, UCSD Campus, and the broader San Diego biotechnology community than all other competitors.
Major Equipment: Precision X-Ray SmART system, Somni Isoflurane Anesthesia Machine
Website: Transgenic Mouse Shared Resource
Primary Contact: Sang Lee
Location: CMM-E, Room 1061
Activity Description: The Transgenic Mouse shared resource is a state-of-the-art facility that has an outstanding track record in the production of genetically altered mice. Transgenic mice carrying new or novel genes are created by microinjection of RNA and/or DNA into the pronuclei of fertilized eggs. Knock-out mice lacking specific genes of interest are created by homologous recombination in embryonic stem cells followed by injection into blastocysts to create chimeric mice. Highly experienced personnel produce transgenic , CRISPR , and knock-out mice for UC San Diego investigators at very reasonable cost and with very short lead times.