The Gladstone Histology and Light Microscopy Core is open to Gladstone, UCSF and the greater Bay Area science community. We provide excellent service, collaboration and support for many histological techniques, light microscopy and advanced imaging, image processing and quantitation.

Provides access and training on two FACS Calibur benchtop cytometers, one FACS Canto II multi-laser digital cytometer, one FACS Aria II cell sorter, one FACS Aria III cell sorter, and one Sony SH800 cell sorter. These systems are primarily used for the rapid analysis and sorting of single-cell suspensions. To analyze the light scatter and fluorescence characteristics of a cell population, one of the benchtop machines is appropriate. For more complex assays requiring more than four differentiating markers, then the high-end multi-laser Canto II system would work well. To rapidly retrieve or sort a particular sub-group of cells from a mixed sample, then a cell sorter would be required.

Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor.

Core includes instrumentation for structural biology with focus on cryo-electron microscopy. Used for imaging ranging from atomic resolution to whole cells, with emphasis on linking structural and dynamics information with biological functions.

The DEM Flow Cytometry Core offers instruments and training in flow cytometer operation and techniques. The core offers two BD LSRII analyzers with up to 17-color capacity, as well as a FACS ARIAII for fluorescent cell sorting. Both the analyzers and sorter are within BSL2 (or above) lab space to allow for analysis and sorting of infected human samples.

The Nikon Imaging Center at UCSF is equipped with several advanced microscopes. We have two super-resolution microscopes, three confocal microscopes, and three widefield systems. One of our super-resolution systems is a Nikon N-STORM microscope which is capable of PALM, STORM, and other variants of single molecule switching and localization microscopy. It is capable of 3-color imaging with up to 20 nm resolution in XY and 50 nm resolution in Z. This system is also capable of high-speed TIRF microscopy with frame rates > 100fps. The other super-resolution system is a Nikon N-SIM structured illumination microscope, which can produce images with ~100 nm resolution in XY and 350 nm in Z. This microscope can acquire four color images and can acquire a super-resolution image in ~2 seconds, so it can be used for live cell imaging.
Our confocal microscopes include a Nikon C1si laser-scanning confocal, capable of 3-color imaging and spectral imaging, and two 4-color spinning disk confocals optimized for video rate data acquisition from live cells. One of the spinning disk confocals is a CSU-W1 equipped with an sCMOS camera for imaging of large fields of view; the other is a CSU-22 with an EMCCD for imaging dim samples. One of our widefield microscopes is optimized for multi-day time-lapse imaging of live cells and one is optimized for five-color imaging (DAPI / FITC / Cy3 / Cy5 / Cy7). Our third widefield microscope is optimized for high speed multicolor Z-stack acquisition. This high speed microscope uses an Andor Zyla camera and is capable of acquiring 5.5 megapixel images at 100 fps, and can acquire multicolor and Z-stack images at this frame rate. This camera can also acquire smaller fields of view at higher frame rates (>1000 fps). It can also rapidly acquire large fields of view by image stitching and acquire data from multiwell plates rapidly. It is also equipped with photoactivation and photobleaching lasers for FRAP and photoactivation experiments. We also have color (RGB) image acquisition capabilities.
We have also developed a light sheet “Ultramicroscope” that allows imaging of cleared tissue samples up to 2 cm on a side, and has 1x, 2x, and 5x objectives, along with an 8x optical zoom system, allowing imaging resolutions from 20 m to 0.5m. Illumination is provided by a four line laser launch, with 405 nm, 488 nm, 561 nm, and 640 nm excitation. We have successfully imaged a number of cleared tissues with this microscope, including cleared mouse embryos, brains, spinal cords, and bone.
We have a full suite of image analysis tools available for data analysis, including Nikon Elements, Metamorph, Huygens, ImageJ/Fiji, Cellprofiler, and Matlab, and high power workstations (up to 8 cores, 128 GB RAM) for data analysis.

The MLK Cores Elemental Analysis Facility provides elemental quantitation and support services (sample preparation, project consultation, and technical writing) in support of a wide range of research projects on a fee-for-use basis at competitive costs. Our flagship instrumentation is an ICP-OES that allows for simultaneous, multi-element measurements over a wide dynamic range with high precision and sensitivity. The instrument is tolerant of high total dissolved solids and complex matrix components, and is compatible with a range of clinical, pre-clinical, basic research, and pharmaceutical samples.

The Parnassus Flow CoLab assists investigators whose research requires molecular marker characterization of cells in suspension as well as the isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are conducted within the Core.

We provide services involved in generating new research models. These range from traditional ES cell targeting and transgenesis, to new genome-editing techniques such as CRISPR and TALEN. A full range of services is available, from training, consultation, and construct design, to targeting, genotyping, and post-targeting QC such as Southern blots to confirm single integrations.

The UCB-EML

The Electron Microscope Laboratory (EML) is an imaging core and shared resource facility of the University of California at Berkeley. Our mission is to provide high-quality electron microscopy services, education, and training for the UC Berkeley campus, other academic institutions, and private companies at-large.

The lab is equipped with a high resolution transmission electron microscope (TEM), scanning electron microscope (SEM), and focused ion beam SEM (FIB-SEM), a high pressure freezer and full suite of ancillary sample preparation equipment to fit most EM-related needs. The equipment can provide nanometer scale analysis for biological, chemical and materials science.

The EML offers multiple levels of service that correspond with the services and training each user desires:

Project consultation
Education and training for new users
Equipment for trained users who anticipate having long-term EM projects
Full service microscopy (as time allows)

All services are available to anyone with an interest in electron microscopy: graduate and undergraduate students, post-doctoral researchers, faculty, staff, and non-UC users.

Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI.

Core microscopy facility managed by Cancer Research Laboratory. Provides campus community with training and access to state-of-the-art light microscopy equipment. Now in two locations: Life Sciences Addition Building (LSA) and the new Li Ka-Shing Center for Biomedical and Health Sciences (LKS). The MIC specializes in live cell imaging, confocal, multi-photon, fluorescent lifetime imaging (FLIM), and equipment for optogenetic research.

The QB3 Cell and Tissue Analysis Facility provides cell culture equipment and instrumentation needed to grow and assess mammalian cells including flow cytometry, hypoxia chambers, automated epifluorescence, confocal, and multiphoton microscopy, as well as a histology suite with cryosectioning equipment.

QB3 Genomics is a partnership between the Vincent J. Coates Genomics Sequencing Laboratory (GSL), the Functional Genomics Laboratory (FGL), and the Computational Genomics Resource Laboratory (CGRL). QB3 Genomics supports genomics research at UC Berkeley and the greater research community.

QB3 Genomics offers consultation on experimental design and data analysis, a full suite of technical services related to high throughput sequencing and genomics experiments, and access to high performance computational infrastructure.

The CRL Molecular Imaging Center is the largest light microscopy facility at UC Berkeley, serving the campus and surrounding community. The MIC offers training, consultation, and guidance on use of high-end instrumentation, including laser scanning confocal microscopy, lightsheet microscopy, Zeiss Airyscan, spinning disk confocal, fluorescent lifetime imaging, 2-photon and in vivo imaging, slide scanning, and optogenetic exerperiments. We have 17 major microscope systems and are located in 2 buildings on campus, Weill Hall and Barker Hall.

The High-Throughput Screening Facility provides expert staff for training, services, and cell culturing space for HT automated cell seeding, liquid handling equipment, multi-label plate reader and high-content automated confocal imaging for any type of multi-well, multi-conditional mammalian cell experiments.

The National Energy Research Scientific Computing Center, or NERSC, is a high performance computing (supercomputer) user facility operated by Lawrence Berkeley National Laboratory for the United States Department of Energy Office of Science. As the mission computing center for the Office of Science, NERSC houses high performance computing and data systems used by 7,000 scientists at national laboratories and universities around the country.

The Cell Culture Facility supports research by providing cell cultures (mammalian and insect), media, supplies and expertise on a recharge basis for more than 40 different laboratories on and off the main campus. The Facility provides cell cultures, provides media and materials for checkout, and also allows use of laminar flow hoods, incubators and microscope for researchers who are using cells provided by the Facility, to use on site.