Core Facilities

The backbone of QB3 consists of shared research facilities: technology centers that promote collaboration and education. The new QB3 buildings and facilities provide scientists with technical know-how and access to state-of-the-art instrumentation, technologies, and materials.

We offer core facilities for nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), advanced imaging, small-molecule drug screening, functional genomics, and proteomics. Each facility is an intellectual commons, managed by seasoned professionals, principal investigators and mentors, aligned to foster scientific interaction and collaboration.

Access to these resources enables scientists and engineers to develop medical devices, drugs, and therapies that improve lives, as well as technologies to alleviate environmental damage and improve energy production and use.

Search all cores at UCSF
Information on facilities and services at Berkeley Lab

QB3 research facilities serve six general research areas:

Structure Determination

Beamline 8.3.1 at the Advanced Light Source at LBNL

This facility is owned jointly by David Agard, professor of biochemistry and biophysics at UCSF; Robert Fletterick, professor of biochemistry, pharmaceutical chemistry and cellular and molecular pharmacology at UCSF; Robert Stroud, professor of biochemistry and biophysics and pharmaceutical chemistry at UCSF; and Jamie Cate, professor of biochemistry, biophysics, and structural biology at UC Berkeley. This is a national facility that generates bright synchrotron light for studies in materials science, biology, chemistry, physics, and environmental sciences. The beamline uses a superconducting bend magnet in the 6-18 keV range to deliver light through an optical obstacle course in order to resolve a protein structure.

Central California 900 MHz NMR Facility at UC Berkeley

Directed by Professor David Wemmer, this Stanley Hall facility features four high-field NMR instruments, including 800 MHz and shielded 900 MHz systems. The instruments are used to study the structures and dynamics of both proteins and nucleic acids at the atomic level, and for probing the formation of biologically important molecular complexes and their functions.

Macromolecular X-ray Crystallography Facility at UC Santa Cruz

Under Harry Noller, professor of molecular, cell, and developmental biology, and Alice Vrielink and Bill Scott, professors of chemistry and biochemistry, the facility houses a state-of-the-art rotating anode/imaging plate X-ray crystallography data collection suite, a cryosystem, and a collection of computer workstations and software for crystallographic computations, molecular visualization, and model building. This facility dovetails with the Lawrence Berkeley National Laboratory’s Advanced Light Source synchrotron radiation facility.

Mass spectrometry facility at UC Santa Cruz

This facility, managed by Ted Holman, professor of bioinorganic chemistry and biochemistry, enables the discovery of new molecular structures directly relevant to understanding and treating diseases, the discovery, design, and manipulation of biologically relevant molecules, and the development of new techniques to probe the behavior of macromolecules central to fundamental biological functions. The facility houses two mass spectrometers: a Thermo Finnigan LC/MS/MS (LTQ) and an Ettan MALDI-TOF. This equipment is capable of determining the molecular weight of both small molecules and peptides, identifying proteins, and characterizing protein modifications.

Membrane Protein Expression Center at UCSF

Directed by Robert Stroud, professor of biochemistry & biophysics and pharmaceutical chemistry at UCSF, the Membrane Protein Expression Center (MPEC) develops and applies the latest innovative methods that yield structurally and functionally intact membrane proteins for subsequent drug development, structural, and functional characterization. The MPEC focuses especially on eukaryotic membrane proteins since these provide many major drug target proteins. The MPEC accepts target genes for expression in functional form from client laboratories, which can introduce a gene choice for expression and then follow the membrane protein expression progress via a password-protected Intranet web site.

The Magnetic Resonance Laboratory at UCSF

Directed by Professor John Gross, the facility includes 600 MHz and 500 MHz spectrometers for high-resolution studies of macromolecules including the solution structure of proteins, nucleic acids, and their complexes.

Nuclear Magnetic Resonance Facility at UC Santa Cruz

This facility in the department of chemistry and biochemistry is used to examine molecular structure and folding in studies involving structure and biochemical mechanisms of cancer and anticancer therapies and environmental toxins. It houses three different high-resolution NMR spectrometers.

QB3/College of Chemistry Mass Spectrometry Facility at UC Berkeley

The facility features state-of-the-art mass spectrometers. It provides routine nominal and accurate mass measurements of biological, organic and inorganic compounds as well as structural elucidation through tandem mass spectrometry. Mass spectral proteomics analysis, mass measurement of intact proteins, lipids, oligosaccharides, and non-covalent protein-protein and protein-ligand complexes are also available.

QB3 MacroLab at UC Berkeley

Directed by Professor Susan Marqusee and managed by Scott Gradia, this Stanley Hall facility offers automated liguid-handling services to enable high-throughput analysis in several key areas. Services are available in 1) cloning and mutagenesis, 2) protein expression and purification, and 3) protein crystallization reagents and other useful consumables.

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High-Throughput Screening

The Small Molecule Discovery Center (SMDC) at UCSF

The SMDC provides University of California scientists with access to innovative discovery technologies, including high-throughput and fragment-based screening and “hit-to-lead” medicinal chemistry. The center is under the direction of UCSF’s Jim Wells, Harry W. and Diana Hind Professor in Pharmaceutical Sciences, and Adam Renslo, Associate Director and Adjunct Assistant Professor of Pharmaceutical Chemistry. The SMDC occupies a custom-built facility on the fifth floor of Byers Hall on the UCSF Mission Bay campus.

Chemical Screening Center at UC Santa Cruz

UC Santa Cruz’s Chemical Screening Center houses high-throughput screening (HTS) robotics that are used to search for biologically active compounds and siRNA targeted toward a variety of biological systems. Investigators can test up to 30,000 chemical compounds per day for biological function and/or usefulness in fighting diseases, such as cancer, malaria, Parkinson’s disease or cholera. The Screening Center houses liquid handling robotics, detectors, imaging equipment, and compound libraries, including a growing collection of unique marine natural products. A detailed list of equipment and compound libraries may be found here.

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Genomics and Proteomics

Microarray Facility at UC Santa Cruz

Established by Manuel Ares, professor of molecular, cell, and developmental biology at UC Santa Cruz, and managed by microarray technology specialist Lily Shiue, this resource facilitates large-scale analysis of alternative splicing and comparative genomics.

The UCSC genome sequencing center

Established by Nader Pourmand, assistant professor of biomolecular engineering, the facility allows researchers to sequence DNA using next-generation high-throughput instrumentation: sequencers, bioanalyzers, and a microarray printer and scanner. The facility can be used for whole-genome resequencing, targeted resequencing, gene expression analysis, and microRNA discovery. These capabilities are useful for research in areas such as genomics, bioinformatics, and environmental biology. The research of the center focuses on both generating high-quality data for the scientific community and improving next generation platform technology.

The UCSF Core Facility for Genomics and Proteomics in the Center for Advanced Technology at UCSF

This facility was established by Joe DeRisi, assistant professor of biochemistry & biophysics at UCSF, Erin O’Shea, professor and vice chair of biochemistry & biophysics at UCSF, and Jonathan Weissman, professor of cellular & molecular pharmacology. The facility is fully equipped to whole genome approaches, in particular expression profiling.

Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley

This facility offers whole genome sequencing, genomic resequencing, ChIP-sequencing, RNA expression, small RNA discovery, and bisulfite sequencing on three Illumina HiSeq 2000 instruments. Don Rio, professor of molecular and cell biology, serves as faculty advisor to the facility.

Vincent J. Coates Proteomics/Mass Spectrometry Laboratory at UC Berkeley

The proteomics / mass spectrometry laboratory (P/MSL) offers full services in protein identification and characterization. These services include protein identification from complex samples through MudPIT analysis, post-translational modification analysis, and identification of proteins from gel bands.

Functional Genomics Laboratory at UC Berkeley

The FGL mission is to conduct state-of-the-art research in functional genomics, with a focus on using DNA microarray technologies, and to make these technologies available to both campus and off-campus users (recharge rates vary depending on affiliation). Complementing the high-throughput DNA sequencing capabilities of the Vincent J. Coates Genomic Sequencing Laboratory, the FGL specializes in the fabrication, use, and analysis of DNA microarrays for large-scale gene expression profiling and genetic profiling, and provides full core lab services for Affymetrix GeneChip arrays and Agilent DNA microarrays. FGL scientists are actively involved in the development of new techniques for microarray-based experimentation and statistical approaches for analyzing complex datasets. Research support services include hands-on training and consultation from the unit’s Director and highly trained staff; software, computational facilities, and databases for gene expression data analysis; prefabricated DNA microarrays; a full complement of robotics technologies for the fabrication of custom microarrays; and Agilent Bioanalyzer sample analysis.

Computational Genomics Resource Laboratory (CGRL) at UC Berkeley

The CGRL provides technical expertise and training opportunities in experimental design and data analysis of projects using next-generation genomic sequencing and other high-throughput technologies. Professors John Taylor and Brian Staskawicz direct this QB3 core facility at UC Berkeley.

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Informatics

Resource for Biocomputing, Visualization, and Informatics at UCSF

This facility was established by Tom Ferrin, professor of pharmaceutical chemistry and biopharmaceutical sciences at UCSF. This facility provides access to state-of-the-art computer graphics hardware and software for research on biomolecular structures and interactions. It houses the Computer Graphics Laboratory, an NIH National Center for Research Resources Biomedical Technology Research Center for the integrated analysis of biological sequence, structure, and functional information. The other major components of the Center include the Babbitt Laboratory and the Sequence Analysis and Consulting Service (SACS).

Michael J. Homer Center for Computational Biology at UCSF

The computer server room in Byers Hall houses a collected, shared resource consisting of over 1000 processors and approximately 20 terabytes of disk storage. This special purpose room has state-of-the-art power, cooling and networking systems. The facility is managed by Joshua Baker-LePain. Potential users can arrange access via the accounts page.

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Imaging

Electron Microscopy Laboratory at UC Santa Cruz

This core facility houses two transmission electron microscopes (TEM) and a scanning electron microscope. One TEM, a JEOL 1200 EX equipped with a 4pi x-ray analyzer and a Gatan Bioscan digital camera, managed by chemistry professor Jin Zhang, is used for general room temperature applications. The other is a state of the art JEOL 1230 equipped with a Gatan cryostage and transfer device, a Gatan Ultrascan digital camera, and a Gatan 626 video camera, managed by MCD biology professor Melissa Jurica. The lab’s ISI WB-6 scanning electron microscope is a conventional, tungsten filament instrument equipped with a 4pi x-ray analyzer and digital imaging system.

Electron Spin Resonance Facility at UC Santa Cruz

Managed by Glenn Millhauser, professor of chemistry and biochemistry, the facility houses a Bruker ESP 380 X-band spectrometer that operates in either continuous-wave or pulsed mode at variable temperatures and a high-sensitivity Bruker ExexSys 500 for limited sample sizes needed for many biological studies. Non-core facility available by special arrangement only.

Hyperpolarized MRI Technology Resource Center at UCSF

Directed by Dan Vigneron, professor in the Departments of Radiology & Biomedical Imaging and Bioengineering & Therapeutic Sciences, this new NIH NIBIB Biomedical Technology Research Technology center focuses on the technological development of new preclinical hyperpolarized carbon-13 MRI. The center funds three projects: 1) the development of new dynamic nuclear polarization (DNP) and hyperpolarized (HP) MRI techniques; 2) new HP probes and cell/tissue HP techniques; 3) specialized HP MRI reconstruction and analysis techniques. These developments will be driven by collaborative projects led by outstanding clinical and basic scientists using hyperpolarized 13C MRI to accomplish their goals. These technical developments will also be disseminated for extramural feedback and then widely to the scientific community via a dedicated website and onsite training. This center also provides state-of-the-art training in this new metabolic imaging field and sponsors a yearly symposium focused on hyperpolarized MR technology.

Nikon Imaging Center at UCSF

The UCSF Nikon Imaging Center (NIC) is a core facility for light microscopy developed in partnership with Nikon Instruments Inc., Technical Instruments, and several other providers of microscopy instrumentation. Opened in September 2006, the facility serves QB3 and UCSF. The NIC will provide investigators access to cutting edge microscopy resources with a particular emphasis on developing novel imaging solutions to systems biology challenges; promote cross-discipline collaborations, training, and courses; and foster collaborations with biopharmaceutical companies.

UCSC life sciences microscopy center at UC Santa Cruz

The microscopy center provides cutting-edge imaging techniques for advanced biomedical research. It has a Leica SP5 X confocal microscope, a Leica DM5500 B wide-field microscope, and a Zeiss live imaging microscope. A PerkinElmer Volocity spinning disk confocal and a Zeiss LSM5 spot scanning Confocal are maintained at different locations, but available for shared use. Biomedical researchers at UCSC have access to a variety of other light microscopy resources maintained by individual faculty members. These include a Leica SP3 confocal microscope in the Sullivan lab, a Prairie Technologies Ultima-IV two-photon microscope in the Zuo lab, and a Delta Vision wide-field fluorescent microscope with iterative deconvolution technology in the Bhalla lab.

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Bioengineering

Biomedical Micro and Nanotechnology Core (BMNC) at UCSF

Operated by Tejal Desai, UCSF professor of physiology and bioengineering, with partial sponsorship from the Sandler Foundation and QB3, this facility houses technologies needed to 1) link soft biomolecular structures to hard material surfaces for biosensors, array technologies, and new medical devices, and 2) topographically and chemically pattern hard and soft substrates for microfluidics, cell patterning, targeted delivery, and tissue engineering. Core equipment in the clean room includes equipment for photolithography, wet chemical etching, polymer spin coating, and reactive ion etching. In addition, the facility has a Nano eNabler™ molecular printer and an atomic force microscopy system with nanolithography capabilities for developing and characterizing micro and nanoscale organic and inorganic surfaces. Located on the second floor of Byers Hall, the facility serves as a resource for those interested in developing new micro/nanotechnology platforms for their research.

Biomolecular Nanotechnology Center at UC Berkeley

Directed by UC Berkeley professor and QB3-Berkeley director Susan Marqusee, the Biomolecular Nanotechnology Center (BNC) is a 11,500 sq ft class 1,000/10,000 cleanroom facility located in Stanley Hall. The BNC features a full range of lithography, deposition, etching, metrology, and microscopy equipment as well as facilities for performing biological experiments. The center focuses on microfluidic processing of glass and polymer materials. Experimentation on proteins, nucleic acids, cells, and tissues is encouraged. In addition to a state-of-the-art research lab, the center also features a teaching lab for hands-on training of both undergraduate and graduate students.

Flow cytometry facility at UC Santa Cruz

Established by Camilla Forsberg, assistant professor of biomolecular engineering, this core facility houses a high-speed cell sorting and analysis system, the BD Biosciences FACSAria. Its four-laser system allows simultaneous detection of up to 14 parameters. Up to four cell populations can be sorted simultaneously at high purity and deposited in bulk or as single cells into a range of standard test tubes, multiwell plates, or slides, allowing convenient and flexible analysis of purified cells. The facility also provides licensed FlowJo software for data analysis and display. This facility is part of the CIRM-funded Shared Stem Cell Facility.

Nanosecond Time-Resolved Laser Spectroscopy Laboratory at UC Santa Cruz

The department of chemistry and biochemistry contains several systems capable of measuring different time-resolved spectra from the far ultraviolet to the near infrared regions for a wide variety of research applications. Non-core facility available by special arrangement only.

CIRM/QB3 Shared Stem Cell Facility at UC Berkeley at UC Berkeley

Designed to enhance stem cell research amongst Berkeley and QB3 investigators, as well as collaborators at Lawrence Berkeley National Lab and Children’s Hospital Oakland Research Institute, the facility provides all of the cell culture equipment and instrumentation needed to grow and assess stem cells from flow cytometry to automated epi-fluorescence, confocal, and multiphoton imaging.

CIRM/QB3 Shared Stem Cell Facility / High-Throughput Screening Facility at UC Berkeley

The CIRM/QB3 Shared Stem Cell Facility provides cell culture equipment and instrumentation needed to grow and assess stem cells from flow cytometry to multiplex ELISA reader to automated epifluorescence, confocal, and multiphoton imaging. The High-Throughput Screening Facility provides cell culturing space for automated cell seeding, and automated liquid handling equipment, multi-label plate reader and high-content imaging for any type of multi-well plate experiments. Both facilities are directed by David Schaffer, Professor in the Departments of Chemical and Biomolecular Biology, Bioengineering, and Neuroscience, and Director of the Berkeley Stem Cell Center.

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