Mini Guide to the UC Berkeley QB3 Core Facilities

This guide provides a brief introduction to the core facilities on UC Berkeley campus. Core facilities feature a diverse array of advanced analytical capabilities including mass spec, microscopy, flow cytometry, NMR, nanofabrication and sequencing. No affiliation with UC Berkeley or Bakar Labs is required, so even after moving out of Bakar Labs, you can still continue to use the services provided. 

Each company must contract with each user facility to gain access. Many of the core facilities participate in the Research Infrastructure Commons (RIC) agreements. The terms and conditions are straightforward and the university doesn’t claim ownership interest in any IP, nor does it claim a right to use materials or data resulting from RIC use by companies. The business-friendly agreements are intended to be non-negotiable and electronically executable. To learn more about the Berkeley RIC, check out their website: https://vcresearch.berkeley.edu/berkeley-ric/about

Please plan well ahead before you need to use any of these services, as some may be in high demand. Additionally, core facilities prioritize access to the UC Berkeley research community, so it’s important to discuss availability. 

To begin, locate the type of service or equipment you require and directly contact the facility director indicating: 

    a) you’re a tenant/startup at Bakar Labs, 

    b) describe the particular capability you’re looking for, 

    c) an estimate of the amount of services you require, 

    d) and the timeline you’d like to work to. 

In some cases users may operate the equipment (‘user facilities’), in others only lab personnel can and provide services, or run your sample on the instrument as a service. Pricing is updated every July. Many of the QB3 facilities listed below---excluding QB3 Genomics and the HTSF---offer a "Startup Partner" rate, which Bakar Labs companies are eligible for. However, please be aware that this is subject to change, so check with the facility manager when setting up your account.

Below is a list of the more common services that tenants of Bakar Labs may find especially useful. For a comprehensive list of all core facilities at UC Berkeley and a map of where to find them, see: https://vcresearch.berkeley.edu/core-facilities 

QB3 Biomolecular Nanotechnology Center:  

A user facility with 11,500 sq ft class 1,000/10,000 cleanroom facility specializing in BioMEMS (Biomedical Micro-electromechanical systems) and Microfluidic devices fabrication and experimentation. 

Cal-Cryo@QB3-Berkeley: 

Cal-Cryo at QB3-Berkeley provides researchers with access to state-of-the-art Cryo Electron Microscopes and related tools for high resolution structural biology imaging experiments. Learn more at their website, here. 

QB3 Cell and Tissue Analysis Facility: 

The QB3 Cell and Tissue Analysis Facility provides cell culture equipment and instrumentation needed to grow and assess mammalian cells including flow cytometry, automated epifluorescence, confocal, and multiphoton imaging, as well as a histology suite with cryosectioning equipment. There are microscopes for fixed and live cell automated epifluorescence, confocal, and multiphoton imaging. Tissue related instrumentation includes cryostats, sliding microtome, paraffin-embedding equipment, and histology processing and staining setup. 

QB3 High-Throughput Screening Facility: 

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.  

Also offers assistance with some siRNA and arrayed CRISPR screening reagents, CRISPR cell line identification, along with other high-throughput fluidics projects. We also provide a lentivirus packaging service, and an amplification service, providing maxipreps of DNA and specialized CRISPR libraries with full validation, upon request. 

QB3 Genomics: 

QB3 Genomics is a partnership between the Vincent J. Coates Genomics Sequencing Lab (GSL – B206 Stanley Hall), the Functional Genomics Laboratory (FGL – 255 Weill Hall, formerly LSA), and the Computational Genomics Resources Facility (CGRL)). QB3 Genomics’ mission is to make genomics research tractable and affordable to UC Berkeley and the greater genomics community. The VCGSL provides QC and sequencing services. It operates Illumina MiSeq, HiSeq, and NovaSeq platforms, as well as a PacBio Sequel II system and Oxford Nanopore Minion system. The GSL also provides PacBio and ONT library preps and high molecular weight extractions.The FGL provides molecular biology services for next-generation sequencing projects, including library preparation, QC, purification, enrichment, and single cell (10X) services. The CGRL provides shared computational infrastructure and technical support in collaboration with Berkeley Research Computing. The CGRL also provides consulting for bioinformatics and genomic analyses. Learn more at their website, here. 

QB3 MacroLab: 

The QB3 MacroLab is a core facility administered by QB3-Berkeley. Located in UC Berkeley’s Stanley Halle, the QB3 MacroLab offers automated gene cloning and recombinant protein expression and purification services. In addition to these services, MacroLab can provide reagents such as competent cells. 

QB3 Central California 900 MHz NMR Facility: 

This facility promotes the understanding of the structures and dynamics of natural products, potential therapeutics, proteins, and nucleic acids at the atomic level. Instruments include a 900 MHz spectrometer equipped with a cryoprobe, along with several other NMR systems. Learn more at their website, here. 

QB3 Vincent J. Coates Proteomics/Mass Spectrometry Laboratory: 

The P/MSL provides proteomics services principally through mass spectrometry.  Currently the facility has two Thermo LTQ XL linear ion trap mass spectrometers and a Thermo Fusion Lumos mass spectrometer. 

QB3/Chemistry Mass spectrometry Facility: 

The combined QB3/Chemistry Mass Spectrometry Facility features state-of-the-art mass spectrometers that are capable of analyzing a wide variety of samples. The facility provides acquisition of mass spectra and accurate mass measurements of biological, organic and inorganic compounds, as well as mass measurements of intact proteins, lipids, oligosaccharides, and non-covalent protein-protein and protein-ligand complexes and supramolecular coordination clusters. The facility also provides advanced proteomics analysis. This involves protein identification using mass spectral data as well as identification of posttranslational modifications. In addition, the facility provides ion mobility spectrometry. The facility also operates an open access MALDI-TOF instrument available to trained users. Electron Impact (EI), Chemical Ionization (CI), Electrospray Ionization, Ion Mobility Spectrometry (IMS), MALDI (Matrix Assisted Laser Desorption Ionization)