University of California San Francisco
Helen Diller Family Comprehensive Cancer Center

Genome Services

About LCA Genome Services

The LCA-Genome Analysis Services offer genetic and genomic biomarker analysis, instruments, and translational research support for preclinical, clinical discovery, and clinical trial enrollment projects with special emphasis on the unique technical needs of tumor biology.

Our research team works with users to develop biomarker strategies and assays collaboratively by functioning seamlessly as an extension of your team. We offer services in mutational analysis, genotyping, and gene expression studies.

Our wet-lab services are focused at the Mission Bay campus. However, we manage instruments at two campuses: Mount Zion and Mission Bay.

Genomic Instrumentation

The LCA-Genome Services oversees several instruments available for use by members of the research community.  As providers, we are responsible for facilitating equal access to these instruments and maintaining proper function and updates.  Maintenance is performed at a regular schedule defined by the manufacturer. As users, you are responsible for following the guidelines issued by the Core.  Please refer back to the information provided by the Core and be respectful to reserve on the MyCORES calendar prior to using an instrument.

Mount Zion Campus:

  • Nanodrop 8000 (ThermoScientific): UV-Vis Spectrophotometer with multi-sample (1-8) micro-volume measurements (1ul).
  • Synergy (HT) Plate Reader (BioTek): Multi-mode microplate reader for fluorescence, absorbance, and luminescence measurements on 96 and 384 well plates.

Mission Bay Campus:

  • EpMotion 5075LH (Eppendorf): Automated liquid handling workstation
  • Agilent 2100 Bioanalyzer (Agilent Technologies): Microfuidics-based (Lab-on-a-chip) platform for sizing, quantification, and quality measurements of DNA, RNA, protein, and cells.
  • QuantStudio 3D (dPCR): Desktop digital PCR instrument for absolute quantification in copies/uL.
  • 4D Nucleofector: High efficiency electroporation of primary cells and cell lines (see application in this webinar)
  • Bioline Mic: Very fast, user-friendly, and low-throughput magnetic induction qPCR Cycler with a maximum of up to 48 samples per run

Agilent Bioanalyzer 2100

Agilent Bioanalyzer 2100The Agilent Bioanalyzer 2100 is a microfluidics-based platform that combines the principles of electrophoresis and flow cytometry to allow quantitative and qualitative analysis of various sample types that include total RNA, mRNA, microRNA, small RNA, and small to large fragments of PCR amplified DNA or fragmented DNA.

Using the Bioanalyzer: Reservations are made in MyCORES. Please contact core personnel at genome2@ucsf.edu if you need training on the platform.

Location: HD330, Helen Diller Building, Mission Bay Campus


Nanodrop 8000

Nanodrop 8000The Nanodrop 8000 is a multi-well (8 total) UV-Vis spectrophotometer used for absorbance detection within 220-750 nm, designed to be used for detecting nucleic acid concentration, proteins and labeling dye. Sample volume input is 1uL. Dynamic range for dsDNA is 2.5-3700 ng/uL, according to the manufacturer.

Using the Nanodrop 8000: Because the instrument is a shared resource of the building, reservation of the instrument is not needed. Please use the sign-in binder next to the Nanodrop, so we can track usage.

Location: S172, Cancer Research Building, Mount Zion Campus


Biotek Synergy (HT) Microplate Reader

Biotek Synergy HT Microplate ReaderThe Synergy (HT) Plate Reader with BioTek software is a multi-mode microplate spectrophotometer for fluorescence, absorbance and luminescence measurements on 96 and 384 well plates. Protocols are designed using the BioTek software to instruct commands for the instrument (shaking/mixing etc). Quantifications using standard curves may be done automatically using the software.

Using the Synergy Plate Reader: Only researchers located in the Cancer Research Building at the Mount Zion Campus may use the instrument. Because the instrument is a shared resource of the building, reservation of the instrument is not needed. Please use the sign-in binder next to the plate reader, so we can track usage.

Location: S176, Cancer Research Building, Mount Zion Campus


Qubit 4 Fluorometer

Qubit 4 Fluorometer

The Invitrogen Qubit 4 is a fluorometer designed to accurately measure DNA, RNA, and protein quantity in less than 3 seconds per sample.  
 
Location: HD250, Helen Diller Building, Mission Bay Campus
 

Eppendorf epMotion 5075

Eppendorf epMotionThe recently upgraded EpMotion 5075 is an automated liquid handling system linked to a desktop computer software is designed for effective, automated liquid handling applications providing a precise, accurate alternative to time-consuming manual pipetting and liquid handling tasks. The combination of accelerated operational speed, new software & hardware features and an increased number of worktable positions make the systems ideal for simple and flexible laboratory use across a wide range of liquid handling applications. This is supported even further by an optical sensor that checks labware, liquid levels and tip counts and type at the start of each cycle, hugely decreasing any risk of error during the run.

The instrument allows for single pipetting using 1uL, 10uL, 100uL, and 1000uL automated pipettors and multichannel pipetting using 50uL and 1000uL automated pipettors.

Possible applications: serial dilutions, real-time PCR set-up, immunoassay set-up, sample pooling, distributing reagents, magnetic beads DNA extractions, NGS-automated library preparation.

Using the epMotion 5075: The LCA-Genome Core will work with you on programming the machine for your own application. Please contact the Genome Core at genome2@ucsf.edu for more information.

Location: HD330 Helen Diller Building, Mission Bay Campus


QuantStudio 3D (dPCR)

QuantStudio 3D dPCRThe QuantStudio 3D is a desktop digital PCR instrument used for absolute quantification in copies/uL. The instrument consists of three parts: a chip loader, a PCR thermal cycler, and the chip reader. One sample is used per chip with the capacity to multiplex. Loading, cycling, and reading 10 chips may be done in 4 hours.

Applications: Rare allele detection; precise copy number variation; absolute quantification of nucleic acid standard; absolute quantification of next‐generation sequencing libraries; low‐level fold change of gene expression (smaller than 2 fold).

Using the dPCR: Reservations are made in MyCORES. Please contact the Genome Core at genome2@ucsf.edu regarding the use of this instrument.

Location: HD330, Helen Diller Building, Mission Bay Campus


QuantStudio 5 qPCR System

QuantStudio 5 PCR System

The Applied Biosystems QuantStudio 5 Real-Time PCR System with 384-well block is a real-time thermocycler that allows quantitative and qualitative detection of nucleic acids based on fluorescent-based technology. The optimized Design and Analysis software is ideal for both first-time and experienced users. The instrument includes wi-fi connectivity and when connected to the Thermo Fisher Cloud, the QuantStudio 5 system provides access to your data wherever and whenever you want. The 384-well format has 5 excitation filters (450-650nm) and 5 emission filters (500-700nm).

QuantStudio 5 has a HRM curve capabilities; a relatively new, post-PCR analysis method used to identify variations in nucleic acid sequences. The method is based on detecting small differences in PCR melting (dissociation) curves. It is enabled by improved dsDNA-binding dyes used in conjunction with real-time PCR instrumentation that has precise temperature ramp control and advanced data capture capabilities. Data are analyzed and manipulated using software designed specifically for HRM analysis. For HRM application mutation scanning and methylation analysis information please see the following links.

Using the QuantStudio 5: Reservations are made in MyCORES following the standardized times for SYBR and Taqman, 3 hours and 2 hours per plate, respectively. Please plan your projects accordingly. There is an inconvenience fee of $5 per cancellation.

Location: HD235, Helen Diller Building, Mission Bay Campus


Lonza 4D-Nucleofector System

Lonza 3D Nucleofector SystemThe 4D-Nucleofector System is the most advanced Nucleofection Platform offering maximum flexibility in regards to cell numbers, throughput, and cell status. The Nucleofector Technology is a highly efficient non-viral transfection method which is based on the momentary creation of small pores in cell membranes by applying an electrical pulse. The comprehensive way in which Nucleofector Programs and cell-type specific solutions are developed enables nucleic acid substrate delivery not only to the cytoplasm, but also through the nuclear membrane and into the nucleus. This allows for high transfection efficiencies up to 99% and makes the transfection success independent from cell proliferation.

Using the 4D-Nucleofector: Reservations are made in MyCORES. Please contact the Genome Core at genome2@ucsf.edu regarding the use of this instrument.

Location: HD327, Helen Diller Building, Mission Bay Campus


Bioline Mic Magnetic Induction qPCR Cycler

Bioline Mic Magnetic Induction qPCR CyclerThe Bioline Mic is a very fast, user-friendly, and low-throughput magnetic induction qPCR Cycler with a maximum of up to 48 samples per run. Mic uses a magnetic induction technology to heat samples and fan forced air for cooling. This means fast qPCR results in less than 25 minutes for 35 cycles.

Using the Bioline Mic: Reservations are made in MyCORES.

Location: HD235, Helen Diller Building, Mission Bay Campus