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 Mount Zion 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:

  • AB 7900HT (Life Technologies/Applied Biosystems): QPCR instrument with exchangeable blocks (96, 384 well).  Fast PCR, Taqman Low Density Array (TLDA).  High-throughput plate loading accessory for >4 plates.
  • Nanodrop 8000 (ThermoScientific): UV-Vis Spectrophotometer with multi-sample (1-8) micro-volume measurements (1ul).
  • Agilent 2100 Bioanalyzer (Agilent Technologies): Microfuidics-based (Lab-on-a-chip) platform for sizing, quantification, and quality measurements of DNA, RNA, protein, and cells.
  • Synergy (HT) Plate Reader (BioTek): Multi-mode microplate reader for fluorescence, absorbance, and luminescence measurements on 96 and 384 well plates.
  • EpMotion 5075LH (Eppendorf): Automated liquid handling workstation

Mission Bay Campus:

  • AB 7900HT (Life Technologies/Applied Biosystems): QPCR instrument with exchangeable blocks (96, 384 well).  Fast PCR, Taqman Low Density Array (TLDA).
  • QuantStudio 3D (dPCR): Desktop digital PCR instrument for absolute quantification in copies/uL.
  • 4D Nucleofector: High efficiency electroporation of primary cells and cell lines
  • Bioline Mic: Very fast, user-friendly, and low-throughput magnetic induction qPCR Cycler with a maximum of up to 48 samples per run

AB 7900HT qPCR System

AB 7900 qPCRThe Applied Biosystems 7900HT is a real-time thermocycler that allows quantitative and qualitative detection of nucleic acids based on fluorescent-based technology. The AB7900HT uses excitation and emission filters to capture the amplification of nucleic acids in real time for quantitative analysis. End-point and dissociative curve analysis can be used to qualitatively assess nucleic acids. Commonly used assays are SYBR Green and Taqman. The instrument can only be used for 384 well plate formats. Applied Biosystems plates are recommended.  

Using the AB7900HT: To use the AB7900HT, please consult the Core’s personnel to complete an online training.  Upon completion of the training, access to the reservation calendar will be granted.  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. Results are exported in text format which can be conveniently opened with Microsoft Excel.

Locations:
S161, Cancer Research Building, Mount Zion Campus
HD235, Helen Diller Building, Mission Bay Campus


Agilent Bioanalyzer 2100

Agilent Bioanalyzer 2100The Agilent Bioanalyzer 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.

The Core hosts the RNA 6000 Nano chip (12 samples/chip, 1 uL sample vol, 30 min run time, Sensitivity: 25-500 ng/uL)

Using the Bioanalyzer: A mandatory online training session is required to authorize the use of the Bioanalyzer and may be set up with the Core’s personnel. Following the session, the Core will enable access to the instrument on the MyCORES calendar for reservation. 

Location: S163, Cancer Research Building, Mount Zion 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: To use the Nanodrop 8000, please reserve the instrument on MyCORES using the Nanodrop 8000 reservation calendar.

Location: S161, 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: S164, Cancer Research Building, Mount Zion Campus


Eppendorf epMotion 5075

Eppendorf epMotionThe epMotion 5075 is an automated liquid handling system linked to a desktop computer software designed to automate routine pipetting tasks. The instrument allows for single pipetting using 10uL, 100uL, and 1000uL automated pipettors and multichannel pipetting using 50uL and 1000uL automated pipettors. 

Using the epMotion 5075: Please contact the Genome Core regarding the use of this instrument. 

Location: S163, Cancer Research Building, Mount Zion 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. 

Using the dPCR: Please contact the Genome Core regarding the use of this instrument. 

Location: HD307, 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: Please contact the Genome Core regarding the use of this instrument. 

Location: HD328, 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 4D-Nucleofector: We are looking for a small number of pilot users to do a few runs free of charge to validate the instrument.  Our first-time users will acquire tubes and reagents free of charge.  Please contact the Genome Core regarding the use of this instrument. 

Location: HD235, Helen Diller Building, Mission Bay Campus