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UCSF Laboratory for Cell Analysis – Genome Analysis Core Services

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San Francisco, California, US

About UCSF Laboratory for Cell Analysis – Genome Analysis Core Services

The UCSF HDFC - Cancer Center Genome Analysis Core provides laboratory services and equipment specializing in wet-lab genome analysis downstream of RNA and DNA isolation. We have years of expertise generating custom assays on clinical research samples starting from a large variety of tissue and sample types. Most recently, we have had success with assaying DNA from circulating tumor cells, plasma (cell free DNA), and cerebrospinal fluid.

We specialize in mid-to high-throughput quantitative and digital PCR, SNP genotyping, and gene expression analyses using a variety of state-of-the-art platforms.

Techniques

We have validated laboratory pipelines with validated SOPs in the following techniques
across the entire wet-lab molecular genomic workflow - assay design to sample processing
to primary data analysis using software packages:

Genome and transcriptome assay design, digital PCR (dPCR), quantitative real time PCR (qPCR), targeted DNAseq, targeted RNAseq, library preparation, sample & library QC, Cancer Hot Spot NGS Panel, multiplex SNP genotyping (1-256 targets), high throughput qPCR (>3,000 rxns), epigenetics (quantitative methylation analysis), SNP discovery, Gene Expression (1‐224 transcripts), Copy Number Variant (CNV) analysis, DNA Quantification, low frequency allele detection, somatic mutation profiling.

Instrumentation
-QuantStudio 5 qPCR System: The Applied Biosystems 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.
-Qubit 4 Fluorometer: A fluorometer designed to accurately measure DNA, RNA, and protein quantity in less than 3 seconds per sample.
-Eppendorf epMotion 5075: 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.
-Quantstudio 3D Digital PCR system: chip-based digital PCR that uses Taqman assays for the most sensitive quantitative and reproducible detection for low frequency variants. Located at 1450 3rd Street.

  • Quantstudio 12K Flex, OpenArray block (Life Technologies): High throughput nanoliter QPCR with >2300 reactions per chip.
  • Two MJ Research tetrad DNA engines with four independent PCR blocks
  • ABI 9600 PCR block with exchangeable 96- and 384-well blocks
  • Nanodrop 8000 (Thermo Scientific): UV-Vis Spectrophotometer with multi-sample (1-8) micro-volume (1ul) measurements. Mt. Zion Campus, Cancer Research Building, 2340 Sutter St, Room S164.
  • Agilent 2100 Bioanalyzer (Agilent Technologies): Microfluidics-based (Lab-On-A-Chip) platform for sizing, quantification and quality control of DNA, RNA, protein, and cells. Mt. Zion Campus, Cancer Research Building, 2340 Sutter St, Room S163.
    -Lonza 4D-Nucleofector System: The most advanced Nucleofection platform offering maximum flexibility in regards to cell numbers, throughput, and cell status.
    -Bioline Mic Magnetic Induction qPCR Cycler: A very fast, user-friendly, and low-throughput magnetic induction qPCR Cycler with a maximum of up to 48 samples per run.

Selected Publications

  • Lopez Jimenez N, Gerber S, Popovici V, Mirza S, Copren K, Ta L, Shaw GM, Trueb B, Slavotinek AM. Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm. Hum Genet. 2010 Mar; 127(3):325-36. PMID: 20024584. PMCID: PMC2893560.
  • DuBois SG, Goldsby R, Segal M, Woo J, Copren K, Kane JP, Pullinger CR, Matthay KK, Witte J, Lessnick SL, Robison LL, Bhatia S, Strong LC. Evaluation of polymorphisms in EWSR1 and risk of Ewing sarcoma: a report from the Childhood Cancer Survivor Study. Pediatr Blood Cancer. 2012 Jul 15; 59(1):52-6. PMID: 21793187. PMCID: PMC3204324.
  • Premasekharan, G; Gilbert, E; Okimoto, R.A.; Hamirani, A; Lindquist, K.J.; Ngo, V.T.; Roy, R; Hough, J; Edwards, M; Paz, R; Foye, A; Sood, R; Copren, K.A.; Gubens, M; Small, E.J.; Bivona, T.J.; Collisson, E.A.; Friedlander, T.W.; Paris, P.L. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer, Cancer Letters, Volume 380, Issue 1, 28 September 2016, Pages 144-152, ISSN 0304-3835.
  • McCreery MQ, Halliwill KD, Chin D, Delrosario R, Hirst G, Vuong P, Jen KY, Hewinson J, Adams DJ, Balmain A. Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nat Med. 2015 Dec; 21(12):1514-20. PMID: 26523969.
  • Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ, Fredlund E, Quigley DA, Adams DJ, Balmain A. The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature. 2015 Jan 22; 517(7535):489-92. PMID: 25363767; PMCID: PMC4304785.

Our Services (15)


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qPCR

Quantitative PCR
Starting at $55.17 per hour

QuantStudio 5 qPCR System-Instrument time

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). 

ABI 7900HT Applied Biosystems 7900HT Fast Real-Time PCR System qPCR

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CRISPR/Cas9 Genome Editing

Starting at $70.19 per hour

Lonza Nucleofector Instrument Time:

The 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.

4D-Nucleofector Lonza Nucleofector CRISPR nucleofection

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Spectrophotometry

Starting at $27.55 per hour

Nanodrop 8000 Instrument Time:

The 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.

NanoDrop 8000 spectrophotometer

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DNA/RNA Analysis and Quality Control

Starting at $37.56 per hour

Bioanalyzer Instrument Time: The 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. 

Agilent Bioanalyzer

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Spectroscopy

Price on request
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Imaging & Spectroscopy

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Nucleic Acid Services

Price on request
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Biochemistry & Molecular Biology

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Biology

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Genetic Engineering

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Equipment

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PCR

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DNA Services

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Omics

Price on request

Single-CellFunctional Proteomics
IsolightSystem

 
The IsoLightis a versatile, precision engineering platform designed to understand and characterize immune function, fitness, and potency. The IsoLight maps thousands of cells per sample to reveal full functional profiles and polyfunctionality among cell subsets to reveal correlative insights into true functional immune biology.
 
Running the IsoCode Chip, the IsoLight system captures single-cell, functional cytokine profiles from thousands of single cells in parallel to better understand complex functional immune response in preclinical and clinical samples.
 
The IsoSpeakbioinformatics software platform helps discover new patient relationships among heterogeneous cells and clearly defines subsets of powerful, polyfunctional cells, secreting 2+ cytokines simultaneously, and has revealed unique functional correlates to in vivoresponse in various studies.
 


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RT-PCR

Reverse transcription polymerase chain reaction
Price on request

Gene Expression Analysis Service

Real-Time PCR asseses the relative abbundance of transcripts to deteremine gene expression patterns between samples. RNA quolity, reverse transcription efficancy, real-time PCR efficiency, quantification strategy, and the choice of a normalizer gene play particularly important roles in gene expression experiment. 


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Emanuela Zacco

LCA-Genome Core Manager

UCSF Laboratory for Cell Analysis – Genome Analysis Core Services has not received any reviews.

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