UCSF Laboratory for Cell Analysis – Genome Analysis Core Services
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San Francisco, California, US
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.
Selected Publications
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).
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.
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.
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.
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.
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.
UCSF Laboratory for Cell Analysis – Genome Analysis Core Services has not received any reviews.
UCSF Laboratory for Cell Analysis – Genome Analysis Core Services has not received any endorsements.