Genomics High Throughput Facility

Direct Lab Website: Genomics High Throughput Facility 

For information regarding iLab usage, please refer to the iLab User Guide

Overview of Services

We offer a wide variety of different services to assist researchers with their genomics related research projects.

DNA and RNA Quality Control
We have several services that can be used to check the quality and quantity of your DNA and RNA samples. Some of the quantification services provided are: Qubit Assays( dsDNA High Sensitivity, dsDNA Broad, and RNA High Sensitivity), Nanodrop, and Kapa qPCR quantification. We also offer Agilent Bioanalyzer services to help visualize your DNA and RNA samples. If concentrations are lower than desired, then we can speed vacuum your RNA or DNA samples via a Speed-Vac Concentrator. If your samples require further cleanup, we also offer cleanup services via Qiagen RNeasy Purification with DNase Treatment and Ampure XP Beads purification. 

Microarray Analysis
Use our Affymetrix Microarray platform to perform microarray analysis using Affymetrix chips, a GeneChip Scanner, and a ScanArray Express. We have several Affymetrix services: Affy 3′-IVT biased Expression, WT & Exon arrays (HuGENE, MuGENE, and RatGene), Affy microRNA/Geneisphere FlashTag Biotin HSR processing, and Cytoscan. 

Digital PCR
Using the Bio-Rad’s QX200 Droplet Digital PCR (ddPCR) System you can perform high-throughput digital PCR without using as much sample and reagents as you would with other means. Droplet digital PCR is essentially when the DNA is partitioned into nanoliter sized droplets, where PCR amplification occurs. 

Single Cell Sequencing
We currently have two options for single cell sequencing: Fluidigm C1 Single Cell Sample Prep and the 10x Chromium Single Cell Gene Expression. Both machines are available for self operation or full service. Reference Worthington Skin Table for more information about sequencing skin cells with 10x Chromium.

Illumina Compatible Library Construction
GHTF offers several different library construction kits in order to create Illumina compatible libraries from a multitude of different sample types. Some of the library construction types offered are: Genomic DNA Library Kapa Hyper and Bioo Scientific, ChIP-seq and ATAC-seq, TruSeq stranded or unstranded mRNA-seq, TruSeq Ribo-Zero Stranded RNA-seq, Illumina Bisulfite, 16S metagenomics, and Whole Exome library construction. 

Illumina Sequencing
GHTF houses several Illumina sequencing instruments: MiSeq, HiSeq4000, and NovaSeq6000. With each sequencing instrument offering a variety of different sequencing chemistry, users can easily find the chemistry and instrument to obtain the amount of data they need.

PacBio Sequencing
Perform long-read sequencing at GHTF with our PacBio Sequel Sequencing system. We can generate SMRTbell templates up to 30kb. 

Nanostring
Perform multiplex analysis of mRNA and miRNA, using our Nanostring services. 

Genome Mapping
Obtain genome mapping data with our Bionano Saphyr platform. Either provide high molecular weight DNA or tissue samples, and we can create labeled DNA for the Bionano Saphyr to image. The mapping data obtain can then be used to create hybrid scaffolds with next generation sequencing data to assist with whole genome sequencing. 

Bioinformatics Services
Confused on what to do with all the sequencing data received? GHTF offers bioinformatic services to assist with the processing of your sequencing data. You can perform analysis by yourself using the Ingenuity Pathway Analysis software or you can request services from our in house bioinformaticians. 

Miscellaneous Services Provided
To make things simpler, GHTF also offers RNA isolation and DNA extraction services. If DNA sample need to be fragmented, we can shear them for you using the Covaris S220 Focused Acoustic Shearer. Click here to learn more.

For custom services not listed please contact Dr. Melanie Oakes (949-824-6023) for a consultation.

 

Acknowledgement Guidelines

It is very important to the continued funding of the Chao Family Comprehensive Cancer Center (CFCCC) that the productive collaboration of CFCCC-supported Shared Resources is acknowledged in publications and presentations, and that resulting publications are processed by the National Institutes of Health Manuscript Submission (NIHMS) to obtain a PubMed Central reference number (PMCID), per NIH Public Access Policy.

Please visit the CFCCC website to learn more about Acknowledging the Cancer Center Support Grant (CCSG) and Shared Resources.

 

Leadership

Director:
Suzanne Sandmeyer, Ph.D.

Location and hours of operation

Hours      Location

Monday - Friday 
8:00 am - 5:00 pm

     340 Sprague Hall
     University of California, Irvine
     Irvine, CA 92697-4035

Sample Drop Off Information:

GHTF is still receiving samples during this pandemic. Samples can be dropped off anytime Monday-Friday between 8:00am-5:00pm on the 3rd floor of Sprague Hall at Bench 20 of Room 340 and 350. Please complete a service request before submitting samples.

Contacts

Name Role Phone Email Location
Melanie Oakes, PhD
Core Lead
 
(949)824-5327
 
mloakes@uci.edu
 
340 Sprague Hall University of California, Irvine Irvine, CA 92697-4035
 

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