Genomics Research and Technology Hub

Direct Lab Website: Genomics Research and Technology Hub

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. 

Beadarray Analysis
Use our Illumina iScan beadarray for mouse or human SNP, methylation and CNV analysis. 

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.  The ThermoFisher Quantstudio Q is available for smaller sample numbers.  The Q uses a micropartitioning plate to generate 20,000 partitions for digital PCR amplification.

Single Cell Sequencing
We currently have several options for single cell sequencing: Fluidigm C1 Single Cell Sample Prep and the Chromium X. Both machines are available for self operation or full service. Additionally, Parse Biosciences Split-seq workflow is available for scRNA-seq.  Reference Worthington Skin Table for more information about sequencing skin cells with Chromium X.

Illumina Compatible Library Construction
GRT Hub 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, Takara low input pico and Smarter v4 for RNA, TruSeq Ribo-Zero Stranded RNA-seq, Illumina Bisulfite, 16S metagenomics, and Whole Exome library construction. 

Illumina Sequencing
GRT Hub houses the Illumina sequencing instruments: MiSeq 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 II 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. 

Spatial Transcriptomics
GRT Hub offers several workflows for spatial transcriptomics, the 10x Genomics Visium the Nanostring GeoMx. 

Bioinformatics Services
GRT Hub offers bioinformatic services to assist with the processing of your sequencing data. You can perform analysis by yourself using the Qiagen CLC Genomics Workbench and the Ingenuity Pathway Analysis software or you can request services from our in house bioinformaticians. 

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

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

Sample Drop Off Information:

GRT Hub 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

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