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Research / Core Facilities

College of Medicine Research Core Facilities

The UC College of Medicine houses several research core facilities designated as core service centers. These facilities exist within multiple departments but are collectively supported by the College of Medicine Office of Research through the Associate Dean for Research Core Facilities: Ken Greis, PhD. (ken.greis@uc.edu; Tel: 513-558-7102).

The service center designation signifies the rates charged by each of these facilities have been reviewed and approved by the UC Government Cost Compliance Office; thus, the service fees can be charged to federal grants and contracts. Details related to the services offered and the internal rates for each of the cores are provided below. Since these rates are substantially subsidized by the University, external investigators should contact individual core directors to get a rate quote.

Resources to offset some of the cost of the core services may be available through a variety of centers and institutes across UC depending on an investigator’s affiliation. Information for support from the CCTST is provided here:

UC invesitgators also hvae full access to shared resource cores at Cincinnati Children's Hospital. Details are provided here:

We have recently transitioned our core facilities booking and management to the PPMS system from Stratocore. To book and access services from the core facilities, please log in or create an account in Stratocore via:

My PPMS Dashboard

Stratocore Account Creation Guides:

Genomics, Epigenomics and Sequencing Core (GES Core)



The Genomics, Epigenomics and Sequencing Core (GES Core), originally named Genomics and Microarray Laboratory, was established in 1999. In 2012, the Core was transformed into the next generation sequencing-based facility, which provides services to researchers at the University of Cincinnati, Cincinnati Children's Hospital Medical Center as well as other institutions nationwide. Since then, the Core has been fully sustainable and always maintains financially healthy status. We now have one of the best equipped laboratories in the College of Medicine for the next generation sequencing, single cell sequencing and many other services in genomics and epigenomics.

GES Core uses UC Stratocore for sample submission and billing. Here are the related links:
Placing an order via UC Stratocore (required): https://ppms.us/uc/start/
How to use UC Stratocore (important): https://med.uc.edu/depart/eh/cores/genomics/services-and-order

 

Grant Information

A general NIH description of facilities and equipment for this core may be accessed with this link - GESC NIH Summary May 2024; however, it is highly recommended that you discuss your specific core needs with the core director or manager while preparing the grant application since they can likely provide tailored information regarding their capabilities to enhance your application.

ServiceCost
RNA/DNA extraction.
$40/sample.
10x Genomics single cell sequencing.
Please inquire.
DNA/RNA Bioanalyzer QC (measure sample size distribution and integrity).
$25
miRNA-seq (standard service; PE2x61 bp, ~10M reads/5M read clusters, >3M pass filter reads).
$195
PolyA RNA-seq (standard service; PE2x61 bp, ~60M reads/30M read clusters, >40M pass filter reads)
$230
Other types of sequencing (varies with experiment approach, kit/reagent, sequencing setting, etc).
Please inquire.
MethylationEPIC and Genotyping.
Please inquire.
Other types of services (supportive DNA/RNA experiments).
Please inquire.
Note 1: The rates are approved by UC Recharging Meeting. Due to the price change of kits, reagents, consumables, etc., they are subject to change without prior notice.
For inquiry, please email xiang.zhang@uc.edu.
Note 2: Collaboration and/or co-authorship maybe required if the Core has significant intellectual contribution.
N/A

Placing an order via UC Stratocore (required): https://ppms.us/uc/start/ How to use UC Stratocore (important): https://med.uc.edu/depart/eh/cores/genomics/services-and-order

GES Core major equipment



GES Core has three Revco high-performance ultra-low freezers, four Revco high-performance freezers, and three refrigerators, which are equipped with Smart-Vue Sensors to monitor and report temperature change in real-time via wireless connection to cell phones and emails. The Core is equipped with a series of instruments to support its service and research, from DNA/RNA isolation to library preparation and sequencing. This includes Illumina NextSeq 2000 sequencer and all the ancillary instruments including:
 
ABI QuantStudio 5 Real-Time PCR System for library quantification, gene expression, genotyping and CNV analyses, Covaris S2 for precise size control of DNA fragmentation, Eppendorf Thermomixer block shakers with heating and cooling (two), 4X microplates shaker (two) incubators (two), Agilent Bioanalyzer and Invitrogen Qubit fluorometers (two) for DNA, RNA and library QC, Veriti and VeritiPro thermal cyclers (total 8) for enzyme reactions and DNA amplification, Labconco entriVap micro IR Vacuum Concentrator for DNA/RNA samples, and Labnet ENDURO GDS Touch Gel Documentation System agarose/PAGE gel electrophoresis systems for library/DNA/RNA analysis and size selection. It has a total of 26 different types of centrifuges to meet different experiment requirements. In addition, it is equipped with MPBio FastPrep-24 5G homogenizer for high quality RNA extraction from all types of samples. The Core has Illumina iScan and its ancillary instruments used in Infinium BeadChip System. Further, the Core has six different types of Schneider Electric Smart-UPS connected to its critical instruments to prevent potential power failure.
 
For single cell sequencing, GES Core has 10x Genomics Chromium Single Cell System and its supportive instruments such as LUNA-FL Automated Fluorescence Cell Counter and fully automated gentleMACS Octo Dissociator with Heaters from Miltenyi.
 
GES Core values the role of lab automation in its service. It continuously invests in the Integra automated pipetting system and has developed many validated apps for large experiments. Combined with the access to NovaSeq X Plus sequencer, the Core efficiently processes large numbers of samples routinely in a cost-effective manner.

How can I submit my samples?

If possible, we suggest contacting us before experiment design and sample preparation. Once your samples are ready, please download and complete the Sample Submission Form. Then, email it to us and let us know the submission date. In this way, we can prepare for your project in advance. Please always download the form from our website to ensure you use the latest version.

Do you provide service to researchers outside your University?

Yes, we provide high quality service with competitive price.

Do you have any suggestions for sample preparation?

Many RNA samples submitted to our core do not pass QC. Please contact us for suggestions specific to your project. We also provide an RNA extraction service.

My total RNA samples are degraded and I do not have replacement samples. Can you still use them to perform RNA-seq and miRNA-seq?

Yes. With degraded RNA, we use alternative approaches for RNA-seq and miRNA-seq. However, more reads are required for analysis, and the cost could be higher.

Which kit would you recommend for total RNA extraction?

Basically, all major brand kits have good performance for total RNA extraction. However, taken the yield, quality and further application into consideration, we recommend using mirVana miRNA isolation kit (Lifetech), and suggest following the manufacturer’s total RNA extraction protocol to extract RNA from culture cells and most types of tissues. In this way, the extracted total RNA can be used for both RNA and small RNA study. Please be reminded that for some special samples such as blood and FFPE samples, special kits may be required.

Why are my RNA samples extracted from blood and other tissues degraded even when I flash-frozen them in liquid nitrogen and stored them in -80C freezer?

It is very important to treat blood samples according to established protocols before storing them for future RNA extraction. GESC suggests our customers to strictly follow the Invitrogen’s protocol by mixing the anticoagulated whole blood with RNAlater, or using other commercially available kits specifically for this purpose. For most types of fresh tissues, it is suggested to treat them with RNAlater rather than liquid nitrogen.

Will genomic DNA contamination affect my RNA-seq data quality?

If your RNA extraction protocol has a phase separation step, please make sure that the interphase which contains gDNA is not disturbed when transferring the aqueous phase. If you have enough RNA, it is always good to leave some aqueous phase. Specifically for Ribo-Zero RNA-seq, please treat the RNA with RNase-free DNase I; for polyA RNA-seq, there is less concern about gDNA contamination, as the protocol only purifies polyA RNA for sequencing.

In regard to your routine polyA RNA-seq, how much total RNA should I submit, what should the concentration be, and what should the quality be?

We run our routine polyA RNA-seq with the total RNA input between 50 ng – 1 ug in 50 ul. In general, the RNA quality determined by Bioanalyzer RIN (RNA Integrity Number) score should be >7. Please adjust all the RNA samples to the same 100 ng/ul (preferred concentration) and submit 1.5- 2 ug RNA, if possible. Please do not adjust the RNA concentration if it is < 20 ng/ul.

Can you give me an exact sequencing turnaround time?

While our goal is to provide short turnaround time, many factors affect it. One consideration is that we have to fill an entire flow cell with the expected number of samples before the final sequencing. As our service began to expand since 2012, there has been a reduction in turnaround time.
For single read sequencing (SR 1x51 bp), our goal is to keep the turnaround time within one month. The pair-end sequencing takes longer time and is more difficult to predict the turnaround time. Please contact us for current turnaround time. Please note bioinformatics analysis takes extra time.
 

Will you be able to generate exact number of reads that I need?

We follow standard protocol and use qPCR to adjust final library concentration for sequencing. Due to the nature of qPCR variation, we are unable to generate exact # of reads. However, we guarantee the # of pass filter reads will be >80% of planned reads (<20% variation). For example, if the plan is to generate 50 million reads, we guarantee the final # of pass filter reads will be >40 million. In case the # of reads is <40 million, we will simply add more reads in the next sequencing.

Bioinformatics analysis

We can send links to you to download them.

What can I expect from the bioinformatics analysis?

After the completion of the sequencing, and if the data pass preliminary QC analysis, we will contact you for sample information. This includes 1) how many groups do you have? 2) the sample IDs in each group; 3) are they paired samples or not? 4) how do you want us to compare different groups? Once we have the information, our bioinformatics team will perform standard analysis, and send you a link to the result.

What are your preferred payment methods?

For payment from UC, please provide the PI’s full grant account string (e.g. G100121-62612XXXXX-1-100XXXX); for payment from VA, only credit card payment is accepted. We will contact you for credit card information. For payment from institutions other than UC and VA, please mark your check with GESC order/invoice #, and mail it to Ben according to the instruction provided in the invoice. 

My grant account will be expired soon. Can you help me to process the payment now?

Please contact us as soon as possible.

How will you adjust your service rate?

Our service rate is reviewed and approved by the Recharge Council. The rate heavily relies on the cost of sequencing consumables and other reagents. While it is our goal to maintain our services at low stable rate, occasionally we may adjust our rate without prior notice based on price changes in the market.

Do you provide support for grant and manuscript writing?

Yes. We provide free supporting letter, service quotes, and our standard Materials & Methods for grant preparation/manuscript writing. We also provide consultation on experiment design and suggestions for sample preparation.

How about collaboration?

We are very interested in collaboration. With our expertise in the field, we are looking for collaboration opportunities in grant application and paper submission. Specifically, if the study needs to establish a novel approach, needs to use a complicated, customized method or extensively requires our expertise, collaboration is required.

Are you interested in method development?

Yes we are very interested in developing or introducing new methods to our core that can benefit both the research community and us. Please contact us if you think we should provide a service that is not on our list.

What is your shipping address?

Xiang Zhang
160 Panzeca Way
Kettering Building Room 336
Cincinnati, OH 45267
 
Tel: 513-558-4764

A total of 69 publications as of 07/01/2024 https://www.ncbi.nlm.nih.gov/sites/myncbi/1XIci6hpXFh5v/bibliography/47307541/public/?sort=date&direction=descending

Location

160 Panzeca Way
Kettering Building Room 336
Cincinnati
45267

Contact Information

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Contact Us

University of Cincinnati
College of Medicine

CARE/Crawley Building
Suite E-870
3230 Eden Avenue
PO Box 670555
Cincinnati, OH 45267-0555

Mail Location: 0555
Phone: 513-558-7333
Fax: 513-558-3512
Email: College of Medicine