Today is Tuesday, Sep. 18, 2018

Research

College of Medicine Research Core Facilities

The UC College of Medicine houses a number of 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: 515-558-7012).  

The service center designation signifies that 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 cross-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 related to some of those opportunities and the website links are provided below:

 

Close up view of neurons
core

Contact Information

Genomics, Epigenomics and Sequencing Core (GESC)

The Genomics, Epigenomics and Sequencing Core (GESC), originally named as Sequencing and Microarray Laboratory, was established in 1999. GESC is a fee-for-service, one-stop facility that provides genomics and epigenomics related service and collaboration to researchers at the University of Cincinnati, Cincinnati Children's Hospital and other institutions.
In 2012, GESC was transformed into the next generation sequencing-based core facility. Since then, it has been expanding its services and seamlessly integrated with the bioinformatics team for handling massive amounts of data generated by these services. Equipped with Illumina sequencer and automated liquid handling system, GESC provides a wide variety of high-quality NGS services and continuously developing new methodologies to meet researchers’ requirements. In addition, it offers Illumina BeadChip assay and a series of other supportive services. The Core manager Xiang Zhang routinely provides consultation to researchers from sample preparation to experiment design.
GESC is a small but highly efficient team. Nearly 100% of its expenses is paid from its service revenue. The Core’s financial status is extraordinary healthy and stable.

ServiceCost
1. Illumina next generation sequencing
contact core manager
2. Illumina Infinium beadchip assay
N/A
3. DNA/RNA extraction and QC analysis
N/A
4. NGS-based multiplexed bisulfite PCR sequencing (new)
N/A
5. Bisulfite PCR sequencing
N/A
6. Real-time qPCR
N/A
7. Grant and manuscript preparation
N/A
8. Other service/collaboration
N/A
Collaboration and/or authorship maybe required if the Core has significant intellectual contribution.
N/A
GES Core major equipment

HiSeq sequencing for the next generation sequencing (Illumina, San Diego, CA)
SMARTer Apollo automatic liquid handling system (Takara Bio USA, Mountain View, CA)
iScan system for Infinium beadchip Assay (Illumina, San Diego, CA)
FastPrep-24 5G homogenizer (MP Bio Solon, OH)
Bioanalyzer for DNA/RNA QC analysis (Agilent, Santa Clara, CA)
CentriVap micro IR Vacuum Concentrator (Labconco, Kansas City, MO)
Qubit 3.0 fluorometer (Thermo Fisher, Waltham, MA)
Covaris S2 Focused-ultrasonicators for precise DNA/chromatin shearing (Covaris, Woburn, MA)
ABI QuantStudio 5 Real-Time PCR System (Thermo Fisher, Waltham, MA)
Veriti thermal cycles (Thermo Fisher, Waltham, MA)
Enduro GDS Touch Gel Documentation System agarose (Labnet Edison, NJ)
Desktop and floor centrifuges
Incubators, heaters and shakers
Revco high-performance ultra-low freezers, freezers and refrigerators (Thermo Fisher, Waltham, MA)
Smart- Uninterruptible Power Supplies (Schneider Rueil-Malmaison, France)
Branson 5800 Series Ultrasonic Cleaner (Danbury, CT)
Servers, high performance computers, massive data storage devices

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?

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