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. (firstname.lastname@example.org; 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:
- Center for Clinical and Translational Science and Training (CCTST) Just-in-Time Core Support
- Cincinnati Cancer Center (CCC) Just-in-Time Shared Facilities Award
- Center for Environmental Genetics (CEG) Integrative Technologies Support
Genomics, Epigenomics and Sequencing Core (GESC)
The Genomics, Epigenomics and Sequencing Core (GES Core), originally named as Microarray Laboratory, was established in 1999. GES Core provides genomics and epigenomics related service and collaboration to researchers at the University of Cincinnati, Cincinnati Children's Hospital and other institutions.
In 2012, GES Core was transformed into the next generation sequencing-focused core facility. Since then, it has been expanding its services. Equipped with Illumina NestSeq 550 sequencer and automated liquid handling system, the Core provides a variety of high-quality NGS services. More recently, the Core introduced single cell sequencing via 10x Genomics Chromium and its supportive system such as LUNA-FL Automated Fluorescence Cell Counter and automated gentleMACS Octo Dissociator with Heaters from Miltenyi. In addition, it offers Illumina BeadChip methylationEPIC assay for epidemiology study.
The Core Director Xiang Zhang routinely provides consultation to researchers from sample preparation to data generation.
GES Core is one of the best equipped laboratories in the College. 100% of its expenses is paid from its service revenue. It is fully sustainable and always maintains financial stability over the past 9 years.
RNA/DNA extraction (depending on sample type and number; human blood and clinical samples: $40).
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10x Genomics single cell sequencing.
DNA/RNA Bioanalyzer QC (measure sample size distribution and integrity).
miRNA-seq (standard service; SR 1x85 bp, ~3M reads)
PolyA RNA-seq (standard service; SR1x85 bp, >20M pass filter reads)
Other types of sequencing (varies with experiment approach, kit/reagent, sequencing setting, etc).
MethylationEPIC/oxBS-methylationEPIC (extra charge for repeated assay (sample #: 8X) if the low data quality is not due to our mistake).
Other types of services (supportive DNA/RNA experiments).
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.
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Note 2: Collaboration and/or co-authorship maybe required if the Core has significant intellectual contribution.
To submit samples, please fill the Sample Form (http://med.uc.edu/eh/cores/genomics/services) and email to firstname.lastname@example.org.
GES Core major equipment
GES Core has 12 benches, three fume hoods, three Revco high-performance ultra-low freezers, four Revco high-performance freezers, three refrigerators with backup. It 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 550 sequencing system and all the ancillary instruments such as Takara SMARTer Apollo system for automated liquid handling, 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), incubators (two), Agilent Bioanalyzer and Invitrogen Qubit fluorometers (two) for DNA, RNA and library QC, Veriti thermal cycles (six) for enzyme reactions and DNA amplification, Labconco entriVap micro IR Vacuum Concentrator for DNA/RNA, 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 24 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 for epigenome-wide DNA methylation association study. Further, the Core has six different types of Schneider Electric Smart-UPS connected to its critical instruments to avoid potential power failure. For single cell sequencing, GES Core has 10x Genomics Chromium Single Cell System and its supportive system such as LUNA-FL Automated Fluorescence Cell Counter and fully automated gentleMACS Octo Dissociator with Heaters from Miltenyi.
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.
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
A total of 54 publications as of 09/08/2021 https://www.ncbi.nlm.nih.gov/sites/myncbi/1XIci6hpXFh5v/bibliography/47307541/public/?sort=date&direction=descending
160 Panzeca Way
Kettering Building Room 336
- Xiang Zhang, PhD; Core Director & Assoc. Prof.