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Genomics Facility

The Genomics Core Facility at the University of Utah provides a variety of cost effective genotyping, fragment analysis, gene expression, copy number, and methylation profiling services to the research community. Many of these services can be customized to meet the needs of individual researchers for projects ranging in scale from single targets to whole genomes. Instrument training and access, along with full service, sample-to-results options, are available. Researchers are encouraged to contact the Genomics Core Facility to discuss the most appropriate and cost effective platform to achieve their study goals.

Genotyping

Whole genome genotyping, an ideal platform for genome-wide association studies and identifying variants associated with disease risk and disorders, is offered using Illumina’s predesigned and custom beadchip arrays on the Illumina iScan instrument. Thousands to millions of SNPs can be genotyped on any number of samples. 

Custom panels of SNPs can be selected for more focused genotyping of genes or regions of interest using the LifeTechnologies OpenArray system and QuantStudio 12K Flex real time PCR instrument. This platform is best suited for studies that involve genotyping dozens to hundreds of SNPs on hundreds of samples.

Predesigned and custom TaqMan SNP genotyping assays from LifeTechnologies are available for genotyping a small number of SNPs on any number of samples using the QuantStudio 12K Flex real time PCR instrument. Assays can be designed for any organism. This platform is ideal for rapidly genotyping a variant of interest in a large set of samples.

Fragment Analysis

DNA fragment size analysis and STR genotyping services are available to researchers who submit PCR product labeled with FAM, VIC, NED, or PET fluorescent tags. Fluorescent labeled PCR products are run on an Applied Biosystems 3730 capillary electrophoresis instrument and analyzed with GeneMapper software. PCR optimization and reaction setup is offered as a full-service option for users who would prefer to submit DNA samples and PCR primers to size and genotype regions of interest.

Gene Expression Analysis

Quantitative real time PCR is routinely used to measure differences in gene expression between samples or groups of samples, and to validate RNA-seq results. Two Life Technologies QuantStudio 12K Flex instruments are available for researchers interested in performing quantitative real time PCR experiments for gene expression studies. Instrument and software training is available to all users, and the instruments can be reserved in two hour time increments. This service is offered as instrument-use only, and researchers are responsible for reaction plate setup prior to using the instruments in the Genomics Core Facility.

Copy Number Analysis

Copy number variations (CNVs) resulting from duplications, deletions, translocations, and inversions can be associated with disease and genetic disorders. For researchers interested in CNV analysis of a specific gene or region, the TaqMan Copy Number Assays from ThermoFisher are available to run on the QuantStudio 12K Flex real time PCR instrument. Genome-wide genotyping arrays from Illumina are available to researchers looking to screen the entire genome for CNVs. 

Methylation Analysis

The methylation of DNA at various sites in the genome regulates the expression of genes and plays an important role in development, X chromosome inactivation, imprinting, and carcinogenesis. The Genomics Core Facility offers researchers an array-based platform for measuring the degree of methylation at various sites throughout human and mouse genomes using Illumina’s Human MethylationEPIC array which targets over 935,000 CpG sites, the Mouse Methylation Array targeting 285,000 CpG sites, and the upcoming Human Methylation Screening Array with 250,000 CpG sites.

Data Retention

As a reminder to our users:  We do NOT store your data long term.  Once your runs are finished and your data given to you, we reserve the right to delete it from our servers to recover space for ongoing runs for other users.  It is the responsibility of the grant holder to archive their data, not the core labs.  We cannot maintain a server farm to archive data for everyone.  For archival purposes, we suggest users contact CHPC about creating storage space for their data there.

ILLUMINA BEADCHIP ARRAY USERS

Illumina BeadChip array users MUST download and backup DMAP files for any arrays expected to be processed beyond the product expiration date.  Illumina DELETES all DMAP files for expired BeadChip lots.  The Genomics Core Facility will not be responsible for storing or backing up DMAP files for expired Illumina BeadChip arrays.  All users are encouraged to download and backup DMAPs for any BeadChip arrays purchased from Illumina, regardless of the expected processing timeline.

Each individual Illumina BeadChip array has a unique DMAP file, generated when the BeadChip array is manufactured.  A DMAP file is REQUIRED for processing any Illumina BeadChip array in the Genomics Core Facility.  Without the DMAP file, a BeadChip array cannot be processed or analyzed.

Learn More About DMAP Files

Service Rates

Requesting Services

If you are new to the Cores, you must complete a work authorization form through the Work Authorization System prior to requesting services. Work authorizations may be used for any services offered by facilities managed by HSC Cores. After your work authorization has been approved you will be able to login to the Resource System.

Existing users may login directly to the Resource Scheduling System to schedule or order services. This system is cores-wide and uses University of Utah uNID authentication.

Work Authorization
System On Campus / UU
Work Authorization
System Off Campus / Business
Resource Scheduling
System

If you encounter financial/account issues, contact the Cores Admin office.
For technical issues with any of the web applications, contact the developers.

Charge Rates Procedure / Federal Facilities and Administration (F&A) Rate

Part of the University’s agreement with the Federal Government regarding F&A is that the University will not offer a lower than F&A rate to other kinds of sponsors. That means that the University has to use, at minimum, the same rates for commercial sponsors as it does for the Federal Government. The University would jeopardize its relationship with the Federal Government (the University’s single largest sponsor) if it were to accept rates lower than the current federal F&A rate.

The current F&A Rate is: 54%

The facility internal rate is used when exclusively internal funding sources are used. The F&A / external academic rate applies when external funding sources are used i.e. Federal Government or other academic universities. For more information about F&A rates at the University of Utah please see: 6.3 Indirect Costs/Facilities and Administrative Costs (F&A)

Derek Warner

Facility Director

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Michael Klein

Laboratory Manager

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Hours of Operation

9:00 am to 5:00 pm
Monday - Friday

Mailing Address

Genomics
30 N 2030 E, Rm 115
Salt Lake City, UT  84112

Recent Mentions

  1. Balakrishnan, B., R. Altassan, R. Budhraja, W. Liou, A. Lupo, S. Bryant, A. Mankouski, S. Radenkovic, G. J. Preston, A. Pandey, S. Boudina, T. Kozicz, E. Morava-Kozicz and K. Lai (2023). AAV-based gene therapy prevents and halts the progression of dilated cardiomyopathy in a mouse model of phosphoglucomutase 1 deficiency (PGM1-CDG). Transl Res 257: 1-14.10.1016/j.trsl.2023.01.004
  2. Demir, M., L. P. Russelburg, W. J. Lin, C. H. Trasvina-Arenas, B. Huang, P. K. Yuen, M. P. Horvath and S. S. David (2023). Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Nucleic Acids Res 51(3): 1034-1049.10.1093/nar/gkac1246
  3. Flack, C. E. and J. S. Parkinson (2022). Structural signatures of Escherichia coli chemoreceptor signaling states revealed by cellular crosslinking. Proc Natl Acad Sci U S A 119(28): e2204161119.10.1073/pnas.2204161119
  4. Fleming, A. M. and C. J. Burrows (2023). Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription. Nucleic Acids Res 51(4): 1914-1926.10.1093/nar/gkad044
  5. Fleming, A. M., R. Tran, C. A. Omaga, S. A. Howpay Manage, C. J. Burrows and J. C. Conboy (2022). Second Harmonic Generation Interrogation of the Endonuclease APE1 Binding Interaction with G-Quadruplex DNA. Anal Chem 94(43): 15027-15032.10.1021/acs.analchem.2c02951
  6. Gerstner, C. D., M. Reed, T. M. Dahl, G. Ying, J. M. Frederick and W. Baehr (2022). Arf-like Protein 2 (ARL2) Controls Microtubule Neogenesis during Early Postnatal Photoreceptor Development. Cells 12(1).10.3390/cells12010147
  7. Giglio, M. L., P. F. Salcedo, M. Watkins and B. Olivera (2023). Insights into a putative polychaete- gastropod symbiosis from a newly identified annelid worm that predates upon Conus ermineus eggs. Contributions to Zoology 92(2): 97-111.https://doi.org/10.1163/18759866-bja10038
  8. Hackney, C. M., P. F. Salcedo, E. Mueller, L. D. Kjelgaard, M. Watkins, L. G. Zachariassen, J. R. McArthur, D. J. Adams, A. S. Kristensen, B. Olivera, R. K. Finol-Urdaneta, H. Safavi-Hemami, J. P. Morth and L. Ellgaard (2022). Identification of a sensory neuron Cav2.3 inhibitor within a new superfamily of macro-conotoxins. bioRxiv: 2022.2007.2004.498665.10.1101/2022.07.04.498665
  9. Happ, J. T., C. D. Arveseth, J. Bruystens, D. Bertinetti, I. B. Nelson, C. Olivieri, J. Zhang, D. S. Hedeen, J. F. Zhu, J. L. Capener, J. W. Brockel, L. Vu, C. C. King, V. L. Ruiz-Perez, X. Ge, G. Veglia, F. W. Herberg, S. S. Taylor and B. R. Myers (2022). A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. Nat Struct Mol Biol 29(10): 990-999.10.1038/s41594-022-00838-z
  10. Howpay Manage, S. A., A. M. Fleming, H. N. Chen and C. J. Burrows (2022). Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair. ACS Chem Biol 17(9): 2583-2594.10.1021/acschembio.2c00511
  11. Howpay Manage, S. A., J. Zhu, A. M. Fleming and C. J. Burrows (2023). Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology. RSC Chem Biol 4(4): 261-270.10.1039/d2cb00233g
  12. Leng, A. M., K. S. Radmall, P. K. Shukla and M. B. Chandrasekharan (2022). Quantitative Assessment of Histone H2B Monoubiquitination in Yeast Using Immunoblotting. Methods Protoc 5(5).10.3390/mps5050074
  13. McKnite, A., H. S. Kim, J. Silva and J. L. Christian (2023). Lack of evidence that fibrillin1 regulates bone morphogenetic protein 4 activity in kidney or lung. Dev Dyn 252(6): 761-769.10.1002/dvdy.578
  14. Radmall, K. S., P. K. Shukla and M. B. Chandrasekharan (2023). A system for <em>in vivo</em> evaluation of protein ubiquitination dynamics using deubiquitinase-deficient strains. bioRxiv: 2023.2006.2018.545485.10.1101/2023.06.18.545485
  15. Reed, M., K. I. Takemaru, G. Ying, J. M. Frederick and W. Baehr (2022). Deletion of CEP164 in mouse photoreceptors post-ciliogenesis interrupts ciliary intraflagellar transport (IFT). PLoS Genet 18(9): e1010154.10.1371/journal.pgen.1010154
  16. Scoles, D. R., M. Gandelman, S. Paul, T. Dexheimer, W. Dansithong, K. P. Figueroa, L. T. Pflieger, S. Redlin, S. C. Kales, H. Sun, D. Maloney, R. Damoiseaux, M. J. Henderson, A. Simeonov, A. Jadhav and S. M. Pulst (2022). "A quantitative high-throughput screen identifies compounds that lower expression of the SCA2-and ALS-associated gene ATXN2." J Biol Chem 298(8): 102228.10.1016/j.jbc.2022.102228
  17. Simeone, C. A., J. L. Wilkerson, A. M. Poss, J. A. Banks, J. V. Varre, J. L. Guevara, E. J. Hernandez, B. Gorsi, D. L. Atkinson, T. Turapov, S. G. Frodsham, J. C. F. Morales, K. O'Neil, B. Moore, M. Yandell, S. A. Summers, A. S. Krolewski, W. L. Holland and M. G. Pezzolesi (2022). "A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia." NPJ Genom Med 7(1): 43.10.1038/s41525-022-00314-z
  18. Shukla, P. K., J. E. Bissell, S. Kumar, S. Pokhrel, S. Palani, K. S. Radmall, O. Obidi, T. J. Parnell, J. Brasch, D. C. Shrieve and M. B. Chandrasekharan (2023). Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. Nucleic Acids Res 51(5): 2117- 2136.10.1093/nar/gkad012 Shukla, P. K., K. S. Radmall and M. B. Chandrasekharan (2023). Rapid purification of rabbit immunoglobulins using a single-step, negative-selection chromatography. Protein Expr Purif 207: 106270.10.1016/j.pep.2023.106270
  19. Shukla, P. K., D. Sinha, A. M. Leng, J. E. Bissell, S. Thatipamula, R. Ganguly, K. S. Radmall, J. J. Skalicky, D. C. Shrieve and M. B. Chandrasekharan (2022). Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 in helix-3 affect ubiquitination activity and decrease enzyme stability. J Biol Chem 298(11): 102524.10.1016/j.jbc.2022.102524
  20. Utzman, P. H., V. P. Mays, B. C. Miller, M. C. Fairbanks, W. J. Brazelton and M. P. Horvath (2023). Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. bioRxiv: 2023.2004.2005.535768.10.1101/2023.04.05.535768
  21. Walker, M. F., J. Zhang, W. Steiner, P.-I. Ku, J.-F. Zhu, Z. Michaelson, Y.-C. Yen, A. B. Long, M. J. Casey, A. Poddar, I. B. Nelson, C. D. Arveseth, F. Nagel, R. Clough, S. LaPotin, K. M. Kwan, S. Schulz, R. A. Stewart, J. J. G. Tesmer, T. Caspary, R. Subramanian, X. Ge and B. R. Myers (2023). GRK2 Kinases in the Primary Cilium Initiate SMOOTHENED-PKA Signaling in the Hedgehog Cascade. bioRxiv: 2023.2005.2010.540226.10.1101/2023.05.10.540226
  22. Workalemahu, T., C. Avery, S. Lopez, N. R. Blue, A. Wallace, A. R. Quinlan, H. Coon, D. Warner, M. W. Varner, D. W. Branch, L. B. Jorde and R. M. Silver (2023). Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study. PLoS One 18(2): e0281934.10.1371/journal.pone.0281934

Citing Our Facility

Acknowledgments

We would like to thank you for acknowledging the our facility. This recognition allows us to highlight the impact of your work and demonstrates the important contributions of our facility makes to research across the University of Utah. The recognition our core receives from your acknowledgments also aids in receiving grants and further funding for equipment and services we can provide to our users.

Self-Run Services / Instrumentation Usage:

In published papers that used instruments at our facility and notably involved staff members please use the following format:

We acknowledge (facility name) at the University of Utah for use of equipment (insert instrument/service details here), and thank (insert any notable staff member – if desired) for their assistance.

Assisted Services:

In published papers where a staff member assisted you in addition to the requested services please use the following format:

We acknowledge (facility name) at the University of Utah for use of equipment (insert instrument/service details here), and thank (insert staff member-required) for their assistance in (service provided).

Collaboration:

For publications resulting from collaborations that assisted with the methodologies, planning process and execution of your experiment in addition to equipment usage we require Co-author attribution on your publication for our facility and any staff members who provided substantial contributions to the originating project.