Genomics Hero

The Genomics Core facility provides support and services to investigators who want to apply genomics technologies to their research projects. A genome is the complete set of an organism's DNA. Genomics is the broad, interdisciplinary field of science that studies the genes contained in the DNA as well as the regulatory sequences and expression of those genes.

We provide:

  • Consultation on experimental design
  • Equipment
  • Training
  • Services
  • New protocol development

How to Access Core Services

Investigators may request trained facility staff to perform experiments or may use available equipment themselves once they have been trained.

USD and South Dakota BRIN/INBRE-affiliated researchers may use the facility for free. However, the cost of supplies is charged back to the investigator. External charge rates may apply for outside entities. Contact Genomics Core director Kathleen Eyster at kathleen.eyster@usd.edu for a quote or for details about available services.

Equipment and Services

Genomics Bioanalyzer
Agilent Bioanalyzer 2100

RNA Extraction and Quantitation

Working with RNA for the first time can be daunting because of the susceptibility of RNA to ribonucleases. To assist new users of RNA to overcome this barrier, Genomics Core personnel will teach RNA hygiene and standard RNA extraction procedures or may perform RNA extractions if requested.

  • The quantity and quality of RNA are analyzed with the Agilent Bioanalyzer 2100. This instrument uses microfluidics to perform the equivalent of an electrophoresis gel, as well as spectrophotometric analysis of the total RNA in one microliter of a sample.
  • Microfluidics chips for DNA and protein can also be analyzed in the Agilent Bioanalyzer 2100.
  • Core personnel will perform RNA analysis with the instrument or will train new users on the use of this equipment.

Microarray
GenePix 4000

DNA Microarray

  • Genomics Core personnel will provide assistance in experimental design to ensure that DNA microarray experiments will yield reliable data.
  • Experienced users may submit purified RNA to the core for DNA microarray processing, or core personnel will extract RNA.
  • Core personnel will carry out the sample amplification, hybridization, post-hybridization processing and scanning of the DNA microarrays.
  • Core personnel will perform in-depth data analysis and bioinformatics analysis and present users with tables of differentially expressed genes as well as any additional bioinformatics analysis and figures desired by the user. Available software packages include GenePix Pro 7, Acuity 4.0, and GeneSpring GX 13.1.1.

Users with experience have access to the software and may analyze their own data if desired.


Real-Time PCR
StepOne Plus Real-Time PCR System

Real-Time PCR

Polymerase chain reaction (PCR) is an important technique for analyzing DNA. Similarly, reverse transcription (RT) PCR is an important technique for analyzing RNA.

  • The Genomics Core maintains a StepOne Plus Real-Time PCR System (Applied Biosystems) for the performance of quantitative PCR or RT-qPCR experiments. A dedicated PCR workstation hood for preparing qPCR plates and a centrifuge fitted with plate carriers (Eppendorf 5810R) are also available to users.
  • Core personnel will train new users of the qPCR system or may perform analyses if requested. Software for PCR primer design (Primer Express 3.0.1) is also available to users.

Available Services/Training

  • Experimental design
  • Training in RNA extraction
  • Training in RNA quantitation
  • Equipment usage
  • Data collection for DNA microarray
  • Data analysis for DNA microarray
  • Data collection and analysis for RT-qPCR
  • New protocol development

Recent Publications

  • Eyster KM, Klinkova O, Kennedy V, Hansen KA. Whole genome deoxyribonucleic acid microarray analysis of gene expression in ectopic vs. eutopic endometrium. Fertility and Sterility 2007;88(6):1505-1533.
  • Eyster KM, Brannian J. Profiling gene expression in the aging ovary. In: "Molecular Endocrinology: Methods in Molecular Biology" (Park-Sarge O-K and Curry T, eds) Humana Press: Totowa, NJ; 2009;590:71-89.
  • Eyster KM, Mark-Kappeler CJ, Appt S, Chalpe A, Register T, Clarkson T. Gene expression signatures differ with extent of atherosclerosis in monkey iliac artery. Menopause 2011;18(910):1087-1095.
  • Mark-Kappeler CJ, Martin DS, Eyster KM. Estrogens and selective estrogen receptor modulators (SERMs) regulate gene and protein expression in the mesenteric arteries. Vascular Pharmacology 2011;55:42-49.
  • Arendt DH, Smith JP, Bastida CC, Prasad MS, Oliver KD, Eyster KM, Summers TR, Delville Y, Summers CH. Contrasting hippocampal and amygdalar expression of genes related to neural plasticity during escape from social aggression. Physiology and Behavior 2012;107(5):670-679.
  • Eyster KM, Mark-Kappeler CJ, Appt S, Register T, Clarkson T. ¬†Effects of estradiol on transcriptional profiles in atherosclerotic iliac arteries in ovariectomized cynomolgus macaques. Menopause 2014;21(2):143-152.
  • Eyster KM, Chalpe A, Appt S, Register T, Clarkson T. Effect of equol on gene expression in female cynomolgus monkey iliac arteries. Nutrition, Metabolism, and Cardiovascular Diseases. 2014; 24(4):423-427.
  • Booze ML, Eyster KM. Compilation and analysis of atherosclerosis gene expression data. Advances in Biological Chemistry 2015; 5:142-150.
  • Zhang Y, Eyster K, Liu J-S, Swanson DL. Cross-training in birds: cold and exercise training produce similar changes in maximal metabolic output, muscle masses and myostatin expression in house sparrows, Passer domesticus. Journal of Experimental Biology, 2015;218(Pt 14):2190-2200.
  • Zhang Y, King MO, Harmon E, Eyster K, Swanson DL. Migration-induced variation of fatty acid transporters and cellular metabolic intensity in passerine birds. Journal of Comparative Physiology B 2015;185(7):797-810.
  • Zhang Y, Carter T, Eyster K, Swanson DL. 2016. Acute cold and exercise training up-regulate similar aspects of fatty acid transport and catabolism in house sparrows, Passer domesticus. Journal of Experimental Biology. 2015;218(Pt 24):3885-3893.
  • Zhang L, Hapon MB, Goyeneche AA, Srinivasan R, Gamarra-Luques CD, Callegari EA, Drappeau DD, Terpstra EJ, Pan B, Knapp J, Chien J, Wang XJ, Eyster KM, Telleria CM. Mifepristone increases mRNA translation rate, triggers the unfolded protein response, increases autophagic flux, and kills ovarian cancer cells in combination with proteasome or lysosome inhibitors. Molecular Oncology 2016; 10(7):1099-1117.
  • Booze ML, Eyster KM. The use of real time reverse transcription-PCR for assessing estrogen receptor and estrogen-responsive gene expression. In: "Estrogen Receptors: Methods and Protocols, Methods in Molecular Biology Volume 1366" (Eyster KM, ed) Humana Press: Totowa, NJ; 2016, 19-28.
  • Eyster KM. DNA microarray analysis of estrogen-responsive genes. In: "Estrogen Receptors: Methods and Protocols, Methods in Molecular Biology Volume 1366" (Eyster KM, ed) Humana Press: Totowa, NJ; 2016, 115-129.
  • Eyster KM (editor). Estrogen Receptors: Methods and Protocols, Methods in Molecular Biology Volume 1366. Humana Press: Totowa, NJ; 2016, 115-129.
  • Eyster KM, Booze M, Drappeau DD, Klinkova O, Rahman MS, Mark-Kappeler C. Estrogen and selective estrogen receptor modulators regulate differential gene expression in the liver. In press in: Estradiol: Synthesis, functions and effectiveness.
  • Zhang Y, Eyster K, Swanson DL. Effects of photoperiod and temperature on pectoralis muscle expression of myostatin and lipid transporters in the dark-eyed junco (Junco hyemalis). In review at Current Zoology.

Contact Us

Name Department & Office Contact
Kathleen Eyster
  • Professor
BASIC BIOMEDICAL SCIENCES
Lee Medicine & Science Hall 146