Gene Expression

The Genome Analysis Core at Mayo Clinic provides comprehensive services and technical support for the measurement of gene expression in clinical and nonclinical samples for customers from both inside and outside Mayo Clinic. Gene Expression accepts RNA from fresh-frozen tissues, formalin-fixed, paraffin-embedded tissues, laser-capture micro-dissected cells, cell lines and blood cells.

The Genome Analysis team has the expertise and qualifications to provide top-quality expression data on a variety of different platforms. With more than 100 years of combined laboratory experience, the staff is well-suited to perform high-complexity gene transcript measurements.

Investigators at Mayo Clinic are engaged in a wide variety of basic and clinical research studies. As a result, the Genome Analysis staff has significant expertise working with human and animal samples of all kinds and performing gene expression analysis on a wide variety of eukaryotic species.

Areas of expertise include:

  • Gene transcript measurement in archival clinical samples. Mayo Clinic has one of the largest repositories in the world for archival tissue samples, providing institutional researchers with an unsurpassed resource for studying disease. As a result, the gene expression team has gained significant expertise by analyzing thousands of RNA samples derived from formalin-fixed, paraffin-embedded tissues.
  • Single cell gene expression by either Fluidigm C1 or 10X Chromium. The team performs a variety of single cell population analyses using the Fluidigm system and highly diverse 10X Chromium platform. Using these platforms, the core can provide comprehensive solutions for characterization and gene expression profiling of single to hundreds and tens of thousands of cells.
  • High-throughput real-time reverse transcription quantitative PCR. The team routinely performs real-time reverse transcription quantitative PCR using instrument platforms from Applied Biosystems and Fluidigm. The Fluidigm system currently analyzes up to 96 samples and 96 targets in a single run and performs the reactions in only 10 nanoliters of reagent.
  • Analysis of microRNA expression. The team has provided services for microRNA expression analysis for several years, including a study comparing the expression levels of several types of samples across multiple platforms. This work provides a cross-platform perspective that enables the core to support genomic researchers.

Services are also available for sample preparation for whole-transcriptome messenger RNA (mRNA) and microRNA (miRNA) profiling by next-generation sequencing. The Genome Analysis Core provides whole-transcriptome and miRNA expression analyses of RNA derived from fresh-frozen tissues; formalin-fixed, paraffin-embedded tissues; laser-capture micro dissected cells and cell lines.


Gene expression utilizes multiple state-of-the-art platforms — including microarray-based technologies from Affymetrix, Illumina and Agilent, and quantitative polymerase chain reaction (qPCR) instrumentation from Fluidigm and Applied Biosystems — for a variety of gene expression analyses. These technologies include:

  • AB 7900HT Fast Real-Time PCR System
  • Affymetrix GeneChip Platform
  • Agilent 2100 Bioanalyzer
  • Eppendorf robotics
  • Fluidigm
  • Illumina BeadArray Reader
  • NanoDrop

Contact GAC Supervisors for more information on using gene expression services.