Alternative Gene Expression Profiling Services

Alternative Gene Expression Profiling Services


ThermoFisher (formerly Affymetrix) Microarray Analysis

For fast RNA expression analysis, we offer a broad range of arrays for whole-transcriptome-, gene-, exon-, or microRNA analysis. All arrays are compatible with RNA from a variety of sample types (e.g., PAXgene blood tubes and fresh-frozen or FFPE tissue).
Arrays are available in single-sample cartridges and multi-sample array strip/plate formats for different throughput needs.

Sample Requirements (in a minimum volume of at least 10 ul)

  • Total mRNA
    • Standard Processing: recommended – 400 ng; allowable range 100 – 500 ng (i.e., 10 – 50 ng/ul).
    • Low-input Processing: recommended – 5 ng; allowable range 0.5 – 10 ng (i.e., 1.67 – 10 ng/ul).
  • MicroRNA: required – 130 ng

Submission Guidelines

Upon submission, all RNA concentrations will be checked via NanoDrop and quality will be assayed via Agilent Tapestation or Bioanalyzer. Core staff will email you the QC results with advice on the suitability of the RNA for proceeding with the arrays. For samples not meeting the minimum quality requirement (RIN > 7), we also offer low input and/or degraded RNA prep options that tolerate both lower input (< 5 ng) and highly degraded (RIN < 5) RNA. Please contact the Gene Expression Microarray Manager (ckrebs@umich.edu) for how best to manage poor quality samples.


qPCR: Qiagen RT2 Profiler Targeted Gene Expression Analysis

RT2 Profiler PCR Arrays enable quick, reliable gene expression analysis of 170+ pathways. The arrays are pathway-focused panels of laboratory-verified qPCR assays, with integrated, patented controls to ensure a successful experiment every time. The arrays can also be modified to suit unique experimental needs.

mRNA Sample Requirements (in a minimum volume of at least 10 ul)

  • Total mRNA: recommended – 400 ng; allowable range 25 – 5000 ng (i.e., 2.5 – 500 ng/ul).
  • Low-input Processing: for RNA in the range from 1 – 25 ng, Qiagen recommends a pre-amplification step using the RT2 PreAMP cDNA Synthesis Kit and RT2 PreAMP Pathway Primer Mix. Additional kits will increase the overall cost, dependent on pricing at the time of submission.

MicroRNA: Human, mouse or rat miFinder miScript miRNA PCR Array profiles the expression of the 84 most abundantly expressed and best characterized miRNAs in miRBase (www.miRBase.org). Each of these miRNAs can regulate one or more messenger RNA transcripts, and conversely a given mRNA can be regulated by one or more miRNAs. Therefore, although they are well-characterized, the complex role played by each miRNA is yet to be completely defined. This array maximizes the likelihood of discovering miRNAs whose expression patterns correlate with the biological phenotypes under study. A set of controls present on this array enables data analysis using the ΔΔCT method of relative quantification, assessment of reverse transcription performance, and assessment of PCR performance. Using SYBR Green-based real-time PCR, the expression of 84 highly researched miRNAs can be easily and reliably analyzed with this miScript miRNA PCR Array.

miRNA Sample Requirements (in a minimum volume of at least 10 ul)

  • Total mRNA: recommended – 125 – 250 ng (i.e., 12.5 – 25 ng/ul).
  • RNA enriched for small RNA: recommended – 12.5 – 25 ng (i.e., 1.25 – 2.50 ng/ul).

Submission Guidelines

Upon submission, all RNA concentrations will be checked via NanoDrop and quality will be assayed via Agilent Tapestation or Bioanalyzer. Core staff will email you the QC results with advice on the suitability of the RNA for proceeding with the arrays. The minimum quality requirement is RIN > 7. Please contact the Gene Expression Microarray Manager (ckrebs@umich.edu) for how best to manage samples with RIN < 7.


qPCR: ThermoFisher OpenArray Targeted Gene Expression Analysis

The TaqMan® OpenArray® Panels enable the identification of differentially expressed genes in key pathways through expression profiling and high-throughput analysis of ~600 genes at once within commonly studied gene families involved in specific disease states, biological processes, and cellular regulation pathways. Panels are also available to identify differentially expressed miRNAs by analyzing 754 miRNAs in parallel.

mRNA Sample Requirements (in a minimum volume of at least 10 ul)

  • Total mRNA: recommended – 2000 ng; allowable range 50 – 2000 ng (i.e., 5 – 200 ng/ul).
  • Low-input Processing: for RNA in the range from < 1 – 50 ng, ThermoFisher recommends a pre-amplification step. Additional kits will increase the overall cost, dependent on pricing at the time of submission.

Pathway Panels Available:

  • Human Kinome
  • Human Stem Cell
  • Human Cancer
  • Human Signal Transduction
  • Human Inflammation
  • Mouse Inflammation

miRNA Sample Requirements (in a minimum volume of at least 10 ul)

  • From tissue or cellular total RNA: recommended – 5 – 10 ng (i.e., 0.5 – 1 ng/ul).
  • From blood, serum or plasma samples: 2 ul of sample eluent.

miRNA Panels Available:

  • Human MicroRNA Panel (for legacy projects)
  • Human Advanced MicroRNA Panel
  • Rodent MicroRNA Panel

How to Request

Login through https://brcf.medicine.umich.edu/cores/dna-sequencing/ and the Submit or Edit Samples option on the left side of the screen. Choose QC Only and Submit QC Samples. On the page showing Sample QC Submission, select one of the Bioanalyzer or TapeStation RNA options. In the Reason pull-down menu, choose one of the following:

  • Affymetrix Microarray Submission
  • Target PCR based array submission
  • Openarray submission

In the Additional Notes section, include:

  1. the array name
  2. the processing method (e.g., “standard” or “low-input”)
  3. any other comments that you feel will be informative for completing your project