Molecular Pathology

Gene expression, DNA and RNA quality assessments, and spatial transcriptomics services

Our molecular pathology services allow for a deeper and holistic understanding of disease pathogenesis of neoplastic, degenerative, congenital, or infectious processes.

Experimental Pathology Facility

Molecular pathology services are offered through the Experimental Pathology Facility, a university-wide resource available to researchers within and outside Colorado State University. Researchers gain access to personal, one-on-one consultation from our team of pathologists and laboratory specialists who provide a multivariant approach to research questions.

If you have questions about our services, our pathologists are here to help.

Contact the Experimental Pathology Facility

nanoString® services

We offer gene expression services via the nanoString® nCounter® Analysis System. This novel analysis system allows for a non-amplification method for multiplex analysis of up to 800 mRNAs, microRNAs, and DNAs using an innovative molecular “barcode system.” By working with nanoString directly, researchers can secure the off-the-shelf or custom gene panels they need for their assays to be run through the technology available through the molecular pathology service at the Experimental Pathology Facility.

Off-the-shelf panels offered by nanoString®

Immunology panels

  • Autoimmune Profiling Panel
  • Autoimmune Discovery Panel
  • Metabolic Pathways Panel
  • Fibrosis Panel
  • Human Organ Transplant Panel
  • Immunology Panels
  • Inflammation Panels
  • miRNA Panels
  • Myeloid Panels
  • NHP Immunology Panel

Neuroscience panels

  • Neuropathology Panels
  • Neuroinflammation Panels
  • Mouse and Human AD Panels
  • miRNA Panels
  • PlexSet™ Pre-selected Panels

Oncology panels

  • Breast Cancer 360™ Panel
  • PanCancer 10 360™ Panel
  • CAR-T Characterization Panel
  • Metabolic Pathways Panel
  • Hallmarks of Cancer Collection:
    • PanCancer Pathways Panel
    • PanCancer Immune Profiling Panel
    • PanCancer Progression Panel
  • PlexSet™ Pre-selected Panels
  • Vantage 3D™ RNA Panels
  • Vantage 3D™ Gene Fusion Panels
  • miRNA Panels
  • Counter Gene Fusion Panels (Ex-US only)

See full list of nCounter® panels and assays.

Sample quantities

For RNA samples we recommend at least 100ng of DNA samples, though samples >20ng can be run. Recommended spectrophotometer 260/280 ratio is 1.7-2.0. nanoString® recommends that 50% of the samples be greater than 200 nucleotides, modifying input RNA to meet this criteria. Sample fragmentation can be assessed via TapeStation analysis at an additional charge. Below is a generalized chart of needed sample input for a variety of nanoString® assays.

Sample TypeQuantity Needed
FFPE-derived RNA300 ng
Total RNA (CodeSets <400 genes)100 ng
Total RNA (CodeSets >400 genes)50 ng
Fragmented DNA300 ng
ChIP DNA (unamplified)10 ng
ChIP DNA (whole-genome amplification)100 ng
Single-cell or low-input materialup to 8 μL of amplified sample

Submission Process

step 1

Questions? Contact the Experimental Pathology Facility.

If you have questions about pricing or which services we offer using the nanoString® nCounter® Analysis System, please contact the Experimental Pathology Facility.

Contact the Experimental Pathology Facility

step 2

Ready to get started? Contact nanoString to acquire gene panels.

Researchers need to work with nanoString directly to acquire specific gene panels needed for assay runs. Once ordered, nanoString will send all required reagents to the Experimental Pathology Facility.

Email nanoString

DNA and RNA quality assessments

We offer different quantification and assessment techniques for a variety of molecular samples. Contact the Experimental Pathology Facility for pricing and use of machines for sample quantification and quality assessments.

Agilent 4200 TapeStation

The Agilent 4200 TapeStation system is an established automated electrophoresis tool for DNA and RNA sample quality control. Fully automated sample processing enables the unattended analysis of size, concentration and integrity. Choose any sample number between 1 and 96 and analyze at constant cost per sample.

The TapeStation system provides a complete solution for true end-to-end sample quality control within any next-generation sequencing (NGS) or Biobank workflow. This covers the full DNA and RNA range and offers high levels of flexibility in a simplified workflow with ready-to-use ScreenTapes.

BioTek Synergy H1 Multimode Microplate Reader

BioTek Synergy H1 is a modular multimode microplate reader, with monochromator-based optics and filter-based optics. The patented Hybrid Technology offers flexibility and sensitivity across a broad range of applications. The machine allows for fast multi-sample colorimetric, fluorescent, and/or luminescent quantification and assessment of a variety of sample types.

Thermo Scientific™ NanoDrop™ One Microvolume UV-Vis Spectrophotometer

Next-gen spectrophotometer that allows researchers to quantify and qualify a variety of samples. Possible sample types include peptides, DNA and RNA, purified protein, toxicology assays, gold nanoparticles, colorimetric protein assays, and optical density measurements.