Expression Profiling

The Translational Genomics Lab (TGL) performs bulk RNA expression profiling using the following technologies and assays.

If submitting RNA, it is our recommendation for us to perform our own quality control of the samples before performing downstream assays to ensure the samples meet the QC requirements for the assays being performed.

Our Laboratory Management System (LIMS) and freezers are designed to accept individually labeled tubes. If possible, please avoid submitting samples in tube strips or PCR plates.

NanoString nCounter MAX Analysis System

• Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE
• Input Material: Total RNA
• Recommended Input:
  • For codesets > 400 targets: (100/%DV200) * 50 ng in 5 µL of Tris buffer
  • For codesets < 400 targets: (100/%DV200) * 100 ng in 5 µL of Tris buffer
    

    

• Instruments
  • NanoString nCounter MAX Prep Station
  • NanoString nCounter Digital Analyzer
• Kit: nCounter Master Kit (Cat 100054)

Except for projects using custom codesets, TGL will purchase all the necessary reagents and consumables required to run the NanoString nCounter System. This includes both off-the-shelf codesets and master kits. For projects using custom codesets, we ask that the investigator provides that codeset with their samples. TGL will still purchase the other reagents and consumables required for those projects as those are included in our rates.

NanoString CosMx Spatial Molecular Imager (SMI) System (In Development)

• Input Material: FFPE Slides and Frozen Specimens
• Recommended Input: 1×5 µm slide
  

  

• Instrument: NanoString CosMx Spatial Molecular Imager (SMI) System
• Kits:
  • 100plex Human Immuno-Oncology RNA Panel
  • 1000plex Universal Cell Characterization RNA Panel
  • 6000plex Human Discovery RNA Panel
  • Whole Transcriptome RNA Panel (estimated NanoString release in 2025)

mRNA Sequencing

• Input Material Source: Snap Frozen Tissue, Cell Pellets
• Input Material: Total RNA
• Recommended Input: 200-1000 ng in 50 µL of Tris buffer
• Recommended Quality: Agilent TapeStation RNA Integrity Number (RIN) > 6
• Instrument: Hamilton NGS STAR Automated Liquid Handlers (Cat 93774-05)
• Kit: Illumina TruSeq Stranded mRNA Library Prep (Cat 20020595)
• Recommended Sequencing Depth: >40 million clusters

Total RNA Sequencing

• Input Material Source: Snap Frozen Tissue, Cell Pellets, FFPE
• Input Material: Total RNA
  

  

• Recommended Input: 1000 ng in 10 µL of Tris buffer
• Recommended Quality: % DV200 > 20%
• Instrument: Hamilton NGS STAR Automated Liquid Handlers (Cat 93774-05)
• Kit: Illumina TruSeq Stranded Total RNA Library Prep Gold (Cat 20020599)
• Recommended Sequencing Depth: >100 million clusters