NanoString Sample Submission Requirements

The Genomics Core is only offering NanoString services to MSU, MSU-affiliated, and Henry Ford Health System researchers.  Researchers that are interested in an nCounter assay should contact the Genomics Core (gtsf@msu.edu) to discuss instrument availability.

NanoString offers several nCounter assay kits for standard and custom sets of protein coding or miRNA genes.  Because these assays are performed in volumes of less than 10 µl, it is essential that samples are provided at very narrow concentrations and volumes.  Instructions for sample requirements for mRNA and miRNA assays are provided below.  If your samples have a mass less than 100 ng, please contact the MSU Genomics Core at gtsf@msu.edu for a discussion about how to proceed.

The NanoString nCounter System can also provide assays for DNA copy number variants and protein levels.  For information about sample requirements for these types of assays, please contact the MSU Genomics Core at gtsf@msu.edu.

The MSU Genomics Core charges a processing fee for all nCounter assays, see our pricing page for information.

The MSU Genomics Core performs the following types of assays with the nCounter System:

• nCounter Elements XT Assays for mRNA Expression Analysis
• nCounter XT Assays for mRNA Expression Analysis (Standard NanoString probe panels)
• nCounter XT Assays for miRNA Expression Analysis

 

nCounter Elements XT Assays for mRNA Expression Analysis

Total RNA samples must be supplied in 1.5 ml microfuge tubes.  Individual sample tubes must be clearly labeled with sample identifiers that are distinct and no longer than 8 characters.  Samples must be registered in our LIMS system before they are submitted or shipped to the Genomics Core.  See our LIMS Project Submission page for instructions and to download the submission form.

For total RNA submissions, all samples must be normalized to approximately 40 ng/µl to 200 ng/µl for Elements XT mRNA assays.  Each sample must be provided in a volume of 10 µl or more.  Sample concentrations must be provided, and concentrations must have been determined with a Qubit or other fluorescence-based quantification method.  UV-based quantification (such as Nanodrop) is unreliable and will result in delay of sample processing.  Samples must be provided in RNase-free water, TE or Tris buffer.  TapeStation/Bioanalyzer assays must be performed before sending samples to the Genomics Core.  DV300 values must be calculated during the TapeStation analysis and must be provided before delivering samples to the Genomics Core.

For sorted cell submissions, all samples should have an accurate count of the number of cells in the submitted samples.  Lysed samples must be provided in a NanoString-approved lysis buffer such as Qiagen's RLT, NanoString's LH buffer, BioRad's iScript RT-qPCR Sample Preparation Reagent or Life Technologies' Cells-to-CT lysis buffer.  Other lysis buffers may interfere with annealing of the probes and RNA.  All cell submissions must be sent as lysates.  The MSU Genomics Core is not a BSL-rated laboratory and cannot accept intact cells.  Such samples will be sterilized and discarded.  NanoString recommends cell lysate concentrations of 6,500 cells/µl RLT lysis buffer or 2,000 cells/µl of LH, iScript or Cells-to-CT lysis buffers.  The maximum volume of lysate that will be used for each assay will be 1.5 µl for RLT-lysed samples and 5 µl for LH-, iScript- or Cells-to-CT-lysed samples.  NanoString has recommendations for cell lysis conditions and may have specific guidance for particular cell types (such as immune cells).  Contact NanoString Support (support@nanostring.com) for more information about cell lysate preparation.  A sample manifest must be supplied with the samples sent to the MSU Genomics Core, and this manifest must indicate the buffer used with the samples.

Samples must be shipped on dry ice directly to the MSU Genomics Core.  The shipment should be made with an excess of dry ice to ensure that the samples remain frozen while in transit to Michigan State University.  The shipment must be made on a Monday, Tuesday or Wednesday to help to avoid the possibility of the package being lost or delayed over a complete weekend.

NanoString Elements XT reagent kit, master reagent kit and Probe A & B Master Mixes from IDT will be purchased by the researcher and sent to the MSU Genomics Core where it will be stored until the researcher's samples also arrive.  Note that the Probe A & B Master Mixes should be prepared by IDT.  The MSU Genomics Core will not prepare Probe A & B Master Mixes from individual probes.

All samples and reagents will be retained for six months.  Samples and reagents may be returned to the researcher by request with a FedEx shipping account number.

 

nCounter XT Assays for mRNA Expression Analysis (Standard NanoString probe panels)

Total RNA samples must be supplied in 1.5 ml microfuge tubes.  Individual sample tubes must be clearly labeled with sample identifiers that are distinct and no longer than 8 characters.  Samples must be registered in our LIMS system before they are submitted or shipped to the Genomics Core.  See our LIMS Project Submission page for instructions and to download the submission form.

For total RNA submissions, all samples must be normalized to approximately 40 ng/µl to 200 ng/µl for XT mRNA assays.  Each sample must be provided in a volume of 10 µl or more.  Sample concentrations must be provided, and concentrations must have been determined with a Qubit or other fluorescence-based quantification method.  UV-based quantification (such as Nanodrop) is unreliable and will result in delay of sample processing.  Samples must be provided in RNase-free water, TE or Tris buffer.  TapeStation/Bioanalyzer assays must be performed before sending samples to the Genomics Core.  DV300 values must be calculated during the TapeStation analysis and must be provided before delivering samples to the Genomics Core.

For sorted cell submissions, all samples should have an accurate count of the number of cells in the submitted samples.  Lysed samples must be provided in a NanoString-approved lysis buffer such as Qiagen's RLT, NanoString's LH buffer, BioRad's iScript RT-qPCR Sample Preparation Reagent or Life Technologies' Cells-to-CT lysis buffer.  Other lysis buffers may interfere with annealing of the probes and RNA.  All cell submissions must be sent as lysates.  The MSU Genomics Core is not a BSL-rated laboratory and cannot accept intact cells.  Such samples will be sterilized and discarded.  NanoString recommends cell lysate concentrations of 6,500 cells/µl RLT lysis buffer or 2,000 cells/µl of LH, iScript or Cells-to-CT lysis buffers.  The maximum volume of lysate that will be used for each assay will be 1.5 µl for RLT-lysed samples and 5 µl for LH-, iScript- or Cells-to-CT-lysed samples.  NanoString has recommendations for cell lysis conditions and may have specific guidance for particular cell types (such as immune cells).  Contact NanoString Support (support@nanostring.com) for more information about cell lysate preparation.  A sample manifest must be supplied with the samples sent to the MSU Genomics Core, and this manifest must indicate the buffer used with the samples.

Samples must be shipped on dry ice directly to the MSU Genomics Core.  The shipment should be made with an excess of dry ice to ensure that the samples remain frozen while in transit to Michigan State University.  The shipment must be made on a Monday, Tuesday or Wednesday to help to avoid the possibility of the package being lost or delayed over a complete weekend.

The appropriate NanoString probe and master reagent kits will be purchased by the researcher and sent to the MSU Genomics Core where it will be stored until the researcher's samples also arrive.

All samples and reagents will be retained for six months.  Samples and reagents may be returned to the researcher by request with a FedEx shipping account number.

 

nCounter XT Assays for miRNA Expression Analysis

Total RNA samples must be supplied in 1.5 ml microfuge tubes.  Individual sample tubes must be clearly labeled with sample identifiers that are distinct and no longer than 8 characters.  Samples must be registered in our LIMS system before they are submitted or shipped to the Genomics Core.  See our LIMS Project Submission page for instructions and to download the submission form.

For total RNA submissions, samples must be provided at a concentration between 50 ng/µl to 100 ng/µl for XT miRNA assays.  Each sample must be provided in a volume of 8 µl or more.  Sample concentrations must be provided, and concentrations must have been determined with a Qubit or other fluorescence-based quantification method.  UV-based quantification (such as Nanodrop) is unreliable and will result in delay of sample processing.  Samples must be provided in RNase-free water, TE or Tris buffer.  TapeStation/Bioanalyzer assays must be performed before sending samples to the Genomics Core.

Contaminants from RNA extraction in total RNA can inhibit the enzymatic steps in the miRNA assay protocol.  Important contaminants to avoid include guanidinium isothiocyanate, guanidinium HCl, phenol and ethanol.  These are all common components of RNA purification methods.  RNA can be checked for contaminants by measuring the A260/A280 and A260/A230 ratios with a device such as a NanoDrop.  NanoString recommends a 260/280 ratio of 1.9 or greater and a 260/230 ratio of 1.8 or greater for optimal results.

Nanostring does not have a protocol for assaying miRNAs from cell lysates.  Nanostring does not recommend using miRNAs as input for the miRNA assay.  Instead, total RNA should be used as input for miRNA assays.

Samples must be shipped on dry ice directly to the MSU Genomics Core.  The shipment should be made with an excess of dry ice to ensure that the samples remain frozen while in transit to Michigan State University.  The shipment must be made on a Monday, Tuesday or Wednesday to help to avoid the possibility of the package being lost or delayed over a complete weekend.

The appropriate NanoString probe and master reagent kits will be purchased by the researcher and sent to the MSU Genomics Core where it will be stored until the researcher's samples also arrive.

All samples and reagents will be retained for six months.  Samples and reagents may be returned to the researcher by request with a FedEx shipping account number.

 

Other nCounter Assay Protocols

For information about sample requirements for other nCounter Assays, please contact the MSU Genomics Core at gtsf@msu.edu.