RNA Sequencing


RNA Sequencing (RNA-Seq) has become the gold standard method for genome-wide gene expression analysis in different biological conditions, as well as the detection of splice variants, transcriptome analysis, and the discovery non-coding RNAs. We provide several different library kit options for RNA-Seq library creation to accommodate varying sample types, including kits for low input and partially degraded samples, as well as options for polyA enrichment or ribosomal reduction. The UMGC offers a complete RNA-Seq workflow starting from RNA extraction through RNA QC analysis, and in partnership with MSI, analysis of RNA-Seq data through streamlined pipelines.

Please see our PacBio service to sequence full-length transcripts up to 10kb or longer and our Single-cell service for gene expression profiling of single cells.

Charter Service

Charter Service is our low-cost RNA-Seq service at $219.58 /sample (UMN rate) that provides a monthly shared sequencing run that departs on the 1st business day of the month, whether the (p)lane is filled or not. Carry-on luggage is restricted to 20 million reads/sample on a 150 PE run, but additional space can be purchased in 20-million-read increments at $64.59/sample.

RNA samples are submitted in increments of 8 with a 16-sample minimum and must pass security (QC) by the 1st of the previous month to start either the TruSeq Stranded mRNA kit or the Pico Mammalian v2 kit. Samples passing QC at the scheduled validation deadline are guaranteed to have data released in 4 weeks. Please see the Charter Service calendar for upcoming submission deadlines and data release turnaround times.

Batching RNA-Seq projects into a shared, scheduled monthly run enables us to offer a competitive RNA-Seq rate with a guaranteed 1-month turnaround time. Samples are sequenced in-house on our NovaSeq 6000 using a 150 PE flow cell. Need a more flexible flight plan with no luggage restrictions? Please see our standard service to purchase a devoted lane of sequencing for your RNA-Seq project.

Standard Service

Unlike the Charter Service, our Standard RNA-Seq Service has no restrictions regarding minimum number of samples, depth or read length, QC cut-off dates, and includes any of the library prep kits available at the UMGC. However, clients who elect for this service will follow our standard sequencing queue turnaround time and will see slightly longer turnaround times than the Charter Service. This is an a-la-carte service where the cost of the library prep and sequencing are priced separately, where clients purchase sequencing in lane increments.

RNA-Seq Kit Options Table w Charter

Comparison of RNA-Seq kits available at the UMGC. 1) Illumina Stranded Total RNA Prep includes the Illumina Ribo-Zero Plus rRNA Depletion Kit, which provides efficient removal of ribosomal RNA from multiple species, including human, mouse, rat, and bacteria. 2) UMGC sample submission requirements.


For questions or a quote, please contact Elyse Froehling at next-gen@umn.edu.



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Charter Service1 Scale Unit UMN External
20 million reads. 150 PE sequencing.        
Illumina TruSeq Stranded mRNA. 16-any sample $219.58  $253.07 
Takara SMARTer Pico Mammalian. V2. 16-any sample $219.58  $253.07 
Additional 150 PE NovaSeq sequencing. 20M sample $64.59  $74.42 
Library Creation Only2 Scale Unit UMN External
Illumina kit options.        
mRNA. TruSeq Stranded. Standard scale.  1-96 sample $148.86  $171.57 
mRNA. TruSeq Stranded. High scale. 97-any sample $136.76  $157.63 
Total RNA. Stranded. Ligation w Ribo-Zero Plus.  1-any sample $196.31  $226.18 
Small RNA. 12-any sample inquire inquire
Takara kit options.        
SMARTer Pico Mammalian. V2. 1-any sample $142.28  $164.02 
Small RNA. 12-any sample $197.75  $227.85 
  1. Charter Service is a shared, scheduled sequencing run the 1st of the month with submission timeline requirements. Samples are submitted in batches of 8 with a 16-sample minimum. Posted rate includes library prep + sequencing. RNA sample QC (Ribogreen + RNA sizing) is additional. 
  2. Library creation rate only for our Standard Service. Please see our sequencing rates for RNA-Sequencing using your own dedicated lane and read length and depth. Standard sequencing queue turnaround applies. RNA sample QC (Ribogreen + RNA sizing) is additional.

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How to Order

1. Please contact next-gen@umn.edu for project specifications.

2. Once project details are finalized, complete the appropriate submission form for submitting samples or submitting client-made libraries and email to next-gen@umn.edu.

Illumina Sequencing Request Form (Libraries)
Illumina Sequencing Request Form (Samples)

Shipping Instructions

Samples should be frozen and shipped on dry ice in a 96-well plate. We recommend using plate tape to seal the wells. Place the plate inside of a plastic bag prior to placing on dry ice. Please give advance notice of submission date and time so staff can be prepared to receive samples. If shipping samples from outside the University of Minnesota, ship via express shipping carrier on dry ice to the address below.

Samples can be dropped off at one of our campus locations

Samples can be shipped to the following address:

Please send the tracking information to next-gen@umn.edu.

University of Minnesota Genomics Center
1475 Gortner Ave.
28 Snyder Hall
St. Paul, MN 55108

FAQ - Charter Service

How do I reserve my seats and how many seats can I request?

Reserve your seats by emailing your request to next-gen@umn.edu. You can request as many seats as you need as long as you are purchasing a minimum of 2 seats (16 samples) and groups of 8 samples thereafter. The flight has a maximum of 48 seats (384 samples). Refer to Sequencer Home to see the availability of the next run.

What samples are acceptable?

We accept eukaryotic total RNA samples only for this service. No bacterial or Ribozero service is currently being offered.

Do you perform QC on samples?

Yes, the UMGC provides QC services for all RNA-seq samples. Samples MUST be pre-validated before they are accepted for the Charter Service.

What is the deadline for submission?

2 weeks (10 working days) prior to the flight date. This allows UMGC the opportunity to perform sample QC and obtain replacement samples, if necessary. Refer to Sequencer Home to see the availability of the next run.

Can I request Express Service for Charter-Seq?

There is no Express service. The dates are set.

What if I miss the deadline for submission?

You will have the option of having your samples processed using our standard RNA-seq service and purchasing a separate lane of sequencing. Or, you can wait until the next Charter Service flight.

I can't seem to get on a Charter-Seq run because they fill up too fast.

We have the ability to increase the frequency of Charter Service runs, and will do so if we find that demand justifies it.

FAQ - Standard Service

What is the turnaround time?

Generally, turnaround is 6-8 weeks for standard NGS projects. However, please contact next-gen@umn.edu for specific project turnaround time.