Sample Submission

When submitting sample submission form through Idea Elan Infinity, it is your responsibility to use naming that matches what you have in your notebook for sample identification. The sample submission form will automatically assign Genomics Core sample ID.

Please note if you are an external user, you should submit this sample submission form.

Whenever replacement samples are being submitted, please abstain from using the SAME identifier as the previously submitted samples. This helps eliminate confusion. If you must use the same name, consider including an R for replacement at the end of the sample ID and description.

We do try and fill up QC chips so there may be a delay in results.

For more information please contact core.

General Submission Guidelines

We strongly recommend that you submit your quality control data before submitting your samples to the Genomics Core (GC). Our core staff will review your data and advise you on the suitability of your samples for Illumina sequencing.

Please follow these guidelines for submission:

1. Complete the online sample submission form and include copies of all QC results, including gel images. Samples must be submitted in nuclease-free 1.5 mL Eppendorf tubes labeled with the sample ID and placed on ice (if you are an external user, you should submit this sample submission form) .
2. Complete the online Core Sequencing Policy.
3. Lab researchers: read our general user guide here.
4. Principal Investigators can see the PI/admin lab guide here.
5. See the instructions here.

Samples can be dropped off at the School of Medicine & Health Sciences, Room W116. There is a freezer there just as you enter to your right. The drop-off hours will be from 8 a.m. to 5 p.m. Sample drop-off other than these hours is possible, but not guaranteed. Please put your samples in one of the sample boxes and use tape to write your sample's information on the box. If you have notes about your sample you wish to leave, there is a notepad available. If you wish to talk to the Core about your samples, please contact us to set up a meeting.

COBRE Genomics Epigenetics Bioinformatics Core
University of North Dakota 
School of Medicine & Health Sciences 
1301 North Columbia Rd, Suite W315 
Grand Forks, ND 58202-9037

We will assess the suitability of your samples upon receipt. Please note that we cannot guarantee that your sample will perform well in downstream procedures even if it passes all QC checks.

Submitting User-Prepared Libraries

If you have prepared your own libraries and have requested cluster generation and sequencing services only, please submit ≥ 10 µL of your undiluted 10 nM library suspended in 10 mM Tris-HCl, pH 8.5 or 0.1X TE. If you have custom primers, please include ≥ 40 µL (10 nM) of your primers with your submission. Prior to submitting your libraries for next-generation sequencing, the GC recommends that you perform the following:

• Use a commercial PCR purification kit to clean up libraries,
• Quantify libraries using qPCR,
• Assess quality by gel electrophoresis and submit a gel image to the core

We will quality check your library before processing and contact you if there are any issues. We will analyze your library using the Agilent 2100 Bioanalyzer. Bioanalyzer results should show a high quality library with a clean single peak and no noticeable adapter dimer or PCR primer peaks. 

Submitting DNA Samples

Sample Input Requirements

• Resuspend DNA samples in nuclease-free water or 10 mM Tris-HCl, pH 8.5 (avoid DEPC-treated water and EDTA as its presence will inhibit some enzymatic reactions; avoid resuspension buffers containing detergents (e.g. SDS) as they may interfere with library preparation and/or sequencing),
• Provide 1 µg or more of high quality DNA (concentration > 50 ng/µL, OD 260/280 close to 1.8

DNA Quality Control

• DNA should be high quality DNA with an OD 260/280 ratio of 1.8-2.0 and an OD 260/230 of 2.0-2.2,
• Assess quantity and purity of samples by fluorometry because spectrophotometric based methods cannot distinguish between sample and common contaminants such as ssDNA, RNA, and oligos. As a result, UV absorbance methods tend to overestimate sample concentration, resulting in an insufficient amount of starting material,
• Use agarose gel electrophoresis loaded with sample and a molecular weight marker to assess integrity and submit a gel image to the core

Submitting RNA Samples

Sample Input Requirements

• Always wear gloves when working with RNA and keep all samples on ice while processing,
• Resuspend RNA samples in RNase-free water or 10 mM Tris-HCl, pH 8.5; avoid DEPC-treated water as chemical additives may interfere with sequencing; avoid resuspension buffers containing detergents (e.g. SDS) as they may interfere with library preparation and/or sequencing,
• Perform a final clean-up of RNA samples using commercially available purification kits,
• Provide at least 1 µg or more of total RNA at a concentration of at least 50 ng/µL (using less starting material is possible, but results are not guaranteed); aim to provide 2 to 5 µg of total RNA if possible

RNA Quality Control

• RNA should be high quality with an OD 260/280 ratio of 1.8-2.0 and an OD 260/230 of 2.0-2.2,
• Quantify RNA using a fluorometric based method,
• Assess RNA integrity using agarose gel electrophoresis and submit a gel image to the core; high quality RNA will show a 28s rRNA band twice the integrity of the 18S rRNA band,
• The RNA Integrity Number (RIN; Agilent 2100 Bioanalyzer) value should be ≥ 8

Sample Submission and Service Request

Contact Core staff here to request an initial consultation for your sequencing project. A Core member will schedule a meeting to discuss your research goals and project expectations with core staff and faculty researchers. After the initial project meeting, the sample submission form needs to be completed and submitted online (if you are an external user, you should submit this sample submission form). Incomplete or missing forms will delay work for your project. Additionally, please refer to our Core Sequencing Policy to review the core sequencing process and sign the policy acknowledgment section.

Sequencing work will begin once all required documentation has been provided and an initial consultation has taken place. Depending on the scope and nature of the project, additional meeting(s) may be necessary. Regardless, we will work closely with you to ensure all of your questions have been answered and your project needs have been addressed.

Preparing Samples for Shipment/Drop Off

Please contact a member of the Genomics Core to arrange submission of external samples.

For those not on the UND Campus, please ship samples for next-generation sequencing to the following address:

For shipping samples to the Core, please use the address below:

COBRE Genomics Core
University of North Dakota
School of Medicine & Health Sciences
1301 North Columbia Rd, Suite W315
Grand Forks, ND 58202-9037

Outside of the UND network, samples are to be shipped Monday-Thursday and delivered by domestic overnight courier service for express next day delivery. Please ship DNA samples on ice packs and RNA samples on dry ice. Samples must be in nuclease-free 1.5 mL Eppendorf tubes and sealed with parafilm to minimize sample loss.

For on campus clients, samples can be dropped off at the School of Medicine Room W116. There is a freezer there just as you enter to your right. The drop off hours will be from 8 am to 5pm, sample drop off other than these hours may be possible but not guaranteed. Please put your samples in one of the sample boxes and use tape to write your sample's information on the box. If you have notes about your sample you wish to leave, there is a notepad available. If you wish to talk to the Core about your samples, please contact them to set up a meeting. Samples must be in nuclease-free 1.5 mL Eppendorf tubes. Please label the tube(s) with the sample ID. Please send only aliquots, not stock samples. Please refer to the preceding sections for sample input and quality requirements.

Please schedule a time to drop off samples for next-generation sequencing to the following address:

COBRE Genomics Core 
University of North Dakota 
School of Medicine & Health Sciences 
1301 North Columbia Rd, Suite W116 
Grand Forks, ND 58202-9037

Storage and Delivery of Data

All data is stored on the Illumina BaseSpace server temporarily. All data is stored locally onsite and backed up to the server for long term storage.

MiSeq raw and quality checked data will be available as demultiplexed FASTQ files. HiSeq/NovaSeq data will be available as FASTQ files. The core staff will work with you to determine workflow and downstream analysis as discussed during the consultation process.