Illumina Sequencing

The GBCF is dedicated to providing high-quality service and offering flexible options that allow personalized service to users. The Core offers Illumina Sequencing using the Illumina MiSeq and NextSeq 500 sequencing platforms. Additionally, the GBCF is equipped to handle most sample types and workflows offering a variety of library preparation solutions, sequencing, and data analysis solutions for characterizing the genome, epigenome, and transcriptome. Our highly trained NGS scientists have direct experience and knowledge operating complex technical instrumentation and balancing the throughput needs of our research community. 

Service Options

In addition to on-site Illumina MiSeq and NextSeq 500 Sequencing Services, the GBCF is able to offer alternative sequencing solutions through collaborative pricing with other institutions.

MiSeq Sequencing

The MiSeq desktop sequencer achieves the longest read length of any Illumina instrument. Its single lane and kit flexibility make it ideal for reduced representation studies and focused applications such as microbial profiling, targeted gene sequencing, small genome, and amplicon sequencing.

NextSeq Sequencing

The NextSeq 550 is a high-throughput benchtop sequencer that offers fast turnaround time and flexibility with run configurations. There are two types of flow cell options (mid and high output) available with a range of outputs to accommodate a wide variety of NGS projects. NextSeq 550 is the ideal platform for small to medium sequencing projects that range in output requirements.

View MiSeq and NextSeq 500 comparison tables.

Service Rates

View internal and external service rates

New Policies and Procedures

Effective January 01, 2021


External Users: Contact Melissa Stephens. We are accepting a limited number of requests until further notice.

Internal Users: Follow all University Re-opening procedures. Access Galvin Life Science Center via the main entrance during regular business days and hours. 

  1. iLab transition complete as of January 06, 2021. Go to InsideND and search for iLab Core Facility Management. Any order submitted to CORES after January 01, 2021 will not be fulfilled.

  2. Communicate with facility staff by email, phone, or Zoom appointment. In-person meetings are restricted until further notice.

  3. Samples delivered contactless. Access to facility space is restricted to facility staff.  On designated days and reserved times, there will be a cooler outside the facility door to receive samples. Do not leave samples if the cooler is absent; we are not responsible for damage or loss.

Submitting Your Order

Consultation is required for this service. Before initiating your experiment, contact Melissa Stephens to discuss project specifics, receive a quote, and coordinate scheduling. Once your request is confirmed and scheduled, follow the instructions for self-prepared libraries below. 

Self-Prepared Illumina Library Submissions

Confirmed and Scheduled Requests

Core Facility will perform its own evaluation of the library to confirm (1) concentration, (2) molarity, (3) average fragment length, and (4) functionality using a combination of Qubit Assay, Bioanalyzer analysis, and KAPA qPCR Library Quantification kit for Illumina.

  1. Schematic of library structure: Submit a diagram that illustrates the position of adapters, barcodes, and read primers relative to the insert.

  2. Adapter and index sequences: Submit the excel spreadsheet listing the P5 and P7 adapter and index sequence within the adapter.

    • Custom sequencing primers: If applicable, provide the sequence of each.

  3. Library Information: Submit an excel spreadsheet listing the Library Pool ID, concentration (ng/ul), molarity (nM), volume provided (ul), and an average fragment size (bp). 

    • If the sample is a multiplexed library pool, list the individual library ID and the index sequence in separate columns within a separate spreadsheet.

  4. iLab Core Facility Management: Reserve a sample drop-off day/time. iLab sends us a notification about scheduled reservations. Do not send us a separate email.

    • Go to InsideND, search for iLab Core Facility Management, and sign in using University of Notre Dame credentials.

    • Schedule a reservation 24 hours in advance by selecting a day and time from the Sample Processing Calendar and attach your completed Excel Submission Form. Within the reservation, include the email of other lab members who should be consulted or notified with results.

      • REQUIRED: If you can not make your reservation, cancel it as soon as possible and select a new time slot.

      • Recommendation: Coordinate within your lab to reduce multiple deliveries to a single drop-off reservation whenever possible.

  5. Deliver a self-prepared library (20 ul of 10 nM) in a 1.7 mL microcentrifuge tube labeled with Library ID, your initials, and date (MM-DD-YYYY).
    • Custom sequencing primers: If applicable, provide 20 ul of 100 uM of each in separate 1.7 mL microcentrifuge tubes labeled with Primer ID, your initials, and date (MM-DD-YYYY).
  6. Deposit the sample inside the cooler outside of the facility door on your reserved day and time.

Library Storage

End users are expected to review sequencing data and report issues as soon as possible. Excess (or leftover) library volume is discarded six months after sequencing data is initially shared. If you would like the excess library volume returned, indicate at the time of submission and provide a recipient's name and shipping address.