Genomics & Bioinformatics Core Facility

Illumina Library Preparation

Introduction

The Genomics Core Facility is dedicated to providing high-quality service and offering flexible options that allow personalized service to our users. The Genomics Core offers NGS Library Preparation Services using both commercial kits and custom workflows, giving our users a variety of library preparation options for a wide range of sample types.


Standard and Speciality Service Options

The Genomics Core Facility supports a variety of NGS library creation methods compatible with Illumina Sequencing Platforms. We encourage researchers to contact us with requests for other services not listed here as we are able to provide our researchers with many custom services. Here we list a subset of our "standard" and our speciality workflows

Genomics

  • PCR-Free Library Preparation
  • Whole Genome DNA Library Preparation
  • Nextera and Enzymatic Library Preparation
  • RAD-tag Library Preparation
  • Nextera Mate-Pair - for long insert of up to 12kb
  • Synthetic Long Read - for synthetically generated long read libraries

 Transcriptomics (Total RNA & mRNA)

  • Classic mRNA Library Preparation
  • Strand-specific mRNA Library Preparation
  • Strand-specific RNA Library Preparation with RiboZero (rRNA Depletion)
  • small RNA Library Preparation
  • TruSeq Exome Library Preparation

Epigenomics

  • Reduced Representation Bisulfite Sequencing (RRBS)
  • ChIP Sequencing
  • Other methods available

Targeted Resequencing (Sequence Capture and Microbiome Profiling)

  • Custom Amplicon Panels and Capture Based Libraries
  • TruSeq Amplicon Cancer Panel 
  • Microbiome Profiling- Marker gene profiling using 16S rRNA gene or custom primers (including 18s, ITS, COI)
  • Environmental Metagenomics

Sample Requirements

Below is a general example of input and quantity requirements for standard RNA and DNA workflows. Please contact us before preparing samples for workflow specifics.

RNA Sample Requirements

  1. RNA must be Dnase-treated to eliminate gDNA.
  2. Minimum volume of 20 ul.
  3. Quantity and purity metrics estimated with the NanoDrop Spectrophotometer:
    • Concentration (ng/ul) greater than 50 ng/ul.
    • A260/280 ratio greater than or equal to 1.8 and less than 2.5
    • A260/230 ratio greater than or equal to 1.8 and less than 2.5
  4. Samples should be placed in 1.5mL tubes. Label your tube with your initials, date (MM/DD/YYYY), and Sample ID.
  5. Complete the Sample QC Form and send to genomics@nd.edu for review.

DNA Sample Requirements

  1. DNA must be Rnase-treated to eliminate RNA.
  2. Minimum volume of 20 ul.
  3. Quantity and purity metrics estimated with the NanoDrop Spectrophotometer:
    • Concentration (ng/ul) greater than 100 ng/ul.
    • A260/280 ratio greater than or equal to 1.6 and less than 2.0
    • A260/230 ratio greater than or equal to 1.6 and less than 2.0
  4. User must provide an annotated agarose gel image for review. The DNA must be high-molecular weight without degradation.
    • In the image, wells must be labeled in some way with the Sample Name and DNA Ladder for identification.
  5. Samples should be placed in 1.5mL tubes. Label your tube with your initials, date (MM/DD/YYYY), and Sample ID.
  6. Complete the Sample QC Form and send it with your agarose gel image to genomics@nd.edu for review.

Turnaround Time

Turn around time is dependent on the complexity and scope of the project research goals, and completion time may vary. In general, the typical turn-around time for most standard projects/services is 4 - 6 weeks following successful completion of initial sample quality control.

Your Results

Upon completion of service, a comprehensive report will be provided with sample quality assessment and library preparation information.

Payment Details

An account number must be provided before service begins. An estimate can be generated on request. All invoicing occurs through the CORES ordering system once work has been successfully completed according to the scope of the project.

Sample and Data Storage

Data Storage Raw data files, including files generated through Bioinformatics pipelines, and Run QC information, will be stored for a period no longer than six months upon successful completion. Please make arrangements to back up your data files.
Sample Storage The genomics core will store samples for a period of six months and then discarded. Please make arrangements with Genomics Core personnel to have your materials returned.

Resources

For additional resources and questions, visit Illumina’s Technical Support.