Genomics & Bioinformatics Core Facility

Illumina & NGS 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 Illumina & NGS Library Preparation Services using both commercial kits and custom workflows, giving our users a variety of library preparation options for a variety of sample types.


Service Options

Illumina Library Services: Illumina Kits

Genomics Core Facility supports a variety of Illumina TruSeq Kits compatible with MiSeq and HiSeq Sequencing Platforms. For input amounts and sample quality recommendations, review the User’s Guide for the specific kit requirements.

Whole-Genome Sequencing

Targeted Resequencing

 Whole-Transcriptome Sequencing

De Novo Sequencing and Genome finishing (Available Only for HiSeq Platform)

NGS Library Services: Restriction-site Associated DNA (RAD) Preparation

Restriction-site associated DNA (RAD) Library Preparation is a type of Reduced Representation Library (RRL) that analyzes DNA markers, or tags, near restriction digest sites. RAD-tag sequencing has been utilized in studies of Quantitative Trait Loci (QTL) mapping, genotype by sequencing, Single-Nucleotide Polymorphism (SNP) analysis, and population and ecological genetics. Our RAD-tag library preparation is compatible with Illumina sequencing. Resources are available for experimental design, library preparation, and data analysis. To learn more about our services, including the RADtag working group, please contact us.


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.