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.

In addition to Illumina & NGS Library Preparation Services, the Genomics Core supports Illumina MiSeq & HiSeq Sequencing.  For more information, see our Illumina Sequencing Services.


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)

Illumina Mate-Pair and Synthetic Long Read Library preparation requires exceptionally high-quality DNA to achieve optimal results. For input amounts and sample quality recommendations, review the User’s Guide for the specific kit requirements

  • Assemble synthetically long reads for de novo assembly
  • Perform genome phasing to identify co-inherited alleles and haplotype

  • Phase de novo mutations

  • Detect structural variants

  • Identify complex genomic rearrangements

  • Genome finishing applications

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.

Sample Requirements

Library preparation kits and workflows require intact high-quality nucleic acid free of impurities and other PCR-inhibiting contaminants. In the case of DNA library preparation, high-molecular weight DNA free of RNA is recommended. Typically, transcriptome libraries require intact DNA-free RNA. Sample input amounts vary for each kit and workflow. Please refer to User’s Guide or Workflow for the specific requirements.

We require qualitative and quantitative assessment of nucleic acid before library preparation. Samples will be assessed and scored according to the unique organism, and the requirements of the selected workflow.

Quantitative Assessment Nucleic Acid purity measured with the Nanodrop Spectrophotometer:

  1. A260/280 ratio greater than or equal to 1.8 and less than 2.5
  2. A260/230 ratio greater than or equal to 1.8 and less than 2.5

Qualitative Assessment Analyze nucleic acid sample with the appropriate electrophoresis method.

  1. DNA – Agarose Gel Electrophoresis to confirm intact high molecular weight material free of contaminating RNA.
  2. RNA – Agilent 2100 Bioanalyzer RNA Chip to confirm intact ribosomal band(s) and the absence of DNA contamination.

Sample Submission

  1. Consultation is required for this service. Request an Appointment, or Contact Melissa Stephens.
  2. Samples should be placed in 1.5mL tubes. Label your tube on the side with your initials, date (MM/DD/YYYY), and chosen sample ID. Label the top lid of your tube with your initials and chosen sample ID information. To avoid sample-processing delays and errors, ensure your tubes are legible and clearly labeled.
  3. Additional Quality Control: A separate aliquot of 4ul, in similarly labeled tubes, should be provided to the Genomics Core for QC purposes and to minimize freeze-thaw on the stock material. For samples >8, an aliquot of the sample in a PCR-strip tube is recommended. This aliquot will be discarded following completion of quality control.
  4. Complete and provide the following document and information along with your samples: Illumina Sample Submission Form.

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 2-3 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 any data files you wish to retain for longer periods.
Sample Storage The genomics core will store completed libraries for a period of six months. Please make arrangements with Genomics Core personnel to collect any raw nucleic acid material you wish to keep. The Genomics Core is not responsible for long-term storage of nucleic acid following successful library completion and sequencing.

 

Resources

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