Genomics & Bioinformatics Core Facility

Illumina Sequencing Services

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 Sequencing using the Illumina MiSeq sequencing platform. Sequencing the entire complement of DNA, or genome, of many animal, plant, and microbial species is indispensable for basic biological and medical research. The Genomics Core 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.
 

In addition to On-Site Illumina MiSeq Sequencing Services, we are able to offer Illumina HiSeq 4000 sequencing through a collaborative agreement with Beijing Genome Institute (BGI). Additional Illumina platforms are also available at collaborative pricing. To obtain a contract for Illumina HiSeq sequencing, Request a Quote or Contact Dr. Michael Pfrender and Melissa Stephens with Subject Line: “Request for Sequencing Contract – PI Name”.

 

To learn more about Illumina HiSeq Sequencing, view Illumina HiSeq Supported Applications and NGS Platform Comparisons Tool


Service Options

MiSeq Sequencing

The MiSeq desktop sequencer allows for more focused applications such as targeted gene sequencing, metagenetics, metagenomics, small genome and transcriptome sequencing, targeted gene expression, and amplicon sequencing. Generating 1 million up to 25 million reads, the MiSeq sequence is ideal for reduced representation studies and narrowly focused applications. View MiSeq Supported Applications. Important: Actual read length and sequencing output vary between samples and sequencing runs.
Illumina MiSeq Reagent Kits and Performance Parameters
Illumina MiSeq Performance

 Single Read

Paired-End Read
Data Size
Reagent kit
Read Length
Single Reads
Read Length
Paired-End Reads
Output
MiSeq Reagent Kit v3 (600 cycles)
1 x 300
22-25 Million
2 x 300
44-50 Million
13.2-15 Gb
MiSeq Reagent Kit v3 (150 cycles)
1 x 150
22-25 Million
2 x 75
44-50 Million
3.3-3.8 Gb
MiSeq Reagent Kit v2 (500 cycles)
1 x 250
12-15 Million
2 x 250
24-30 Million
7.5-8.5 Gb
MiSeq Reagent Kit v2 (300 cycles)
1 x 150
12-15 Million
2 x 150
24-30 Million
4.5-5.1 Gb
MiSeq Reagent Kit v2 (50 cycles)
1 x 25
12-15 Million
2 x 25
24-30 Million
750-850 Mb
MiSeq Reagent Micro Kit v2 (300 cycles)
1 x 150
4 Million
2 x 150
8 Million
1.2 Gb
MiSeq Reagent Nano Kit v2 (500 cycles)
1 x 250
1 Million
2 x 250
2 Million
500 Mb
MiSeq Reagent Nano Kit v2 (300 cycles)
1 x 150
1 Million
2 x 150
2 Million
300 Mb

 

Sample Requirements

We require qualitative and quantitative assessment of the library prior to sequencing. Library quality will be assessed and scored according to the requirements of the chosen sequencing approach.

Quantitative Assessment Determine library concentration with Qubit High-Sensitivity Assay, Invitrogen. Typically, library concentration is ≥ 5ng/ul. Ensure the library is dissolved in a low salt solution, such as Qiagen Elution Buffer (Buffer EB), Illumina Resuspension Buffer (RSB) or 1xTE Solution, pH 7 – 8. 
Qualitative Assessment Determine average library fragment length with Agilent Bioanalyzer High-Sensitivity DNA Kit. Examine the 50bp to 150bp region to confirm the absence of adaptor contamination.
 

Sample Submission

  1. Consultation is required for this service. Request an Appointment, or Contact Melissa Stephens.
  2. Library should be placed in 1.5mL tubes. Label your tube on the side with your initials, date (MM/DD/YYYY), and chosen Library ID. Label the top lid of your tube with your initials and chosen Library 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 Library Submission Form. Important: Please include Index/Barcode ID and Sequence (5’-3’) for each library; this is required information.

 

Turnaround Time

Turn around time is dependent on the complexity and scope of the project research goals, and completion time may vary. In general, turn-around time for most standard projects/services is 2-3 weeks following successful completion of initial library quality control.
 

Your Results

Upon completion of service, a comprehensive report will be provided with library quality control and sequencing instrument setup/run information. Data in the form of unprocessed FastQ files for each indexed/barcoded library will be available to download from a secure BaseSpace link. If Bioinformatics services are sought, please visit our Bioinformatics page for policies, requirements, and data delivery options.
 

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.