School of Freshwater Sciences
Great Lakes Genomics Center
School of Freshwater Sciences

Call: (414) 382-1774

Illumina MiSeq

Massive Parallel/Next Generation Sequencing

The Great Lakes Genomics Center offers NGS library preparations and sequencing services on our Illumina MiSeq for:

  • 16S Amplicon Seq
  • Small Whole Genome Resequencing
  • Amplicon Seq
  • Small Genome Stranded RNA Seq

The MiSeq v3 can generate up to 15 Gb of output with 25 million sequencing reads and 2×300 base pair read lengths.

Available Sequencing Read Lengths (Flowcells):

  • 2×150 v3
  • 2×300 v3
  • 1×50 v2
  • 2×150 v2
  • 2×250 v2

Each MiSeq library preparation and sequencing run is unique to the needs of the researcher and project. We strongly suggest consulting with GLGC staff before samples are collected and processed so that the experiment can be set up in the best way possible.

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Sample submission requirements are below.

Library Type Nucleic Acid Quantity Concentration Quality Measure and Score
16S 100 ng Microbial DNA 5 ng/μl Nanodrop (260/280): 1.8-2.0 Gel image
Small Genome Resequencing 5 ng Genomic DNA 0.2 ng/μl Nanodrop (260/280): 1.8-2.0 Gel image
Amplicon 5 ng Genomic DNA 0.2 ng/μl Nanodrop (260/280): 1.8-2.0 Gel image
Small Genome RNA 1 μg total RNA* or 2 ng mRNA 50 ng/μl total RNA* or 0.25-2 ng/μl mRNA Bioanalyzer RNA 6000 Pico chip, RIN ≥ 8 Nanodrop (260/280): 1.8-2.0

*total RNA must be rRNA depleted before libraries can be made

Sequencing Experiment Design and Coverage

Multiplexing is available for for some sequencing applications. The level of multiplexing depends on the number of samples, desired coverage, and genome size.

The flowcell/read length to use for your project depends on what type of experimental question you are trying to answer, genome size, desired coverage, and budget. Generally, 30X coverage is desired for a re-sequencing project. However, if you are trying to identify rare variants, have a mixed population or are looking for low expression transcripts, you may need higher coverage of your genome or transcriptome.

Data Analysis

We will provide sequence data in FASTQ files. Adapters are trimmed.

Bioinformatics is available through the Great Lakes Genomics Center if you require different file types or data processing.


The Great Lakes Genomics Center strives to provide the best data possible in a timely manner. Turn around time is typically 6 weeks after samples are received.

In the advent of failed services, GLGC staff will work with the researcher to identify the cause. If sample quality or researcher error is identified as the cause, the user will be responsible for the full contractual agreement. If the cause is due to equipment failure of GLGC staff error, the service will be repeated without additional cost to the user. GLGC is never financially responsible for the cost associated with sample obtainment (ie DNA prep, RNA prep, experiment costs, etc.).

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