Illumina MiSeq Next-Generation Sequencer

The Illumina MiSeq next generation sequencer is now in the Genomics division of the OUHSC core facilities! The MiSeq is identical to other Illumina sequencers like the HiSeq but costs and turnaround time are much less since the MiSeq is a single lane machine.  Each paired-end run on the MiSeq results in a single sequencing lane yielding  7.5-8.5 Gb of sequence data (500 cycle paired end run).  In addition, samples can be run individually or multiplexed using Illumina indexing chemistry which can further reduce per sample run costs. Cost estimates are given below for library construction, sequencing, and  bioinformatic analysis.

Applications Offered:

  • small genome resequencing
  • de novo sequencing and assembly of clinical isolates and other unknowns
  • small RNA profiling
  • whole transcriptome analysis
  • microbial community studies using multiplexed 16s amplicon pools
  • TruSeq amplicon Cancer panels (48 gene validated panel)
  • ChIP-Seq

Sample Submission Instructions

DNA Samples

Submit no less than 100 ng of purified, RNAse treated, genomic (prokaryotic or viral) DNA at a concentration of at least 20 ng/ul in nuclease-free water.

Whole Transcriptome Samples

Submit no less than 1 ug of high quality Total RNA at a concentration of at least 100 ng/ul in nuclease-free water. If you are unable to obtain this amount please contact us before submission.

Small RNA Samples

Total RNA: Please submit no less than 1 ug of high quality Total RNA at a concentration of at least 100 ng/ul in nuclease-free water. If you are unable to obtain this amount please contact us before submission.

Enriched Small RNA: The minimum amount that can be used for library constuction is 100 ng of enriched Small RNA.  Illumina’s protocol has been optimized for 500ng -1ug of enriched sRNA, and higher amounts of starting material typically increase quality of the resulting library.  If you are unable to obtain these higher amounts, please contact us before submission so that we can discuss expected results for this type of sample.

16s Metagenomic Samples

Please submit no less than 20ng of purified Microbial Genomic DNA at a concentration of at least 5 ng/ul in nuclease-free water. Samples are processed in batches of 10.

ChIP DNA Samples

Please submit 20-50 ng of ChIP DNA. If you are unable to obtain this amount please contact us before submission.

Online Submission Instructions

Request services by logging onto the OUHSC Core site via our iLab Solutions portal:

If you are an internal user, log in using your OUHSC username and password.   If you are an external user and do not already have an iLabs account, please register for an account.  Once you have logged in, please request the service of your choice.  If you have any questions, please email us at

Current Pricing

Pricing (Current OUHSC Prices)

Library Building

Library Type Input Internal 
External Pricing
DNA (Nextera) genomic DNA $200.00/sample $304.00/sample
RNA (TruSeq) Total RNA $300.00/sample $476.00/sample
Small RNA (TruSeq) Purified Small RNA, Total RNA $350.00/sample $484/sample
ChIP-Seq (TruSeq) IP DNA fragments $250.00/sample $353.20/sample
16S rRNA (TruSeq) Microbial DNA $300/(1-10) samples $750/(1-10) samples
Human genomic DNA, FFPE DNA Inquire for pricing    


Read Length (BP) Output Internal Pricing   External Pricing 
2 x 300 (600 Cycles) 14-15Gb $1950.00/run $2045.00/run
2 x 250 (500 Cycles) 7.5 - 8.5 Gb $1465.00/run $1554.00/run
2 x 150 (300 Cycles) 4.5 - 5.1 Gb $1300.00/run $1380.00/run
1 x 50 (50 Cycles) 750 - 850 Mb $1015.00/run $1081.00/run


Service Internal Pricing  External Pricing 
Primary Analysis/Data Handling & Storage $300.00/run $350.00/run

MiSeq Data Analysis and Data Storage

 Once a MiSeq Run is complete, we will transfer the raw data to CLC Genomics Workbench (Qiagen) version 10.0.1 and newer for analysis

         The analysis will include aligning the data to your reference genome of choice or de novo assembly, and initial analysis will be performed.  Below are files that can be expected for each type of sample analysis.

DNA Samples:  Mapping files, Summary Report, Mapping Report, Variant Reports when possible, and Unmapped Reads upon request                                                       

Whole Transcriptome Samples: Gene Expression list, Differential Expression list; and initial PCA plot, Heat Map, and Venn Diagram images                           

Small RNA Samples: small RNA Report, small RNA Sample list, Comparison lists               

16S Samples:  OTU Report, Trim Report, OTU Table, Comparison Tables                         

ChIP Samples: Summary Report, Peaks, QC Report, Peak Shape Filter, Peak Shape Score, Peaks Annotated                       

             ** Many files are interactive in the CLC Genomics Workbench Software.  Customers are responsible for additional analysis and may schedule a time to use the CLC software.      

·      Once the analysis has been performed, the files will be exported and either emailed to the customer or backed up to an encrypted drive provided by either the customer or purchased through our Core (8GB - 2TB recommended for most projects).  The customer must also back up the raw data files (.fastq) and be responsible for keeping any files that might be needed in the future.  We will keep raw data files (.fastq) for up to 3 months but if analysis has to be repeated due to a customer not saving his or her data, a charge might be applied.