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Illumina Miseq

Genomics Sequencing Facility


We offer DNA sequencing services using Illumina NextSeq 500 and MiSeq platforms. We have the capability to prepare several common library types. We can also perform automated DNA and RNA extractions as well as perform PCRs for amplicon sequencing projects using a pipetting robot. We QC all samples and libraries.

We can help you with detailed experimental design and bioinformatic analysis on a collaborative basis. If you are interested in that possibility make sure to discuss it with us.

This facility is funded through a Major Research Instrumentation grant from the National Science Foundation with support from the South Dakota Agricultural Experimental Station. Additionally, BioSNTR (a regional Biosciences virtual center funded through the NSF-EPSCOR and the South Dakota Governor’s Office for Economic Development) is making a significant investment in the facility. 

Please include our RRID# (RRID:SCR_023959) when citing our facility on manuscripts. Citing our core facility helps us to generate support and facilitates future funding for new equipment.

Workshops/Training: We can accommodate individual training opportunities while we work on your project, please contact us. 

We also offer group workshops. Apply using the Facility Workshops Application form.

Fees:(As of Oct. 19, 2023. Costs may change without previous notice.)

* We can work with multiple library preparation protocols and kits. The ones shown below are examples. Contact us for other options.

*We also offer single-cell RNAseq with a 10X Genomics system. Inquire about project costs.

Instrument/ApplicationCost per unit ($)Comments
RNA Seq library prep88Multiples of 6
DNA library prep (Nextera Flex)85Other options are available for specific applications, please inquire cost
Sample QC (Bioanalyzer)942 runs per RNA sample required. Multiples of 12
Sample quant. (Qbit)22 per RNA sample required.
NextSeq 500run
H.O. 1x75bp (up to 30Gb)
2,266Output: Up to 400M clusters
NextSeq 500run
H.O. 2x150bp (up to 120Gb)
NextSeq 500run
H.O. 2x75bp or 1x150bp (up to 60 Gb)
NextSeq 500run
M.O. 2x75bp
1,773Up to 130M clusters
NextSeq 500run
M.O. 2x150bp
V3 2x300 bp
2,161Up to 25M clusters
V2 2x250
1,735Up to 18 M clusters
Other MiSeq runs
Nanopore MinIon1,100Includes 1 DNA library prep
16S RNA metagenomics (from DNA to sequence)
v4-v5 amplicon
5,00096 samples. Uses MiSeq run 2x300bp. Other amplicons are welcome (max length 550bp), please inquire cost.
16S RNA metagenomics (from DNA to sequence)
Full length
1,600Nanopore, 24 samples
Size selection (Blue Pipin)501 gel (5 wells per gel)

Here is what researchers say about having these services available locally:

“Having a sequencing center in South Dakota allows researchers to rapidly acquire genomic data, conduct bioinformatics analyses and then refine their experimental designs,”

Adam Hoppe, director of BioSystems Networks and Translational Research Center

“The next-generation sequencing facility will increase the precision in gene transfers. It will help us develop genomic prediction models so that we can deliver better genetics and varieties to the producers of the South Dakota.”

SDSU winter wheat breeder Sunish Seghal

The availability of an in-house sequencing facility means shorter turn-around time in getting sequencing results.

Professor Senthil Subramanian of Agronomy, Horticulture and Plant Science