Genomic Technologies Facility Plant Sciences Institute Iowa State University

Genomic Technologies Facility › Services

2025 Roy J. Carver Co-Laboratory, Iowa State University
1111 WOI Road, Ames, Iowa 50011-1085
Tel: (515) 294-7491 | Email:

Next Generation Sequencing Services

Ion Torrent Proton

With the Ion Torrent Proton, libraries can be templated and sequenced in two days. Templated library sequences are amplified on Ion Sphere Particles and checked for quality. An enrichment step purifies the amplified template, and sequencing is performed using Ion Torrent's semiconductor ion chips. During this process, nucleotides are sequentially incorporated into DNA, causing a hydrogen ion to be released. Detection of the voltage change allows for genotypic calls to be made. With the Ion Torrent™ Proton P1 chip, 200 bp single end sequencing can provide up to 80-100 million reads per run. Sequencing runs can be conducted by GTF staff on a fee-for-service basis, or on-campus customers can undergo training to become certified to run the instrument themselves. More information on sample submission and Ion Torrent Sequencing chips is available on the FAQ page.

NGS Library Preparation and Quantification

The GTF offers custom library preparation and quantification services for both the Illumina and Ion Torrent platforms.

Illumina library preparations available: TruSeq Small RNA, TruSeq Targeted RNA, TruSeq Stranded Total RNA with Ribo-Zero, TruSeq DNA PCR-Free, TruSeq DNA Nano, TruSeq Custom Amplicon, Nextera XT DNA, Nextera DNA, Nextera Exome Enrichment, and Nextera Rapid Capture Exome and Expanded Exome.

Ion Torrent™ preparations available: Ion Xpress Plus Fragment Library and Ion Total RNA-Seq.

After preparation, libraries are quantified to ensure proper loading of the library. GTF can quantify libraries by Bioanalyer or RT-PCR using the KAPA library quantification kits.

High Throughput Nucleic Acid Manipulation

Plant DNA Extraction:

GTF provides high throughput DNA Extraction using the Qiagen BioSprint96. Qiagen DNA Extraction is suitable for Ion Torrent or Illumina Sequencing and Sequence Capture. Once the lysate is prepared, a single plate can be extracted in 30 minutes. Extraction can be conducted by GTF staff on a fee-for-service basis, or on-campus customers can undergo training to become certified to run the instrument themselves. GTF will provide Qiagen DNA Plant Kits, which includes all necessary reagents and plates to extract DNA from ground tissue. Grinding and quantification services are not included in the price of a run, but GTF can provide this service for an additional fee. Certified users must provide their own pipets and tips. The BioSprint is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF or a printed copy is available by the instrument to be filled out at the time of your appointment.

Plant RNA Extraction:

GTF provides two options for Plant RNA extraction: Qiagen RNeasy Plant Extraction Kitsand high-throughput BioSprint RNA Extraction. Either option is suitable for Ion Torrent or Illumina Sequencing. With Qiagen RNeasy kits, GTF can extract 1-24 samples using spin columns in three hours. With the BioSprint, 96 samples can be extracted in 30 minutes. BioSprint extraction can be conducted by GTF staff on a fee-for-service basis, or on-campus customers can undergo training to become certified to run the instrument themselves. GTF will provide Qiagen Plant Kits, which includes all necessary reagents and plates to extract RNA from ground tissue. Grinding and quantification services are not included in the price of either kit, but GTF can provide this service for an additional fee. Certified users must provide their own pipets and tips. The BioSprint is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF or a printed copy is available by the instrument to be filled out at the time of your appointment.

Eppendorf AF2200 Plate Reader:

GTF offers the AF2200 Plate Reader for nucleic acid quantification in a high-throughput format. The Eppendorf µPlate 0.5 is available for measuring the absorbance of small volume samples. GTF supplies both absorbance and fluorescence filters for use. Users must provide their own supplies and consumables (pipets, tips, tubes, plates, reagents, etc.). The Plate Reader is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times.

PCR Instruments

Real-Time PCR Systems:

The GTF provides two quantitative real-time PCR machines for customer use: The Roche LightCycler 480 Real-Time PCR System and Stratagene's Mx4000 multiplex quantitative PCR system. Machines are available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. A one-hour training session with GTF staff is required for new users. Users must provide their own supplies and consumables (pipets, tips, tubes, plates, reagents, etc.). Sign up for time in the scheduler's page. User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF.

Miscellaneous Services and Instruments

Single SNP/Indel Genotyping:

The GTF provides KASPar Single SNP/InDel genotyping using KBioscience reagents. The KASPar method can be used to detect single base polymorphisms and small InDels, and is most suitable for genotyping a large number of samples for a few markers.

Sage Science's BluePippin:

GTF provides the Blue Pippin for customers for use in the collection of DNA fragments. 1.5% Agarose gel cassettes contain 5 wells with run times of 30-100 minutes. i1.5% gel cassettes are able to target 250bp - 1.5kb fragments and 2% gel cassettes target 100-600 bp fragments. Other cassette sizes may be available for purchase; please contact GTF staff before planning your experiment. A one-hour training session with GTF staff is required for new users. The Blue Pippin is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. Users must provide their own consumables (pipet tips, tubes, etc.) User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF or a printed copy is available by the instrument to be filled out at the time of your appointment.

Invitrogen's E-Gel SizeSelect System:

GTF provides an E-Gel Size Select System from Invitrogen for customers to use. 2% agarose gels contain 8 loading wells, and are suitable for separation ranges from 50bp - 1kb, with collection in ~10-30 minutes. A one-hour training session with GTF staff is required for new users. The E-Gel System is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. Users must provide their own consumables (pipet tips, tubes, etc.). User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF or a printed copy is available by the instrument to be filled out at the time of your appointment.

Agilent Bioanalyzer:

GTF provides an Agilent Bioanalyzer for customers to use with the DNA 1000, DNA 7500, DNA High Sensitivity, RNA 6000 Nano, and RNA 6000 Pico Chips. A one-hour training session with GTF staff is required for new users. The Bioanalyzer is available to customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times. Users must provide their own consumables (pipet tips, tubes, etc.). User Forms are available to be printed and filled out prior to your scheduled appointment in the GTF or a printed copy is available by the instrument to be filled out at the time of your appointment.

Eppendorf epMotion M5073:

GTF offers the Eppendorf epMotion M5073 automated liquid handling system for routine pipetting uses. The epMotion system is equipped with 50 µL and 1000 µL high precision dispensing pipettes, a ThermoMixer and ThermoRack, and a MagSep module that can be utilized for separation and nucleaic acid purifiecations. A one-hour training session with GTF staff is required for new users. Users may purchase certified tips from the facility, and use the instrument at no additional cost. Any additional supplies needed must be provided by the user. The epMotion is available for customers for use 8 AM to 5 PM Monday through Friday when the University is in session. Please contact GTF staff if services are required outside of these times.