DNA Facility Research Division
The IIHG DNA Facility Research Division, centrally located in the Eckstein Medical Research Building adjoining the Carver College of Medicine, provides a broad spectrum of services and resources designed to make the techniques of genomics, functional genomics, and recombinant DNA technology readily available to the University of Iowa research community. The primary objective of the DNA core’s services is to enable investigators to obtain accurate results from the samples they provide. The services are operated with equal emphasis given to quality, expediency, and affordability. Trained scientists who are able to offer technical support, training, and consultation related to sample preparation and data interpretation staff the core. The activities and services of this core focus around five major areas of support: 1) Genome Sequencing using Illumina HiSeq, Roche GS-FLX, and Life Technologies Ion Torrent Systems. 2) DNA Sequencing and Genotyping, 3) Custom Oligonucleotide Synthesis, 3) DNA microarray using the Affymetrix GeneChip and Illumina iScan BeadArray Systems, and 5) Real-Time PCR. Each of these areas of support is described in more detail below.
The IIHG DNA Facility Research Division provides genomic or massively parallel DNA sequencing services using the Roche Genome Sequencer FLX (a.k.a. “the 454 Sequencer”), the Illumina HiSeq 2000 and MiSeq Genome Sequencing Systems, and Life Technologies Ion Torrent Personal Genome Machine. Included is comprehensive support from experimental design and sample preparation through to downstream analysis. Highly skilled technicians process the samples and perform the sequencing reactions. A custom LIMS has been developed that facilitates sample management throughout the workflow. Users receive all information regarding their sample preparations along with their sequencing results. All data, including the images, are backed up and archived. A powerful computer cluster supports data analysis. Members of the Bioinformatics Division of the IIHG perform a preliminary analysis (e.g., assembly, alignment, etc.) on all runs to ensure the run worked properly. Further bioinformatic support is also available.
The IIHG DNA Sequencing/Genotyping Service is a fee-for-service operation. The service maintains two Applied Biosystems autosequencers that include a Model 3730 and a Model 3730xl instrument. For DNA sequencing, investigators submit DNA samples and the sequencing service then performs the sequencing reactions, loads and runs the reactions on an autosequencer, and analyzes and provides the sequencing data. For genotyping, investigators provide PCR products, the core adds the sizing ladder and loads and runs the reactions. Following the sequencing run, data are transferred to the IIHG DNA data server and an email with a password-protected link to their results is sent to the users. Result files are in a format compatible with most sequence analysis software packages.
Custom Olignucleotide Service
The IIHG DNA Facility Research Division has negotiated with commercial oligonucleotide synthesizing companies to provide custom oligonucleotides for University of Iowa investigators at a bulk-rate discount. Investigators submit their oligonucleotide requests to the IIHG DNA Facility electronically by web browser or e-mail. All the synthesis options (e.g., scales, purification, and modifications) are available to investigators. The IIHG DNA Facility compiles all orders into a single large order request. The synthesized oligonucleotides are delivered to the IIHG DNA Facility, which then delivers the oligonucleotides to the investigator.
DNA Microarray Service
The IIHG DNA Facility Research Division provides DNA microarray services using the Affymetrix GeneChip and the Illumina iScan Microarray Systems on a fee-for-service basis. The Affymetrix GeneChip Service presently maintains two Model 3000 GeneChip Scanners (with the 7G upgrade for high density array scanning), two Model 450 GeneChip fluidics stations, and a GeneChip Model 640 hybridization oven. Both scanning instruments can be used to process and analyze the new small feature size arrays including the whole genome expression arrays, 1000K mapping arrays, exon arrays, and tiling arrays. The Illumina Bead Array service houses the iScan array scanner as well as the equipment necessary to run the Infinium Bead Arrays. The Infinium arrays can be used for expression, genotyping, and methylation profiling studies.
Investigators using the microarray service may submit purified total/polyA RNA or DNA, depending on the type of experiment, and the service will perform all the steps necessary to complete data collection. Alternatively, the investigator may elect to perform their own sample processing and then provide their sample to the service for hybridization to the array and scan. The microarray results are provided in formats that are compatible with most commercial or freeware microarray analysis programs.
Real-time PCR
The IIHG DNA Facility Research Division houses five “real-time” or kinetic PCR instruments: two Model 7900HT, one Model 7500, and two Model 7000 Applied Biosystems sequence detection systems. Investigators are charged a flat fee per run. Access to the instruments is obtained by reserving a time slot through our real-time PCR on-line calendar reservation system. The investigator provides PCR reactions in a 96-well plate ready to be loaded on the instrument at the appointed time. The IIHG DNA Facility loads the instrument, collects data, and performs preliminary data analysis. Alternatively, the investigator can elect to perform these tasks themselves. A hard copy “Experimental Report” and/or an electronic version of the data in the form of a Microsoft Excel workbook file are provided. Additional data analysis is the responsibility of the user; however, core personnel are available to assist users in performing further analyses. Two full time employees and the director assist real-time PCR users in their primer/probe design, instrument setup, data collection, and downstream analyses.
Contact Information
Kevin Knudtson, PhD
Research Scientist
323 EMRB
(319) 335-7251
kevin-knudtson@uiowa.edu