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Facilities Resources

The Genomics Division in the Iowa Institute of Human Genetics provides a broad spectrum of technologies and resources to support nucleic acid- and genomics-based initiatives to the research and clinical communities.  These technologies include:

  • Genome Sequencing (NGS-based)
  • DNA Sequencing (Sanger-based)
  • DNA Microarray
  • Oligonucleotides
  • Nucleic Acid quality assessment
  • Quantitative DNA/RNA Analysis

The laboratory occupies a total of ~2950 sq ft of space over 6 rooms. The division director (Kevin Knudtson, PhD), the oligonucleotide service and support staff occupy at total of ~650 sq ft of office space over four rooms.

Genome & Sanger Sequencing

The IIHG Genomics Division provides all University of Iowa investigators access to a NovaSeq 6000 that features dual-flow cells to deliver the highest throughput and lowest price-per-sample across multiple applications. The MiSeq benchtop sequencer permits low throughput genome sequencing. The Covaris E220 96-well plate sonicator and SciClone sample preparation robots facilitate high throughput.  The 10X Genomics Chromium system, drop-seq based technology, is used to for single-cell RNA-Seq applications. A custom LIMS has been developed that facilitates sample management throughout the workflow.  Users receive all information regarding their sample preparations along with their data.  At this time, all data, including the images, are backed up and archived. The service has processed samples using NGS technologies for a complete range of applications including: 1) whole genome sequencing, 2) Whole exome and targeted sequencing, 3) RNA-Seq (quantification of transcripts, i.e., expression analysis), 4) microRNA discovery and quantification, 5) ChIP-Seq, 6) SNP (variant) detection and discovery studies, and 7) Single-cell RNA-seq.

The division houses the Applied Biosystems Model 3730 (48-capillary) and Model 3730xl (96-capillary) DNA Sequencers used for Sanger sequencing and genotyping applications.  A LIMS system is used for the submission of sequencing requests and results that can be downloaded via a web browser through our website. Access to the data files is password protected.

DNA Microarray

The division uses the Illumina iScan BeadArray system to support array-based genotyping and methylation profiling projects. Following hybridization, the core scans the array and provides preliminary analysis of the data. These data are provided in a format that is compatible with most commercial or freeware microarray analysis programs.

Nucleic Acid Quality Assessment

The division maintains and supports two Agilent Bioanalyzers, a Trinean DropSense 16, a Nanodrop spectrophotometer, a Qubit fluorometer, and an Advanced Analytical Fragment analyzer used to asses nucleic quality and quantity.  Results are either acquired directly by the investigator or sent electronically.

Quantitative DNA/RNA Analysis: Real-time and Digital PCR and NanoString

The division offers access to the ABI QuantiStudio 7 Flex, QuantStudio 7 Pro and a ABI Model 7900 real-time PCR instruments used for relative quantification and allelic discrimination studies.  The service supports array card, 96- and 384-well formats. The Fluidigm EP1 and BioMark system use a nanoscale technology to deliver high throughput genotyping at a low cost.  The division maintains controllers to run the 48x48, 96x96, and 192x24 (target x sample) BioMark Dynamic arrays. Digital PCR is provided using the BioRad QX200 droplet digital PCR system. Used to perform ultrasensitive and absolute quantification of nucleic acid targets. The system uses the same hydrolysis probe (Taqman)- or EvaGreen (SYBR-like)-based assays gives the ability to quantify template molecules that may be undetectable using the traditional real-time PCR techniques. The division maintains the NanoString nCounter that is used for RNA and DNA quantification and sequence analysis.  Investigators reserve time on these instruments using the online calendaring system. Division personnel set up and runs the instrument, send the data to the user, and will assist with analysis, as needed. 

The major equipment used to support these technologies are summarized in Table 1.

Table 1. Major Instrumentation at the Genomics Division

Techology

Major Instrumentation

Genome Sequencing llumina NovaSeq 6000 & MiSeq genome sequencers, 2 Perkin Elmer SciClone liquid handling systems, Covaris E220 & S2 sonicators and 10X Genomics Chromium System
Sanger Sequencing Applied Biosystems (ABI) 3730 and 3730xl DNA sequencers, Beckman Biomek FX liquid handling system, 6 ABI thermocyclers
DNA Microarray Illumina iScan BeadArray System
Nucleic Acid Quality Assessment 2 Agilent Bioanalyzers, Trinean DropSense 16, Advance Analytical Fragment Analyzer, Qubit Fluorometer and a Nanodrop spectrophotometer
Quantitative DNA/RNA Analysis ABI Quant Studio 7 Flex, QuantStudio 7 Pro and ABI Model 7900 sequence detection systems, Fluidigm EP1 system, BioRAD QX200 droplet digital PCR system, and NanoString nCounter system