The Genomics Division at 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)
• Single-Cell & Spatial Omics Analysis
• Sanger Sequencing
• 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 Sequencing

Next Generation Sequencing (NGS) services are provided using the Illumina short-read and Oxford Nanopore long-read technologies. The Illumina NovaSeq 6000 features high density dual-flow cells to enable massively parallel high throughput sequencing. The Illumina MiSeq benchtop sequencer permits low throughput genome sequencing.   The Oxford Nanopore PromethION, MinION and Flongle platforms facilitate long-read sequencing and base modification analyses of DNA and RNA to fit all project sizes. Liquid handling robots are used for high throughput sample processing.  A LIMS is used for project submission and sample management, while allowing users an overview of their project along with workflow information and data links. Data is backed up and archived as described in the NGS Data Storage policy.

The division has processed samples using NGS technologies for a complete range of applications including: 

• RNA-Seq 
• Whole Genome Sequencing
• Whole Exome and Targeted Sequencing
• microRNA Discovery and Quantification
• ChIP-Seq
• SNP (variant) Detection and Discovery Studies
• Long Read Sequencing

Single-Cell & Spatial Omics 

Single-cell/nuclei and Spatial Omics analyses are provided using the 10X Genomics Chromium Single-cell and Visium platforms, respectively. Comprehensive support is available to include experimental design, sample processing and sequence data collection, through downstream analysis.

Single-Cell Gene Expression, Immune Profiling,  snATAC-Seq, and other assays supported by using the Chromium X controller system are provided.  The single-cell applications that can be performed using this technology include the measurement of gene expression, cell surface protein characterization, immune clonotyping, antigen specificity determination, and/or chromatin accessibility. 

In partnership with the Iowa NeuroBank Core and the Iowa Neuroscience Institute (INI), Spatial Transcriptomics analysis is offered using the original and HD Visium platforms.  Spatial gene expression and/or spatial protein profiling applications using fresh-frozen or FFPE samples can be conducted.

Sanger Sequencing

The Genomics Division houses 2 Applied Biosystems Model 3730xlu (96-capillary) DNA Sequencers used for Sanger sequencing and genotyping applications.  A LIMS 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, two Agilent TapeStations, a Trinean DropSense 16, a Nanodrop spectrophotometer, a Qubit fluorometer, and an Agilent 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 and QuantStudio 7 Pro  real-time PCR instruments used for relative quantification and allelic discrimination studies.  The service supports array card, 96- and 384-well formats. 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 by Technology