Policies

Core Facility Resource Grant Insert Statement

UNMC Genomics Core Facility Resources Durham Research Center II, Rooms 1010, 1012, 1015, 1017, and 1021 (total of ~2200 square feet). The UNMC Genomics Core facility is a comprehensively equipped facility that serves the regional research community. A wide variety of RNA/DNA samples are processed in the core for a number of different applications including RNA sequencing (traditional and single cell), exome, genomic resequencing, metagenomics, methylation and ChIP sequencing. The core operates the Illumina NovaSeq6000, NextSeq550 and MiSeq systems (Illumina, San Diego, CA). In addition to next generation sequencing systems, the core houses a Nanostring EnCounter, ideal for rapid targeted gene expression experiments for pathway profiling and validation of next generation sequencing experiments. 

Staff Associated With the Genomics Core:

The laboratory has six full-time research technologists that perform a variety of tasks in the laboratory including the processing of samples for the Illumina NovaSeq6000, NextSeq550, and MiSeq systems. These applications include RNA/DNA quality assessment and preparation of samples for gene expression profiling and preparation of DNA samples for sequencing. Major Scientific Instruments Located Within the Genomics Core.

Next Generation DNA Sequencing Instruments:

NovaSeq6000 – The NovaSeq is a high capacity sequencer ideal for projects that benefit from the throughput and capacity. NextSeq550 – The NextSeq is for medium capacity projects and the MiSeq System is optimized for a variety of applications, including targeted gene, small genome and amplicon sequencing, 16S metagenomics, and more.

Targeted Gene Expression Instrumentation:

Nanostring – Nanostring Encounter targeted gene expression panel services. This system is an outstanding system for quickly and efficiently profiling gene expression in pathway specific panels of genes. A wide variety of panels (ranging from 400 to 800 genes per panel) are available including a number of different panels related to oncology, immunology, and neuroscience. Custom panels are available as well.

Robotics / Liquid Handling for Next Generation Sequencing Library Construction:

SciClone NGS Library Production Robot (Perkin Elmer): This instrument is used for producing next generation sequencing libraries for sequencing. The Sciclone® G3 NGS / NGSx workstations are the most capable automated solution for high-throughput sequencing sample preparation. The EpMotion 5075 automated pipetting system from Eppendorf is used for generating NGS libraries.

qPCR Instruments:

Applied Biosystems VIIa Real Time PCR Instrument (Life Technologies, Grand Island, NY). The instrument is utilized for real time PCR, quantification of gene expression and validation of gene expression identified by microarrays or next generation sequencing. It is also valuable for the quantification of next generation sequencing libraries prior to sequencing.

DNA / RNA Quantification and Sizing Instruments:

Fragment Analyzer Automated CE System (Advanced Analytical Technologies, Inc. Ames, IA): This instrument works well for sizing nucleic acids extracted from tissues as well as from single cells in a high throughput fashion. Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA): The Bioanalyzer instrument is used in a variety of NGS applications, including initial RNA integrity assessments as well as checking the size distribution of libraries for next generation sequencing applications. Nanodrop Spectrophotomer Instrument: This instrument is used for measuring the concentration and purity of nucleic acids prior to using them in experiments. Qubit Instrument: The Qubit is used for measuring double stranded DNA for use in next generation sequencing experiments.

DNA Shearing Instrumentation:

Covaris S220 Ultrasonicator (Covaris Inc., Woburn, MA): The Covaris S220 Ultrasonicator is used to generate DNA fragments prior to library generation.

Single Cell Genomics Instrumentation:

The Genomics Core Facility at UNMC has the instrumentation necessary to enable single cell genomics experimentation. 10x Genomics: The 10x genomics system can be used for either single cell RNA expression experiments or ATAC or multi-omic applications. This instrument at UNMC was just upgraded to the newest version the 10X “X”. Tens of thousands of individual cells can be captured simultaneously and individually barcoded for RNA seq and the other applications. This instrument is set up in a BCL2 level facility and the director of the lab has an IBC protocol in place to enable work with HIV infected live cells.

Bioinformatic Resources at UNMC Campus:

The Genomics Core interfaces extensively with the Bioinformatics and Systems Biology Core at UNMC. This is an important resource for assistance with analysis as additional PhD and MS level analysts are available for consultation.

Bioinformatic Resources Accessible at University of Nebraska at Omaha:

 The University of Nebraska at Omaha is located within three miles of UNMC. Researchers are encouraged to utilize resources at the University of Nebraska at Omaha for assistance with next generation sequencing data analysis and interpretation as needed. In particular, the Holland Computing Center at the University of Nebraska at Omaha allows researchers within the University of Nebraska network to utilize the supercomputing resource. This resource allows the next generation sequencing Core bioinformatician to run computational tasks in a massively parallel fashion, thus providing investigators with analysis in a very timely manner.  

Acknowledgement Statement

The University of Nebraska DNA Sequencing Core receives partial support from the National Institute for General Medical Science (NIGMS) INBRE - 5P20GM103427-21 grant as well as The Fred & Pamela Buffett Cancer Center Support Grant - 5P30CA036727-36. This publication’s contents are the sole responsibility of the authors and do not necessarily represent the official views of the NIH or NIGMS.

Rigor & Reproducibility Statement

For all of our laboratory procedures, quality controls are run as part of standard operating procedures. The nature of the control is dependent upon the assay, as described below. Next Generation Sequencing on the Illumina Instrument Quality Metrics: There are a variety of metrics utilized during the entire next generation sequencing procedure beginning with RNA and DNA input quality metrics to determine purity (A260/280 and A260/230 values) as well as processing a sample of the RNA using an Agilent Bioanalyzer to determine the potential degradation state of the incoming sample. During the library production procedure, the concentration and yield, as well as the size distribution of the resultant product, is monitored. Other metrics are continually monitored during sequencing, such as cluster numbers, numbers of clusters passing the filter, and Phred scores of the individual reads. The next generation sequencing facility periodically processes control samples and technical replicates to test the quality of the library production and instrument operations.

Data Management & Sharing Statement

The data generated by the Genomics Core facility is managed on a daily basis by the Bioinformatics and Systems Biology Core. Users are directed to that core for direction and management of their data.