Policies

Core Facility Resource Grant Insert Statement

The UNMC Genomics Core Facility is located in Durham Research Center II (DRC II), Rooms 1010, 1012, 1015, 1017, and 1021 (approximately 2,200 square feet). The Core is a comprehensively equipped shared resource that supports a regional research community and processes a wide variety of RNA and DNA samples for applications including bulk RNA-seq, single cell genomics, whole genome sequencing, metagenomics, methylation-related workflows, and chromatin profiling libraries (for example, CUT and RUN and ChIP-like libraries). The Core operates high-throughput and flexible short-read sequencing platforms, including the Illumina NovaSeq 6000 and the Element Biosciences AVITI24 System. The Core also supports targeted gene expression using the NanoString nCounter platform and single cell workflows using the 10x Genomics Chromium X system.

Staff Associated With the Genomics Core

The Genomics Core is staffed by a Scientific Director and an Assistant Director, supported by four full-time research technologists and technicians who perform day-to-day laboratory operations. The team supports sample intake and QC, library preparation, sequencing operations, run monitoring, and project communication through the Core’s tracking and billing systems.

Major Scientific Instruments Located Within the Genomics Core

Next Generation DNA Sequencing Instruments

Element Biosciences AVITI24 System
A flexible dual-flow-cell sequencing platform designed to support cost-effective mid-throughput sequencing and faster turnaround for many short-read applications. The AVITI24 is used for common bulk sequencing applications (for example, RNA-seq and DNA sequencing workflows) and enables efficient scheduling due to its independent flow cell architecture.

Illumina NovaSeq 6000
A high-capacity sequencing platform used for large-scale projects that benefit from high throughput and strong economy of scale.

Single Cell Genomics Instrumentation

10x Genomics Chromium X
The Core supports single cell RNA sequencing (scRNA-seq) and single cell multiomics workflows depending on project design and sample type. The Core team works with investigators to optimize cell suspensions, evaluate viability, and support library generation and sequencing.

Targeted Gene Expression Instrumentation

NanoString nCounter
Used for targeted gene expression profiling on pathway-focused panels and for rapid validation of sequencing experiments. A wide variety of pre-designed panels are available, and custom panels may be supported depending on project requirements.

Robotics and Liquid Handling for Library Construction

SciClone NGS Library Production Robot
Used for scalable, high-throughput library preparation workflows.

Eppendorf epMotion 5075
Used for automated pipetting steps in library preparation and related workflows where appropriate.

Opentrons OT-2
Used for flexible, scriptable liquid handling to support standardized and reproducible workflows (for example, normalization, pooling, and other repeatable pipetting tasks) as appropriate for the assay and sample type.

DNA and RNA Quantification and Sizing Instruments

Agilent TapeStation
Used for nucleic acid sizing and QC, including RNA integrity and library size distribution checks.

NanoDrop Spectrophotometer
Used for rapid assessment of nucleic acid purity metrics (A260/280 and A260/230).

Qubit Fluorometer
Used for accurate quantification of nucleic acids, especially dsDNA used in library preparation and sequencing workflows.

Bioinformatic Resources

Bioinformatics support is provided through a separate campus resource, the Bioinformatics and Systems Biology Core. The Genomics Core transfers sequencing data and run outputs to designated storage locations, and investigators may engage the Bioinformatics and Systems Biology Core for downstream analysis, interpretation, and consultation as needed. Additional computational resources may also be available through University of Nebraska system high-performance computing environments, depending on project needs and user access.

Rigor and Reproducibility Statement

For all laboratory procedures, quality controls are performed as part of standard operating procedures. Controls and QC steps vary by assay and may include: verification of input nucleic acid purity (NanoDrop), integrity and sizing (TapeStation), quantification (Qubit), library size distribution confirmation, and review of platform run metrics. Sequencing run QC includes monitoring platform-appropriate performance indicators (for example, base quality, yield, index performance, and control library metrics when used). The Core periodically processes control materials and technical replicates as part of ongoing performance monitoring and to support consistent operations across workflows.

Data Management and Sharing Statement

Sequencing outputs (for example, FASTQ files and run metrics) are delivered to investigators through Core-approved storage and transfer pathways. The Genomics Core facilitates data transfer and ensures that required run outputs are made available to investigators. Investigators are responsible for long-term data retention and downstream analysis planning, and may coordinate directly with the Bioinformatics and Systems Biology Core for analysis support.