Instruments and Services

Instruments

The UNMC Genomics Core provides high-throughput and flexible next-generation sequencing, single-cell, and targeted expression platforms to support a wide range of genomic applications.

High-throughput short-read sequencing

• Element Biosciences AVITI24
  The AVITI24 platform provides highly flexible, mid- to high-throughput short-read sequencing (2×75, 2×150, 2×300) with dual independently addressable flow cells. It offers very competitive cost per billion reads, low duplication rates, and optional UltraQ (Q50) high-accuracy mode for sensitive variant detection and low-noise applications.
• Illumina NovaSeq 6000
  Our large-capacity Illumina system is optimized for high-throughput whole-genome sequencing (WGS), exome, large RNA-seq cohorts, and complex metagenomic studies. Multiple flow-cell formats (SP, S1, S2, S4) allow efficient scaling from hundreds of millions up to billions of read pairs per run.
• Ultima Genomics platform
  We now also support sequencing on the Ultima platform for selected projects, enabling an additional high-throughput, cost-efficient short-read option. Please contact the core to discuss suitability for your specific application and current availability.

Single-cell genomics

• 10x Genomics Chromium X
  The Chromium X system supports:
  • Single-cell RNA-seq (3' and 5'),
  • Single-cell multiomics (gene expression + ATAC, V(D)J),
  • Experiments from a few thousand to millions of cells.

The core provides end-to-end support from cell-suspension QC through library preparation.

Targeted gene expression

• NanoString nCounter
  The nCounter system is used for highly multiplexed, targeted gene expression profiling (up to ~800 genes). This is ideal for hypothesis-driven pathway panels, validation studies, and projects where RNA quality or quantity is limiting.

Services

The UNMC Genomics Core offers end-to-end services, including library preparation, sequencing, and basic QC for:

• Bulk RNA-seq (polyA-selected, rRNA-depleted, total RNA, low input)
• Genomic DNA sequencing (WGS for bacteria, virus, human, and other genomes)
• 16S and whole-genome metagenomics
• Single-cell RNA-seq and multiome assays (10x Genomics)
• Targeted expression profiling (NanoString nCounter)

Key service areas:

• RNA Sequencing
  Genome-wide gene expression profiling from standard or low-input RNA. Library prep is performed with xGen/IDT and related chemistries; sequencing is typically performed on AVITI24 or NovaSeq 6000 depending on scale.
• Genomic DNA Sequencing (WGS)
  Resequencing of bacterial, viral, plant, and mammalian genomes using Illumina NovaSeq and AVITI24. Capacity can be tuned from small bacterial genomes to large human cohorts.
• 16S and Whole Genome Metagenomics
  Amplicon (16S) and shotgun metagenomic workflows for profiling bacterial, viral, and fungal communities.
• Single-Cell RNA-seq and Multiomics
  10x Genomics Chromium X assays for single-cell gene expression, immune profiling with V(D)J, and multiome (GEX+ATAC) experiments.
• NanoString nCounter Expression Profiling
  Targeted, hybridization-based expression panels (up to ~800 genes) for pathway-level profiling and validation.