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The Genomics & Bioinformatics Core Facility at Notre Dame offers comprehensive support for generating and analyzing genomic data across a broad range of research applications. The Genomics team offers full-service support for genomic data generation and analysis. The Bioinformatics team provides custom software solutions, data management, and access to high-performance computing resources to support projects from experimental design through data interpretation.

Our services are organized into three major categories, featured below. Click a button to jump to a particular section.

10x Genomics: Single-Cell & Spatial Platforms Illumina Sequencing & Library Preparation Standard Services

10x Genomics: Single-Cell & Spatial Platforms

Advanced gene expression technologies for high-resolution and spatially-resolved data

10x Genomics Single-Cell RNA-seq

Single-cell gene expression profiling

Applications

• Single Cell Transcriptome Profiling: Analyzing the expression of genes in individual cells or nuclei

• Developmental biology

• Pathogen-host interactions

• Cancer heterogeneity

• Single Cell Immune Profiling: Analyzing the expression of immune-related genes and proteins in individual immune cells

• Single Cell Multiome ATAC + Gene Expression: Combining scRNA-seq with ATAC-seq to simultaneously measure gene expression and chromatin accessibility in the same cell

• CRISPR Screens: Identifying genes that are important for specific cellular functions or responses in conjunction with CRISPR screens.

10x Genomics Visium Spatial Transcriptomics

Whole-transcriptome spatial expression in intact tissue of known and unknown genes

Applications

• Cancer Research: Understanding tumor heterogeneity, microenvironment, and response to therapy.
• Developmental Biology: Studying gene expression patterns during development and differentiation.
• Neuroscience: Investigating brain structure and function.
• Drug Discovery: Assessing drug efficacy and toxicity within a tissue context.
• Immunology: Analyzing immune cell interactions and responses in tissues.

10x Genomics Xenium In Situ

High-plex RNA detection at subcellular resolution of known genes

Applications

• Fine-resolution mapping in FFPE tissues
• Characterizing cell types and their spatial distribution within tissues
• Studying cell-cell interactions and communication
• Analyzing tumor microenvironments and immune responses
• Identifying potential drug targets and therapeutic strategies
• Monitoring treatment efficacy

Illumina Sequencing & Library Preparation

Illumina Next-Generation Sequencing Platforms

High-throughput short-read sequencing for DNA and RNA libraries

Available Platforms

• Illumina MiSeq
  • Max Read Length: 2 × 300 bp
  • Max Output: ~15 Gb per run
  • Max Reads: ~25 million reads
  • Best for: small genome sequencing, targeted amplicon sequencing, 16S/ITS metagenomics, pilot RNA-seq studies

• Illumina NextSeq 2000
  • Max Read Length: 2 × 150 bp
  • Max Output: up to 360 Gb per run
  • Max Reads: up to 1.2 billion reads
  • Best for: bulk RNA-seq, exome sequencing, moderate-throughput population studies, microbial genomics

• Illumina NovaSeq X Plus
  (via collaboration with IUSM Center for Medical Genomics)
  • Max Read Length: 2 × 150 bp
  • Max Output: up to 16 Tb per run
  • Max Reads: up to 50 billion reads
  • Best for: large-scale whole-genome sequencing, high-throughput transcriptomics, cancer genomics, population-scale studies

Library Preparation Services

Standard and custom protocols for DNA, RNA, amplicon, and low-input samples

We support a wide range of library prep workflows tailored to specific sample types and research goals. Many of our protocols are compatible with UMI add-ons for improved quantification and error correction, and automation-friendly options are available for high-throughput studies.

Applications & Coordinated Library Kits

*Xenium workflow does not utilize Illumina Sequencing Platform

Capabilities

• Project consultation to match your sample type and research question with the optimal prep method

• Support for low-input, degraded, and FFPE samples

• UMI integration available for most RNA and DNA workflows

Standard Services

Essential tools for validation, fragment sizing, and nucleic acid quantification

Sample Quality Assurance

Nucleic acid quantification and integrity checks

Services include:

• DNA/RNA concentration measurement using spectrophotometry (e.g., Nanodrop, SpectraDrop) and fluorometry (e.g., Qubit, PicoGreen)
• Fragment size analysis using TapeStation
  • Pre- and Post-QC for all sequencing and library prep workflows to assess suitability of samples for processing

Biomolecule Disruption

• Covaris S220 focused-ultrasonicator
• Highly reproducible acoustic shearing of DNA and RNA for controlled fragmentation
  

Size Selection and Cleanup

• SPRIselect Beads (magnetic bead-based) – tunable size selection for NGS libraries
• BluePippin (Sage Science) – automated gel-based size selection with high precision

Resources

Explore guidelines for projects, iLab GBCF user guides, video tutorials, and guidelines for submissions on our Resources page.