Epigenomics and Spatial Biology Core

The Epigenomics and Spatial Biology Core of the Center for Cell Signaling in Gastroenterology provides novel epigenomics and spatial biology technologies and expertise to support faculty research through three main objectives:

  • Delivering comprehensive, turnkey, user-friendly epigenomics assays and spatial biology services.
  • Accelerating research with expert consultation, guidance through the project lifecycle from design to execution, and analysis.
  • Developing and implementing cutting-edge epigenomics and spatial biology methods in response to rapidly emerging technical advances and implementation of additional single-cell and subcellular spatial biology platforms.

Core leadership


The core offers a variety of services, mainly to center faculty members and their laboratory team members. These services include:

  • Study design consultations.
  • Seamless coordination with the C-SiG Clinical Core for tissue acquisition and processing.
  • Execution of epigenomics and spatial profiling assays.
  • Sequencing library preparation.
  • Facilitating cost-effective and timely next-generation sequencing (NGS) in coordination with the Genome Analysis Core at Mayo Clinic.
  • High-performance computing workflow to accommodate high-volume data analysis and storage via Mforge.
  • Facilitating secondary and tertiary bioinformatic analysis of NGS data and the continuing development of related pipelines in collaboration with the Bioinformatics Core at Mayo Clinic.
  • Data interpretation consultations.
  • Assistance with writing the methods sections for grants and publications.


  • Chromatin immunoprecipitation-sequencing (ChIP-seq).
    • Single-stranded ChIP-seq (eSPAN).
    • Low-input methods that offer high signal-to-noise ratios, such as TAF-ChIP and CUT&RUN.
    • Quantitative ChIP-seq using drosophila chromatin for normalization (ChIP-Rx).
  • DNA immunoprecipitation-sequencing (DIP-seq).
    • 5-methylcytosine (5mC).
    • 5-hydroxymethylcytosine (5hmC).
    • 5-formylcytosine (5fC).
    • 5-carboxylcytosine (5caC).
  • Nucleosome positioning and Open Chromatin assays.
    • Micrococcal nuclease digestion with next generation sequencing (MNase-seq).
    • Analysis of transposase-accessible chromatin by sequencing (ATAC-seq).
    • Omni-ATAC.
  • Single cell epigenomic and transcriptomic assays.
    • Single cell (sc) ATAC-seq.
    • Single-cell ATAC-seq combined with gene expression (scATAC+GEX).
    • Single-cell GEX Flex, a single-cell transcriptome assay for cells and frozen or fixed tissues.
  • Spatial biology assays.
    • Nanostring GeoMx Digital Spatial Profiler (DSP) Assays.
    • 10x Genomics Visium Spatial Gene or Gene + Protein Expression Assays.
    • 10x Genomics Visium CytAssist Assays.

External research access to services

Research teams outside of Mayo Clinic can access services from the Epigenomics and Spatial Biology Core. Email us for information.