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Epigenomics Development Laboratory and Recharge Center

The Epigenomics Development Laboratory and Recharge Center provides collaborative and end-to-end epigenomic services to Mayo Clinic researchers and external investigators. Investigators need only send in their samples, and the facility staff does the rest, up to and including next-generation sequencing library preparation.

All epigenomic services provided follow the Encyclopedia of DNA Elements (ENCODE) Consortium guidelines.

Chromatin immunoprecipitation sequencing (ChIP-seq)

ChIP-seq is a valuable and widely used epigenetic approach for studying genomewide protein-DNA interactions in cells and tissues. The Epigenomics Development Laboratory and Recharge Center offers standard or Tn5 transposase-based ChIP-seq services, depending on sample size (50,000 to 10 million cells). Suitable samples include:

  • Cell lines.
  • Fluorescence-activated cell sorting (FACS)-purified cells.
  • Whole blood.
  • Buffy coat samples.
  • Peripheral blood mononuclear cells (PBMCs).
  • Frozen tissues.
  • Formalin-fixed, paraffin-embedded (FFPE) tissues.

Spike-in normalization also is available.

Cleavage under targets and release using nuclease (CUT&RUN)

CUT&RUN is a new and cost-effective technique to profile genomewide occupancy of chromatin proteins and histone modifications for low-input samples — typically 50,000 to 500,000 cells. The CUT&RUN technique uses an antibody to capture the target of interest in situ on nonfixed cells. It also uses a protein A-micrococcal nuclease recombinant protein to enhance DNA fragmentation of targeted genomic loci. Suitable samples include:

  • Cell lines.
  • FACS-purified cells.
  • PBMCs.

DNA immunoprecipitation-sequencing (DIP-seq)

DIP-seq is an antibody-based technology to profile genomewide distribution of DNA-associated epigenetic marks such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The Epigenomics Development Laboratory and Recharge Center offers DIP-seq services using genomic DNA (2.5 to 10 mcg) isolated from:

  • Cell lines.
  • FACS-purified cells.
  • Buffy coat samples.
  • Tissues.
  • FFPE archived tissues.

Assay for transposase-accessible chromatin using sequencing (ATAC-seq)

ATAC-seq provides information about open and accessible regions of chromatin that are indicative of active regulatory regions. Sample types suitable for this assay are around 50,000 cells or equivalent and include:

  • Cell lines.
  • Buffy coat samples.
  • Sorted cells.
  • Frozen tissues.

Single-cell ATAC-seq (scATAC-seq, 10X) and single-cell multiome ATAC + gene expression (scMultiome, 10X)

scATAC-seq provides information about genomewide chromatin accessibility of thousands of individual cells in parallel, identifying subpopulations of cells within a heterogenous population that would otherwise be lost in standard bulk ATAC-seq. Sample types suitable for this assay include cell lines and sorted cells. It requires approximately 250,000 to 500,000 cells.

scMultiome combines scATAC-seq and scRNA-seq assays to accomplish simultaneous profiling of gene expression and chromatin accessibility from the same cell. Sample types suitable for this assay include cell lines and sorted cells. It requires approximately 250,000 to 500,000 cells.

Single-cell gene expression flex (fixed-cell scRNA-seq)

Single-cell gene expression flex (10X Genomics) is a new standard assay to analyze gene expression on the single cell level. It involves sample preservation by fixation and probe hybridization. This approach is particularly useful in scenarios in which live-cell analysis is challenging or when there is a need to capture transient or dynamic cellular states. It enables analysis of samples that cannot be processed as live cells, such as archived or preserved specimens. Sample types suitable for this assay are around 250,000 cells or equivalent and include:

  • Cell lines.
  • PBMCs.
  • Sorted cells.
  • Frozen tissues.
  • FFPE archived tissues.

Library preparation

Library preparation services are offered for nanogram-range DNA or single-stranded DNA. If you choose to perform your own epigenomics assay, consider the Epigenomics Development Laboratory and Recharge Center for the final sequencing library preparation step.