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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 genome-wide 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 (PBMC)
  • Frozen tissues
  • Formalin-fixed, paraffin-embedded (FFPE) tissues

Spike-in normalization also is available.

DNA immunoprecipitation-sequencing (DIP-seq)

DIP-seq is an antibody-based technology to profile genome-wide 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 µg) 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 (sc)ATAC-seq provides information about genome-wide chromatin accessibility of thousands of individual cells in parallel, allowing identification of 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, requiring approximately 50,000 to 100,000 cells.

Single cell multiome ATAC + gene expression assay provides simultaneous profiling of gene expression and open chromatin from the same cell. Sample types suitable for this assay include cell lines and sorted cells, requiring approximately 50,000 to 100,000 cells.

Hi-C chromatin immunoprecipitation (HiChIP)

HiChIP assay combines the benefits of ChIP-seq with the long-range information of Hi-C (high-throughput chromosome conformation capture), enabling genome-wide mapping of protein-directed topological 3D chromatin features in regulatory interactions among promoters and enhancers or genetic variants and the gene or genes they regulate. Sample requirements are similar to that of standard ChIP-seq service.

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.