Bulk Epigenomic Assays

Epigenomic sequencing introduction

Bulk epigenomic assays measure regulatory features averaged across a population of cells or nuclei. The three epigenetic assay types the Genomic CoLab supports are: 1. ATAC-seq that identifies accessible chromatin, 2 CUT&RUN and 3. CUT&Tag that map genomic regions associated with a selected histone modification, transcription factor, or other chromatin-bound proteins.

Bulk ATAC-seq is used to compare genome-wide chromatin accessibility without choosing a target protein in advance, which allows genome-wide inspection of putative active gene regulatory elements. CUT&RUN or CUT&Tag are used when the question concerns a specific histone mark or chromatin-associated protein and a suitable antibody is available. CUT&RUN is more suitable for transcription factors, while CUT&Tag is more suitable for histone modifications. Bulk assays are most interpretable when a population-level average is appropriate or when a sufficiently purified population can be submitted.

Bulk measurements can obscure differences among cell types in heterogeneous tissue. Consider cell sorting, single-nucleus ATAC, or Multiome (ATAC-seq paired with RNA-seq) when cell-resolved regulatory states are central. ATAC-seq does not directly demonstrate that a particular protein occupies an accessible site. CUT&RUN and CUT&Tag depend strongly on antibody performance and should not be scaled to precious samples without appropriate pilot data.

Compatible sample types

Depending on the validated workflow, projects may begin with compatible fresh or cryopreserved cells, isolated nuclei, or tissue-derived nuclei. Acceptance of fixed, archived, or low-input material is may be possible but require pilot experiments to demonstrate feasibility. Investigators are highly encourage to consult the CoLab before collection as cell quantity and viability can greatly impact the success of the experiment.

Genomics CoLab offerings

Active Motif ATAC-seq: Genome-wide measurement of accessible chromatin.
Active Motif CUT&RUN: Antibody-directed nuclease cleavage near a selected chromatin target.
Active Motif CUT&Tag: Antibody-directed tagmentation near a selected chromatin target.

See out bulk epigenomics pricing.

Below is a table of assays with functional antibodies that we have successfully used in experiments.  

Design considerations

When you start your project you will discuss with Genomics CoLab term the following items to assure we can meet your project needs: 

- Accessibility versus a specific histone mark or chromatin-bound protein.
- Cell or nucleus input, preservation, fixation, and nuclei-isolation method is compatible with the desired method.
- Biological replicates, a matched negative control, and an appropriate positive control.
- Evidence that the antibody works in CUT&RUN or CUT&Tag; success in western blotting, immunofluorescence, or ChIP alone does not guarantee compatibility.
- Whether an initial pilot is needed for a new antibody, unusual tissue, limited input, or unsupported preservation condition.
- Sequencing depth and analysis appropriate for broad histone marks versus narrow transcription-factor peaks.

What the CoLab performs

The CoLab reviews sample and antibody suitability, performs the library preparation, completes library quality control and pooling, coordinates sequencing, and provides the agreed primary processing or analysis. Nuclei isolation, antibody evaluation, and pilot work may be separate services.

What the investigator supplies

The investigator supplies the cells, nuclei, tissue, or other approved material; biological replicates; project metadata; the target and antibody information; and the agreed negative and positive controls. Investigators should provide antibody validation evidence and disclose fixation, freezing, and storage history.

Data and analysis delivered

Deliverables include raw reads, and may be expanded to aligned data, library quality metrics, peak or enrichment calls, signal tracks, sample-comparison summaries, motif or annotation results, and standard visualizations. Deliverables differ among ATAC-seq, CUT&RUN, and CUT&Tag and are defined during project planning.

Pricing and sequencing considerations

Costs depend on the assay, sample count, batch structure, upstream nuclei or sample preparation, controls, antibodies or reagents, sequencing depth, and analysis. Controls are part of a valid experimental design and must be included when estimating sample count and sequencing. New targets or unusual material may require a separately priced pilot before the full study.

To start a project 

Please download our project description form, fill it in with the as much detail as you can and then send it along with a consultation request to the [email protected] email address.