Yale Pathology Epigenomics Core
BML 338, 310 Cedar Street
About the core
The Yale Pathology Epigenomics Core provides a streamlined, high-throughput service for Cleavage Under Targets and Release Using Nuclease (CUT&RUN) assays.
As a superior alternative to traditional ChIP-seq, CUT&RUN offers several key technical advantages: it provides a higher signal-to-noise ratio by eliminating artifacts associated with crosslinking and physical shearing; its low input requirements enable robust data acquisition from significantly fewer cells, making it ideal for rare cell populations or limited clinical samples; and its inherent cost efficiency allows for high-quality results with substantially lower sequencing depth.
Our facility leverages the Beckman Biomek i5 automation system to manage the entire workflow, from initial sample preparation to sequence-ready libraries. By centralizing this complex assay, we provide the speed, throughput, and expert bioinformatic support necessary to accelerate epigenetic discovery at Yale while ensuring reproducible, high-resolution mapping of histone modifications and transcription factor binding.
Available to Yale researchers & external researchers
Workflow
Service workflow & responsibilities
The core uses automated 96-well execution to ensure maximum consistency across samples.
| Phase | Task | Responsibility |
|---|---|---|
| 1. Consultation | Project design, antibody selection, and quote generation. | Core & user |
| 2. Preparation | Cell permeabilization and overnight antibody/bead incubation. | User |
| 3. Execution | Automated CUT&RUN assay and library generation (2 days). | Core |
| 4. Quality control | Library assessment via TapeStation and final pooling. | Core |
| 5. Sequencing | Submission to YCGA or user-preferred facility. | Core or user |
| 6. Analysis | Alignment, peak calling, and data visualization. | Core or user |
Guidelines
Sample submission guidelines
To ensure the highest data quality, please adhere to the following requirements:
- Consultation: Required for all new projects to discuss targets and antibody validation.
- Cell preparation: Users provide cells (ideally 500,000–1,000,000) in 8-strip PCR tubes or 96-well plates.
- Antibodies: Users provide primary antibodies. We recommend "ChIP-grade" or "CUT&RUN-validated."
- Forms: A completed request form and COA must be submitted at drop-off.
Rates
Pricing & consultation
The core offers competitive tiered pricing for Yale-affiliated labs, external academic institutions, and industry partners. Fees are structured per sample. Internal users can find rates here (CAS login required).
Contacts
BML338, 310 Cedar Street
New Haven, CT 06510
-
Core/facility
Keck Biophysical Resource
As of 2026, the Keck Biophysical Resource will no longer be available for services except for NIDA investigators, who will still have access to some technologies.
Ewa Folta-Stogniew, PhD, MSc
Director (Retired) -
Core/facility
Yale Center for Molecular Discovery
We provide resources for assay development and high-throughput screening with small molecules and arrayed siRNA and sgRNA/CRISPR libraries in biochemical, cell-based and image-based assays (primarily 384-well format).
-
Core/facility
Chemical Metabolism Core
Previously called the Islet, Oxygen consumption, Mass Isotopomer flux Core (IOMIC), the Chemical Metabolism Core offers targeted and untargeted metabolomics, stable isotope-based metabolic flux analysis, quantitative metabolic panels of central carbon metabolism and adjacent pathways, measurements of cellular bioenergetics, islet isolation and functional studies. Services include study assistance and data analysis.