Center for Epigenomics:
The Epigenomics Platform

The Epigenomics Platform at the Center for Epigenomics is a cutting-edge research laboratory specializing in high-throughput genomic and epigenomic data generation, with a primary focus on human tissue biopsies and clinical samples. A hallmark of our platform is the ability to support sequencing-based bulk, single-cell, and spatial workflows across a broad spectrum of tissue types, from minute needle biopsies to large fibrotic tumor resections. 

We excel in delivering optimized workflows for a wide variety of human tissues and cell types, enabling rapid and efficient optimization of assay conditions.

While we are dedicated to delivering high-quality data, we believe that the next generation of epigenomic discoveries — particularly those that will significantly impact human health — will require profiling epigenomes at scale. Our platform is uniquely positioned to support large cohort and population studies as well as longitudinal research. We are focused on uncovering the clinically actionable discoveries that will emerge from studying the epigenomes of diverse populations over time. This mission is one of our main goals, and we work collaboratively with investigators to drive these future discoveries forward.

In addition to our research aims, our infrastructure ensures precision and reliability, featuring integrated sample tracking systems and quality control (QC) infrastructure that seamlessly manage complex projects. We develop and apply robust bioinformatic pipelines tailored for discovery across diverse biological contexts, allowing researchers to derive meaningful insights from their data. These strengths enable us to assay hundreds to thousands of samples in a cost-effective and efficient manner, driving innovation in epigenomic research.

As a next-generation high-content epigenomic phenotyping platform, we strive to empower research across cross-sectional and longitudinal population studies, compound screening, and disease diagnostics. The Epigenomics Platform has extensive expertise in handling human tissue types including, but not limited to, healthy and diseased lung, liver, heart, pancreas, and blood, collaborating with researchers from across the United States. Each year, we process more than 1,000 samples using advanced techniques such as ATAC-seq, snRNA-seq, snATAC-seq, 10x Multiome, Visium HD, etc. to generate large, high-quality datasets.

Our capabilities extend beyond bulk sequencing to include a strong emphasis on single-cell techniques, producing more than 1,000 datasets annually through workflows such as scRNA-seq, scATAC-seq, and 10x Multiome. As a key data production facility, we contribute to major research consortia, including the Molecular Atlas of Lung Development Program (LungMAP), Human BioMolecular Atlas Program - Lung (HubMap - Lung), the International Mouse Phenotyping Consortium (IMPC), Single Cell Opioid Responses in the Context of HIV (SCORCH) for both human and primate studies, the FNIH Accelerating Medicines Partnership Program in Common Metabolic Diseases (AMP CMD), the Cellular Senescence Network (SenNet) and Trans-Omics for Precision Medicine (TOPMed).

The Epigenomics Platform offers a fully integrated pipeline from experimental design to data analysis, with a focus on ensuring high-quality outcomes at every stage. We support research by providing experimental design tailored to minimize batch effects, alongside robust project management. Our platform is equipped with custom sample tracking systems designed to efficiently categorize and monitor samples throughout the workflow. We also specialize in nuclei isolation, purification, and quantification from various tissue types, followed by high-quality library preparation and sequencing. Additionally, our platform supports data processing, wrangling, analysis, and secure storage, offering both raw and processed data formats for collaborative research and service.