Technology

We create and instantiate technologies to enable both large-scale mapping and mechanistic understanding of the epigenome. These fit into the broader toolkit of the Cell Circuits & Epigenomics programs. We have instantiated some of our core technologies for large scale epigenome mapping projects, such as ENCODE4. We also devote significant effort to protocol development in order to work with diverse, complex and rare tissues and cell types.

We currently work with many collaborators to create epigenetic profiles of both healthy and diseased cell populations using the following technologies.

Transcriptomics

RNA-Seq
Single-cell RNA-Seq (including and from the )

Chromatin mapping

ChIP-Seq (transcription factors, chromatin regulators, and histone modifications)
Microfluidic-ChIP

DNA methylation mapping

; including single-cell RRBS)
Whole-genome bisulfite sequencing (WGBS)

Genome topology

Other Assays

Dual (RRBS+RNA)-Seq of low-input samples
Massively parallel reporter assay (MPRA) of enhancer activity

Perturbations

Epigenome engineering
Chromatin regulator CRISPR screens
High throughput small molecule targeting of chromatin factors

How to work with us

The Epigenomics Program operates on a collaborative model. To work with us, please contact Liz Gaskell, Chuck Epstein, or Andi Gnirke with a brief description of your project, your scientific question, funding opportunities, and an idea of scale.