About: Goals

The overall aim of the UW ENCODE Project is to create comprehensive, high-quality catalogues of human and mouse DNasel hypersensitive sites (DHSs) spanning all major tissue lineages and key developmental time points.

A key focus of our production effort is on data quality, a strategy that served the Human Genome Project well. Accordingly, samples are rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection.

Independent validation by a definitive technique provides the ultimate quality standard. Therefore, we are validating the human DHS catalogue in a statistically rigorous fashion using hypersensitivity Southerns, a well-established gold-standard assay, aiming to benchmark both sensitivity and specificity of the next-generation "-seq" DNaseI assay.

Since DNasel hypersensitive sites are generic markers of a broad spectrum of human and mouse cis-regulatory sequences, the utility of the catalogue is greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, etc.), and insulators. Toward this end we are also performing parallel profiling of transcription (RNA), histone modification (H3K4me3, H3K27me3, H3K26me3), and occupancy by the pleiotropic genomic regulator CTCF.

We release all data rapidly to the ENCODE Data Coordination Center (DCC) at UCSC. Release logs are available through the home page of this website.

Collectively, we aim to establish a high-quality public resource of human and mouse regulatory DNA for all to use and explore.