Assays and standards Glossary File formats Software tools Pipelines Data organization Release policy Schemas Help Using the portal Cart REST API Citing ENCODE FAQ Project Overview …

All data generated by the ENCODE consortium is submitted to the DCC and available from the ENCODE portal (http://www.encodeproject.org). The data are reviewed for quality and released to …

The ENCODE Consortium has adopted shared experimental guidelines for the most common ENCODE assays. The guidelines have evolved over time as technologies have changed, and current …

The ENCORE project aims to study protein-RNA interactions by creating a map of RNA binding proteins (RBPs) encoded in the human genome and identifying the RNA elements that the RBPs bind to.

Antibodies must be characterized according to standards set by the ENCODE Consortium. Please see the linked documents for transcription factor standards (May 2016), histone modification and …

The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment.

The ENCODE Data Coordinating Center has developed data processing pipelines for major assay types generated by the project: RNA-seq, RAMPAGE 1, ChIP-seq, DNase-seq, ATAC-seq 2 , and WGBS.

The ENCODE consortium has developed two analysis pipelines to study two different classes of protein-chromatin interactions. The histone ChIP-seq pipeline, described here, is suitable for proteins that …

The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells …

The ENCODE Project aims to map all functional elements of the human and mouse genomes. Progress toward this goal has involved over ten thousand epigenomic experiments utilizing a wide array of …