The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states.
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 and circumstances in which a gene is active.
The ENCODE Portal, developed and maintained by the Data Coordination Center (ENCODE DCC), is the canonical source for all experimental metadata and data from ENCODE and associated projects.
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 scientific community.
The ENCODE Data Coordinating Center Uniform Processing Pipelines are designed to create high-quality, consistent, and reproducible data. Pipelines are composed of discrete steps that can represent an algorithm, a software tool, or a file format manipulation.
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 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.
