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.
Lab: John Stamatoyannopoulos, UW Project: ENCODE Treatments: 10 ng/mL Interleukin-2 (UniProtKB:P60568) for 5 days, anti-CD3 and anti-CD28 coated beads for 7 days Experiment ENCSR856UND
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 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 adopted shared experimental guidelines for the most common ENCODE assays. The guidelines have evolved over time as technologies have changed, and current guidelines are informed by results gathered during the project.
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.
