ENCODE
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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 …
Project Overview – ENCODE
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 …
Data standards – ENCODE
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 …
ENCORE Matrix – ENCODE
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 …
eCLIP Data Standards – ENCODE
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 …
ATAC-seq Data Standards and Processing Pipeline – ENCODE
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.
Whole-Genome Bisulfite Sequencing Data Standards and
The WGBS pipeline was developed as a part of the ENCODE Uniform Processing Pipelines series 1. The full WGBS pipeline code is available on Github and can be run on DNAnexus …
publications – ENCODE
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 …
Getting Started – ENCODE
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 …