ENCODE
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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 …
Search – ENCODE
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 …
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 …
Data Processing Pipelines – ENCODE
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 , …
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.
Access to ENCODE data
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 …
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 …
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 …