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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 stages from 10 5 days after conception until birth, including transcriptomes, methylomes and chromatin states
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 ENCSR856UND
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 associated projects
Data – ENCODE FAQ Project Overview Collaborations ENCODE workshops About the DCC Sign in Create account Listed carts
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 released to the scientific community
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 , and WGBS
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
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 current guidelines are informed by results gathered during the project