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- ENCODE
Assays and standards Glossary File formats Software tools Pipelines Data organization Release policy Schemas Help Using the portal Cart REST API Citing ENCODE FAQ Project Overview Collaborations ENCODE workshops About the DCC
- Search – ENCODE
Project: ENCODE Library construction method: capped RNA enrichment Experiment ENCSR841GXY released PRO-cap in peripheral blood mononuclear cell Homo sapiens peripheral blood mononuclear cell Lab: Haiyuan Yu, Cornell Project: ENCODE Library construction method: capped RNA enrichment Experiment ENCSR740DLY released PRO-cap in neutrophil Homo
- 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
- 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 RBPs bind to
- 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 and chromatin-associated protein standards (October 2016), and RNA binding protein standards (November 2016)
- 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
- 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
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