NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

ENCODE Standards and Policies

From Encode2 Wiki
Jump to: navigation, search

This page contains final standards and policies for the ENCODE Project. Some standards may be revisited in the future if necessary.

Data Release Policy

ENCODE-modENCODE Data Release Policy

Data Standards

Multiplex Survey Results 2011

Multiplex Survey Results 2011

Chromatin and Transcription Factor Data Standards

ChIP Data Standards Manuscript

Current version, submitted to Genome Research (this manuscript is in the review process, please do not make public)

ChIP, DNase, FAIRE, methylation standards

and DNA Methylation Genome Wide Location Data

The above document contains the following sections (many of which were previously independent data standards documents):
Table of Contents
I. Standard Measurements for Common ENCODE Cell Types
II. ENCODE and modENCODE Standards for ChIP-chip and ChIP-seq Experiments

IIa. Antibody characterization measures for antibodies to chromatin and transcription factors
IIb. ChIP-chip and ChIP-seq data production, including and standards for biochemical validation

III. Requirements for a DNase-seq and FAIRE-seq experiments
IV. Standards for determining DNA methylation status
V. Recommended Standards for Reporting mod/ENCODE Data

Appendix I. Recommended Standards for ChIP-seq including depth of sequencing recommendations, biological replicate requirements and data verification standards
Appendix II. Validation of Commercial Histone Modification Antibodies to be Used for ChIP

OLD data standards documents

NOTE that the below documents are now incorporated into the chromatin/transcription factors standards document above.

RNA-seq Standards

RIP Data Standards