Data analysis Standard ChIP-seq

The following lists the standard ENCODE ChIP-seq data analysis, immunoprecipitation of different types have different standards, the following describes the two directions histones and transcription factors:

A histone

Biological replicates :

At least two

Antibody :

Meet the standards of the ENCODE Consortium. May further refer to the following standards documents: https: //www.encodeproject.org/documents/4bb40778-387a-47c4-ab24-cebe64ead5ae/@@download/attachment/ENCODE_Approved_Oct_2016_Histone_and_Chromatin_associated_Proteins_Antibody_Characterization_Guidelines.pdf

input control :

ChIP assays each input control sample must have

Library complexity :

The Non-Redundant Fraction (NRF), PCR Bottlenecking Coefficients 1 and 2, or PBC1 and PBC2 calculated criteria: NRF> 0.9, PBC1> 0.9 , and PBC2> 10.

Data volume :

For narrow-peak histone experiments, each repetition ≥ 20M available insert

For broad-peak histone experiment was repeated for each available insert ≥45 M

With further reference to: https: //www.encodeproject.org/data-standards/terms/#read-depth

Note ! H3K9me3 is an exception, which is enriched in repeat region of the genome. Relative to other markers of broad, the H3K9me3 peaks located only a few non-overlapping regions.

This led to many ChIP-seq data can not be compared to a unique region of the genome. Organizations and primary cells (primary cells) better than on the need to ensure 45M reads.

The following table wide (broad), narrow (Narrow) peak of histone type:

Types of histones

Second, the transcription factor

Most indicators with histone

The following is a unique index:

Data volume :

At least 20M available insert

    Low depth: 10-20 M

    Inadequate: 5-10 M

    Very low depth: <5 M

Repeatability:

IDR values (Irreproducible Discovery Rate)

And assume that IDR repeated values ​​between the average repeat is less than 2

IDR

With further reference to: https: //sites.google.com/site/anshulkundaje/projects/idr

Third, Reference:

https://www.encodeproject.org/chip-seq/histone/#standards

https://www.encodeproject.org/chip-seq/transcription_factor/