ChIP-Seq

ChIP-seq data analysis

ChIP-sequencing is a method used to analyze protein interactions with DNA. Here, we propose some materials to learn how to analyze ChIP-seq data.

Slides

Several deck of slides are available for this topic:

• General introduction about ChIP-seq data analysis

Tutorials

A tutorial with hands-on is available for this topic:

• Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) with ChIP-sequencing

Input datasets

The input datasets for the tutorial are available on Zenodo.

Galaxy instance

For these tutorials, you can use the dedicated Docker image:

docker run -d -p 8080:80 bgruening/galaxy-chip-seq-training

It will launch a flavored Galaxy instance available on http://localhost:8080 .

References

Papers

Stephen G. Landt et al: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

A very useful "encyclopedic" paper with many details about the tools the (mod)ENCODE consortia use and also contains a long section about antibody validation etc..

Gabriel E Zentner and Steven Henikoff: Surveying the epigenomic landscape, one base at a time

Overview of popular sequencing techniques with very nice descriptions of DNase-seq, MNase-seq, FAIRE-seq.

Benjamin L Kidder et al: ChIP-Seq: technical considerations for obtaining high-quality data

Nice, readable introduction into all aspects of ChIP-seq experiments (from antibodies to cell numbers to replicates to data analysis)

Marion Leleu et al: Processing and analyzing ChIP-seq data

Fairly detailed review of key concepts of ChIP-seq data processing (less detailed on analysis)

Peter J. Park: ChIP-seq: Advantages and challenges of a maturing technology

Peter V Kharchenko et al: Design and analysis of ChIP-seq experiments for DNA-binding proteins

Edison T Liu et al: Q&A: ChIP-seq technologies and the study of gene regulation

Short overview of several (typical) issues of ChIP-seq analysis

Thomas S. Carroll et al: Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

Shirley Pepke et al: Computation for ChIP-seq and RNA-seq studies

First comparison of peak callers, focuses on the explanation of basic principles of ChIP-seq data processing and general workflows of peak calling algorithms

Elizabeth G. Wilbanks & Marc T. Facciotti Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

Another comparison of peak callers - focuses more on the evaluation of the peak callers performances than Shirley Pepke et al.

Mariann Micsinai et al: Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

How to choose the best peak caller for your data set - their finding: default parameters, surprisingly, yield the most reproducible results regardless of the data set type

Jianxing Fen et al: Identifying ChIP-seq enrichment using MACS

How to use MACS

Yong Zhang et al: Model-based Analysis of ChIP-Seq (MACS)

Original publication of MACS

Modan K Das & Ho-Kwok Dai: A survey of DNA motif finding algorithms

Review of motif analysis tools

Philip Machanick and Timothy L. Bailey: MEME-ChIP: motif analysis of large DNA datasets

MEME-ChIP-paper

Timothy L. Bailey and Philip Machanick: Inferring direct DNA binding from ChIP-seq

Centrimo: position-specific motif analysis, especially useful for ChIP-seq data

Morgane Thomas-Chollier et al: Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs,

How to use TRAP

Helge G. Roider et al: Predicting transcription factor affinities to DNA from a biophysical model.

Theoretical background of TRAP

Contributors

This material is maintained by:

• Mallory Freeberg
• Mo Heydarian

For any question related to this topic and the content, you can contact them.

The following individuals have contributed to this training material:

• Mallory Freeberg
• Mo Heydarian
• Friederike Dündar
• Bérénice Batut