ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

By S. Landt, G. Marinov, Anshul B Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, Peter J. Bickel, James B. Brown, Philip Cayting and 38 more. 2012

1,852 citations recorded by the source corpus.

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.

Subfields: Molecular Biology

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, background): “Moreover, invariance of decision trees to monotone transformations (12) to a large extent mitigates normalization issues that are a major concern in the analysis of genomics data, where signal-to-noise ratios vary widely even between biological replicates (22, 23).”
deepTools2: a next generation web server for deep-sequencing data analysis (2016, background): “The average fragment size of a sample is also an important parameter for many downstream analyses, such as peak calling (8,9).”
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences (2014, positive): “Further investigation of these two sites using the ENCODE annotation from UCSC genome browser (36,37) revealed that R-30 Off-4, which had high off-target activity, targeted a site within 400 bp of the 3′ end of a long non-coding RNA (RP4-756H11.”
Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila (2015, positive): “The IDR, a standard technique for the analysis of IP data developed by the ENCODE Project Consortium, is analogous to the false-discovery rate (FDR) and leverages biological replicates to measure quantitative reproducibility (Li et al. 2011; Landt et al. 2012).”
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse (2016, methodology): “In the ChIP layer, the FRiP score (23) (fraction of non-mitochondrial reads in peak regions) and the number of high quality peaks with 10- or 20-fold enrichment over background were calculated to show data quality at the ChIP level.”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, methodology): “The ChIP-seq technology was partly adapted from microarray ChIP-chip technology and first implemented in 2007 and since then has been used widely to analyze transcription factor binding sites, histone modifications, and chromatin-modifying complexes and sequences in a wide variety of organisms [154]”
Ensembl 2020 (2019, background): “This includes statistics on raw read files, QC reports generated by FastQC (https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/), CHANCE (27) and FRIP (28), and finally statistics on the results of peak calling and segmentation.”
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data (2014, methodology): “Similar results were observed on mouse ChIP-seq experiments downloaded from the ENCODE project (data not shown).”