CSSQ: a ChIP-seq signal quantifier pipeline [PDF]
Frontiers in Cell and Developmental Biology, 2023 Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized the studies of epigenomes and the massive increase in ChIP-seq datasets calls for robust and user-friendly computational tools for quantitative ChIP-seq. Quantitative ChIP-
Ashwath Kumar +5 more
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Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection
Genome Biology, 2022 Background The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq).
Thomas Eder, Florian Grebien
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Nucleic Acids Research, 2022 ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape.
Zhaonan Zou, Tazro Ohta, Fumihito Miura
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Model-based Analysis of ChIP-Seq (MACS)
Genome Biology, 2008 We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of ...
Yong Zhang, Tao Liu, Jerome Eeckhoute
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intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
BMC Genomics, 2020 Background RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions.
Yingying Cao +2 more
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Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
Molecular Biomedicine, 2020 Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high ...
Shaoqian Ma, Yongyou Zhang
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RACS: rapid analysis of ChIP-Seq data for contig based genomes
BMC Bioinformatics, 2019 Background Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA sequences on a genomic scale.
Alejandro Saettone +3 more
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ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae [PDF]
Bio-ProtocolChromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a widely used technique for genome-wide analyses of protein–DNA interactions. This protocol provides a guide to ChIP-seq data processing in Saccharomyces cerevisiae, with a focus
Kris Alavattam +4 more
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An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells
STAR Protocols, 2021 Summary: Integrative analysis of next-generation sequencing data can help understand disease mechanisms. Specifically, ChIP-seq can illuminate where transcription regulators bind to regulate transcription.
Lorane Texari +5 more
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An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition. [PDF]
PLoS ONE, 2016 Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require ...
Brian Egan +16 more
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