ArticleBioinformatics and biology insights2016
Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks.
Article in Bioinformatics and biology insights, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Crossover designation recruits condensin to reorganize the meiotic chromosome axis.Current biology : CB · 2025Article
- Crossover designation recruits condensin to reorganize the meiotic chromosome axis.bioRxiv : the preprint server for biology · 2025Article
- SEAseq: a portable and cloud-based chromatin occupancy analysis suite.BMC bioinformatics · 2022Article
- Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum).Plant molecular biology · 2020Article
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Authors and funding
6 authors.
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Abstract
As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. We developed an analysis pipeline that utilizes our unique, enrichment-type specific approach to peak calling. With the help of this pipeline, we managed to accurately describe the advantages and disadvantages of the iterative refragmentation technique, and we successfully identified possible fields for its applications, where it enhances the results greatly. In addition to the resonication protocol description, we provide guidelines for peak calling optimization and a freely implementable pipeline for data analysis.
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