SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin
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- dc.contributor.author Blanco, Enrique
- dc.contributor.author Di Croce, Luciano
- dc.contributor.author Aranda Aragón, Sergio
- dc.date.accessioned 2021-12-02T06:48:50Z
- dc.date.available 2021-12-02T06:48:50Z
- dc.date.issued 2021
- dc.description.abstract In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using the standard ChIP-seq scheme, which lacks a reference for the control of biological and experimental variabilities. While several studies have recently proposed different solutions to circumvent this problem, substantial analytical differences among methodologies could hamper the experimental reproducibility and quantitative accuracy. Here, we propose a computational method to accurately compare ChIP-seq experiments, with exogenous spike-in chromatin, across samples in a genome-wide manner by using a local regression strategy (spikChIP). In contrast to the previous methodologies, spikChIP reduces the influence of sequencing noise of spike-in material during ChIP-seq normalization, while minimizes the overcorrection of non-occupied genomic regions in the experimental ChIP-seq. We demonstrate the utility of spikChIP with both histone and non-histone chromatin protein, allowing us to monitor for experimental reproducibility and the accurate ChIP-seq comparison of distinct experimental schemes. spikChIP software is available on GitHub (https://github.com/eblancoga/spikChIP).
- dc.description.sponsorship Spanish of Economy, Industry and Competitiveness (MEIC) (BFU2016-75008-P, and PID2019-108322GB-100), “Fundación Vencer El Cancer” (VEC), the European Regional Development Fund (FEDER), and from AGAUR to L.D.C. The Ramon y Cajal program of the Ministerio de Ciencia, Innovación y Universidades and the European Social Fund under the reference number RYC-2018-025002-I, and the Instituto de Salud Carlos III-FEDER (PI19/01814), to S.A. We acknowledge the funding support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme / Generalitat de Catalunya.
- dc.format.mimetype application/pdf
- dc.identifier.citation Blanco E, Di Croce L, Aranda S. SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin. NAR Genom Bioinform. 2021;3(3):lqab064. DOI: 10.1093/nargab/lqab064
- dc.identifier.doi http://dx.doi.org/10.1093/nargab/lqab064
- dc.identifier.issn 2631-9268
- dc.identifier.uri http://hdl.handle.net/10230/49131
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof NAR Genom Bioinform. 2021;3(3):lqab064
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-75008-P
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-108322GB-100
- dc.rights © The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.title SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion