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Grant support

Spanish of Economy, Industry and Competitiveness (MEIC) (BFU2016-75008-P, and PID2019-108322GB-100), "Fundacion 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, Innovacion y Universidades and the European Social Fund under the reference numberRYC-2018-025002-I, and the Instituto de Salud Carlos III-FEDER (PI19/01814), to S.A. We acknowledge the funding support of the SpanishMinistry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya.

Analysis of institutional authors

Blanco, EnriqueAuthorDi Croce, LucianoCorresponding AuthorAranda SCorresponding Author
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Article

SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin

Publicated to:Nar Genom Bioinform. 3 (3): lqab064- - 2021-09-01 3(3), DOI: 10.1093/nargab/lqab064

Authors: Blanco, E; Di Croce, L; Aranda, S

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Dr Aiguader 88, Barcelona 08003, Spain - Author
Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain. - Author
Inst Catalana Recerca & Estudis Avancats ICREA, Pg Lluis Co 23, Barcelona 08010, Spain - Author
Univ Pompeu Fabra UPF, Barcelona 08002, Spain - Author

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).© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

Keywords
encyclopediaArticleCabotegravirChromatinChromatin immunoprecipitation sequencingControlled studyDna elementsDrosophila melanogasterEstrogen receptor alphaFulvestrantGenome-wide association studyHistone h3HumanHuman cellHuman genomeInsect genomeJurkat cell lineLysineNoiseNonhistone proteinNonhumanPinometostatSpikeTranscription factor

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nar Genom Bioinform, Q4 Agency Scopus (SJR), its regional focus and specialization in Genetics, give it significant recognition in a specific niche of scientific knowledge at an international level.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 1.8, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions May 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-05-02, the following number of citations:

  • WoS: 6
  • Scopus: 7
  • Europe PMC: 4
  • OpenCitations: 7
Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-05-02:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 40.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 40 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 9.35.
  • The number of mentions on the social network X (formerly Twitter): 17 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (BLANCO GARCÍA, ENRIQUE) and Last Author (ARANDA ARAGÓN, SERGIO).

the authors responsible for correspondence tasks have been DI CROCE, LUCIANO and ARANDA ARAGÓN, SERGIO.