دورية أكاديمية
Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0.
| العنوان: | Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0. |
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| المؤلفون: | Dickson BM; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA. bradley.dickson@vai.org., Kupai A; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA., Vaughan RM; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA.; Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI, USA., Rothbart SB; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA. scott.rothbart@vai.org. |
| المصدر: | Scientific reports [Sci Rep] 2023 May 09; Vol. 13 (1), pp. 7508. Date of Electronic Publication: 2023 May 09. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : Nature Publishing Group, copyright 2011- |
| مواضيع طبية MeSH: | Nucleosomes*/genetics , Histone Code*, Chromatin Immunoprecipitation ; Chromatin Immunoprecipitation Sequencing ; Genomics |
| مستخلص: | We recently introduced an absolute and physical quantitative scale for chromatin immunoprecipitation followed by sequencing (ChIP-seq). The scale itself was determined directly from measurements routinely made on sequencing samples without additional reagents or spike-ins. We called this approach sans spike-in quantitative ChIP, or siQ-ChIP. Herein, we extend those results in several ways. First, we simplified the calculations defining the quantitative scale, reducing practitioner burden. Second, we reveal a normalization constraint implied by the quantitative scale and introduce a new scheme for generating 'tracks'. The constraint requires that tracks are probability distributions so that quantified ChIP-seq is analogous to a mass distribution. Third, we introduce some whole-genome analyses that allow us, for example, to project the IP mass (immunoprecipitated mass) onto the genome to evaluate how much of any genomic interval was captured in the IP. We applied siQ-ChIP to p300/CBP inhibition and compare our results to those of others. We detail how the same data-level observations are misinterpreted in the literature when tracks are not understood as probability densities and are compared without correct quantitative scaling, and we offer new interpretations of p300/CBP inhibition outcomes. (© 2023. The Author(s).) |
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| معلومات مُعتمدة: | F99 CA245821 United States CA NCI NIH HHS; K00 CA245821 United States CA NCI NIH HHS; R35 GM124736 United States GM NIGMS NIH HHS |
| المشرفين على المادة: | 0 (Nucleosomes) |
| تواريخ الأحداث: | Date Created: 20230510 Date Completed: 20230511 Latest Revision: 20240531 |
| رمز التحديث: | 20240531 |
| مُعرف محوري في PubMed: | PMC10169836 |
| DOI: | 10.1038/s41598-023-34430-2 |
| PMID: | 37160995 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 2045-2322 |
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| DOI: | 10.1038/s41598-023-34430-2 |