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Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
Citation
Statham, AL and Taberlay, PC and Kelly, TC and Jones, PA and Clark, SJ, Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines, Genomics Data, 3 pp. 94-96. ISSN 2213-5960 (2015) [Refereed Article]
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Copyright Statement
Copyright 2014 The Authors Licenced under the CC BY-NC-ND license http://creativecommons.org/licenses/by-nc-nd/4.0/
DOI: doi:10.1016/j.gdata.2014.11.012
Abstract
DNA methylation and nucleosome positioning are two key mechanisms that contribute to the epigenetic control of gene expression. During carcinogenesis, the expression of many genes is altered alongside extensive changes in the epigenome, with repressed genes often being associated with local DNA hypermethylation and gain of nucleosomes at their promoters. However the spectrum of alterations that occur at distal regulatory regions has not been extensively studied. To address this we used Nucleosome Occupancy and Methylation sequencing (NOMe-seq) to compare the genome-wide DNA methylation and nucleosome occupancy profiles between normal and cancer cell line models of the breast and prostate. Here we describe the bioinformatic pipeline and methods that we developed for the processing and analysis of the NOMe-seq data published by (Taberlay et al., 2014 [1]) and deposited in the Gene Expression Omnibus with accession GSE57498.
Item Details
| Item Type: | Refereed Article |
|---|---|
| Keywords: | Bioinformatics, DNA methylation, nucleosome positions, histone modifications |
| Research Division: | Biological Sciences |
| Research Group: | Bioinformatics and computational biology |
| Research Field: | Bioinformatic methods development |
| Objective Division: | Health |
| Objective Group: | Clinical health |
| Objective Field: | Clinical health not elsewhere classified |
| UTAS Author: | Taberlay, PC (Associate Professor Phillippa Taberlay) |
| ID Code: | 101261 |
| Year Published: | 2015 |
| Deposited By: | Medicine |
| Deposited On: | 2015-06-15 |
| Last Modified: | 2017-11-02 |
| Downloads: | 339 View Download Statistics |
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