A simple ATAC-seq protocol for population epigenetics v1 (protocols.io.bae6ibhe)

protocols.io ◽  
2019 ◽  
Author(s):  
Ronaldo De ◽  
Aki MINODA ◽  
Christoph Grunau
Keyword(s):  
Population Epigenetics

scholarly journals Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Katarzyna Murat ◽  
Björn Grüning ◽  
Paulina Wiktoria Poterlowicz ◽  
Gillian Westgate ◽  
Desmond J Tobin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Methylation Analysis ◽  
Web Based ◽  
Array Platform ◽  
Complex Evaluation ◽  
The Galaxy ◽  
Population Epigenetics ◽  
Analyse Data ◽  
Dna Methylation Analysis

Abstract Background Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG locus in the human genome based on Illumina’s bead technology and is one of the most common techniques used in epigenome-wide association studies. Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850,000 CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured >450,000 and 27,000 loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable. Results We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy (http://galaxyproject.org), a web-based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. Conclusions The pipeline provides a group of integrated analytical methods wrapped into an easy-to-use interface. Our tool is available from the Galaxy ToolShed, GitHub repository, and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.

scholarly journals Population epigenetics, ecotoxicology and human diseases

2012 ◽  
Vol 10 (4) ◽  
pp. 14-28
Author(s):  
Eugene L Patkin ◽  
Henry A Sofronov
Keyword(s):  
Environmental Factors ◽  
Chemical Compounds ◽  
External Factors ◽  
Human Diseases ◽  
Epigenetic Mechanisms ◽  
Epigenetic Variability ◽  
Current State ◽  
Population Epigenetics

The review critically examines the current state of population epigenetics. Possible mechanisms of intergenerational inheritance of epigenetic and epigenomic modifications as a condition of population epigenetics reality are examined. Special attention is paid to the role of external factors, including diet and various chemical compounds as modulators of the epigenome, and the possible inheritance of epigenetic variability characteristics under the influence of such environmental factors. The role of epigenetic mechanisms in the etiology and susceptibility to complex human diseases is considered.

scholarly journals A simple ATAC-seq protocol for population epigenetics

2020 ◽  
Vol 5 ◽  
pp. 121
Author(s):  
Ronaldo de Carvalho Augusto ◽  
Aki Minoda ◽  
Christoph Grunau
Keyword(s):  
Molecular Biology ◽  
High Throughput ◽  
Biological Samples ◽  
High Throughput Sequencing ◽  
Population Epigenetics ◽  
Accessible Chromatin ◽  
Comparable Size

We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size, and it requires little molecular biology handling expertise.

Population Epigenetics

2015 ◽  
pp. 165-179 ◽  
Author(s):  
Christy M. Foust ◽  
Aaron W. Schrey ◽  
Christina L. Richards
Keyword(s):  
Population Epigenetics

scholarly journals A simple ATAC-seq protocol for population epigenetics

2021 ◽  
Vol 5 ◽  
pp. 121
Author(s):  
Ronaldo de Carvalho Augusto ◽  
Oliver Rey ◽  
Céline Cosseau ◽  
Cristian Chaparro ◽  
Jérémie Vidal-Dupiol ◽  
...  
Keyword(s):  
Molecular Biology ◽  
High Throughput ◽  
Chromatin Structure ◽  
Biological Samples ◽  
High Throughput Sequencing ◽  
Environmental Cues ◽  
Structure Changes ◽  
Population Epigenetics ◽  
Accessible Chromatin ◽  
Comparable Size

We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.

scholarly journals Population epigenetics

2017 ◽  
Vol 1 ◽  
pp. 84-89 ◽  
Author(s):  
John M. Greally
Keyword(s):  
Population Epigenetics

Population Epigenetics and Aging

2019 ◽  
pp. 75-87
Author(s):  
Carsten Carlberg ◽  
Ferdinand Molnár
Keyword(s):  
Population Epigenetics

Population epigenetics

2008 ◽  
Vol 18 (2) ◽  
pp. 221-226 ◽  
Author(s):  
Eric J Richards
Keyword(s):  
Population Epigenetics
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