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Bos taurus

ABSTRACT: Reduced representation bisulfite sequencing (RRBS) data from cattle monocytes, fibroblasts and sperm cells

PROVIDER: PRJNA396902 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5890540_1.fastq.gz	Fastqsanger.gz
	SRR5890540_2.fastq.gz	Fastqsanger.gz
	SRR5890541_1.fastq.gz	Fastqsanger.gz
	SRR5890541_2.fastq.gz	Fastqsanger.gz
	SRR5890542_1.fastq.gz	Fastqsanger.gz

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High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism

Project description:Dietary folate is a major source of methyl groups required for DNA methylation, an epigenetic modification that is actively maintained and remodelled during spermatogenesis. While high dose folic acid supplementation (up to ten times the daily recommended dose) has been shown to improve sperm parameters in infertile men, the effects of supplementation on the sperm epigenome are unknown. To assess the impact of six months of high dose folic acid supplementation on the sperm epigenome, we studied 30 men with idiopathic infertility. Blood folate concentrations increased significantly after supplementation with no significant improvements in sperm parameters. Methylation levels of the differentially methylated regions of several imprinted loci (H19, DLK1/GTL2, MEST, SNRPN, PLAGL1, KCNQ1OT1) were normal both before and after supplementation. Reduced representation bisulfite sequencing (RRBS) revealed a significant global loss of methylation across different regions of the sperm genome. The most marked loss of DNA methylation was found in sperm from patients homozygous for the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, a common polymorphism in a key enzyme required for folate metabolism. RRBS analysis also showed that most of the differentially methylated tiles were located in DNA repeats, low CpG density and intergenic regions. Ingenuity Pathway Analysis revealed that methylation of promoter regions was altered in several genes involved in cancer and neurobehavioral disorders including CBFA2T3, PTPN6, COL18A1, ALDH2, UBE4B, ERBB2, GABRB3, CNTNAP4 and NIPA1. Our data reveal alterations of the human sperm epigenome associated with high dose folic acid supplementation, effects that were exacerbated by a common polymorphism in MTHFR. Reduced representation bisulfite sequencing of 28 human sperm samples before and after 6 month of high dose folic acid supplementation.

2015-09-10 | E-GEOD-72606 | biostudies-arrayexpress

Chronic cadmium exposure induces differential methylation in mice spermatozoa

Project description:We used Reduced Representation Bisulfite Sequencing (RRBS) to comprehensively investigate the impact of chronic, low-dose Cd exposure on mice spermatozoa DNA methylation. Adult male C57BL/J6 mice were provided water with or without cadmium chloride. We purified genomic DNA from sperm samples collected after nine weeks of treatment. We found 1,788 differentially methylated sites present at regulatory regions in sperm of mice exposed to chronic, low-dose of Cd compared to vehicle (control) mice. Our results present a comprehensive analysis of the sperm methylome in response to chronic Cd exposure

2021-01-25 | GSE158455 | GEO

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation

Project description:To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family. Reduced representation bisulfite sequencing was applied to genomic DNA from leukocytes of 6 family members and two unrelated individuals.

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The Myonuclear DNA Methylome in Response to an Acute Hypertrophic Stimulus

Project description:We conducted reduced representation bisulfite sequencing (RRBS) on myonuclei and interstitial nuclei and observed stark differences in methylation patterns during adaptation

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Genome-scale DNA methylation maps of mouse chromaffin cells with or without Sdhb knock-out.

Project description:We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype. Reduced representation bisulfite sequencing of 4 mouse chromaffin cell samples (2 Sdhb wild-type and 2 Sdhb knock-out).

2013-05-06 | E-GEOD-44350 | biostudies-arrayexpress

Profiling the DNA methylation pattern in naïve induced Pluripotent Stem cells and somatic cells

Project description:We analysed by Reduced Representation Bisulfite Sequencing (RRBS) the genome methylation pattern in human fibroblast and in naïve induced pluripoent stem cells (niPSCs)

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Epigenome screen suggests DNA methylation may affect beef tenderness through signal transduction in Bos indicus

Project description:Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the genetic and epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs and deliver a better product quality to consumers. However, little is known about epigenetic effects in the muscle of Bos taurus and their implications in tenderness, and no studies have been conducted in Bos indicus. Therefore, we analyzed Reduced Representation Bisulfite Sequencing (RRBS) to search for differences in the methylation profile of Bos indicus skeletal muscle with extreme values for beef tenderness (tender = 6 animals, tough = 6 animals).

2022-05-27 | GSE190966 | GEO

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