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Mus musculus

ABSTRACT: Reduced Representation Bisulfite Sequencing in DNA methylation deficient mouse embryonic fibroblasts

PROVIDER: PRJNA191567 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR768243_1.fastq.gz	Fastqsanger.gz
	SRR768243_2.fastq.gz	Fastqsanger.gz
	SRR768244_1.fastq.gz	Fastqsanger.gz
	SRR768244_2.fastq.gz	Fastqsanger.gz
	SRR768245_1.fastq.gz	Fastqsanger.gz

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Mus musculus

Project description:Reduced Representation Bisulfite Sequencing in DNA methylation deficient mouse embryonic fibroblasts

| PRJNA191567 | ENA

Two distinct modes of DNMT1 recruitment ensure the stable maintenance DNA methylation

Project description:DNA methylation profiling by reduced representation bisulfite sequencing of PAF15KRKR and wild type mouse embryonic stem cells

2020-01-28 | E-MTAB-7930 | biostudies-arrayexpress

Comparison of genome-wide DNA methylation in MEFs derived from wildtype or estrogen receptor beta null mice using reduced representation bisulfite sequencing

Project description:Estrogen receptor beta (ERÎ²) is a ligand inducible transcription factor regulating gene expression in response to the female sex hormone estrogen. Previously, we found that ERÎ² deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERÎ² in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function. Using reduced representation bisulfite sequencing (RRBS), we compared genome-wide DNA methylation in mouse embryonic fibroblasts (MEFs) derived from wildtype (wt) and ERÎ² knock-out (Î²erko) mice, and identified around 8000 differentially methylated positions (DMPs). This suggests that ERÎ² is involved in regulating DNA methylation at specific sites in the genome. Genome-wide DNA methylation was analysed in MEFs derived from wildtype and ERbeta null mice by educed representation bisulfite sequencing (RRBS) on an Illumina Genome Analyser IIx platform.

2016-02-22 | E-GEOD-72230 | biostudies-arrayexpress

Mus musculus

Project description:mRNA-seq in DNA methylation deficient mouse embryonic fibroblasts

| PRJNA191560 | ENA

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

Mus musculus

Project description:Reduced representation bisulfite sequencing

| PRJNA347548 | ENA

Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

Project description:DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

2013-03-21 | E-GEOD-45361 | biostudies-arrayexpress

Mus musculus

Project description:Reduced representation bisulfite sequencing data of mouse genome

| PRJNA306687 | ENA

Using DNA methylation profiling to evaluate biological age and longevity interventions.

Project description:We utilized Reduced Representation Bisulfite Sequencing to profile DNA methylomes from whole blood of mice to develop a robust predictor of mouse biological aging. Based on DNA methylation profiles of mice from various ages, strains, genetic backgrounds, and diets, an aging methylation signature was observed and an epigenetic clock was created with elastic net linear regression. Profiles from fibroblasts and iPSCs showed that the aging clock can be reset.

2017-04-05 | GSE80672 | GEO

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

Project description:Purpose: The aim of this study was to determine the DNA methylation state of wildtype female mouse embryonic fibroblasts with nonsilencing shRNA mediated knockdown and Setdb1 geneTrap heterozygous cells with Setdb1 shRNA mediated knockdown. Methods: Enhanced Reduced Representation Bisulfite Libraries (eRRBS) were produced as previously descirbed (Akalin et al. 2012). Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads with dark cycle parameters (Boyle et al. 2012). Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data. Determine the DNA methylation state of mouse embryonic fibroblasts (MEFs) with wildtype MEFs and nonsilencing shRNA mediated knockdown or Setdb1 geneTrap heterozygous MEFs with Setdb1 shRNA mediated knockdown. Single-end with dark cycle protocol (Boyle et al. 2012)

2016-05-18 | E-GEOD-66524 | biostudies-arrayexpress

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