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Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

ABSTRACT: Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

PROVIDER: PRJNA205186 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR867069_1.fastq.gz	Fastqsanger.gz
	SRR867069_2.fastq.gz	Fastqsanger.gz
	SRR867070_1.fastq.gz	Fastqsanger.gz
	SRR867070_2.fastq.gz	Fastqsanger.gz
	SRR867071_1.fastq.gz	Fastqsanger.gz

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Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.

Project description:DNA methylation is crucial for a wide variety of biological processes, yet no technique suitable for the methylome analysis of DNA methylation at single-cell resolution is available. Here, we describe a methylome analysis technique that enables single-cell and single-base resolution DNA methylation analysis based on reduced representation bisulfite sequencing (scRRBS). The technique is highly sensitive and can detect the methylation status of up to 1.5 million CpG sites within the genome of an individual mouse embryonic stem cell (mESC). Moreover, we show that the technique can detect the methylation status of individual CpG sites in a haploid sperm cell in a digitized manner as either unmethylated or fully methylated. Furthermore, we show that the demethylation dynamics of maternal and paternal genomes after fertilization can be traced within the individual pronuclei of mouse zygotes. The demethylation process of the genic regions is faster than that of the intergenic regions in both male and female pronuclei. Our method paves the way for the exploration of the dynamic methylome landscapes of individual cells at single-base resolution during physiological processes such as embryonic development, or during pathological processes such as tumorigenesis.

| S-EPMC3847781 | biostudies-literature

Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

Project description:We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes. In total, 36 samples were analyzed, including 8 single mouse embryonic stem cells (mESCs), pooled-5, 10, 20 mESCs, bulk mESCs, 7 single sperms, 10 single pronuclei from 5 individual zygotes, 2 metaphase II oocytes, 2 the first polar bodies and 3 negative controls.

2013-08-31 | E-GEOD-47343 | biostudies-arrayexpress

Reduced representation bisulfite sequencing of equine tissue

Project description:Reduced representation bisulfite sequencing of equine tissue

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Reduced Representation Bisulfite Sequencing analysis of human necrotizing enterocolitis

Project description:Reduced Representation Bisulfite Sequencing was used to assess that changes in intestinal DNA methylation associated with NEC outbreak.

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Reduced representation bisulfite sequencing of equine tissue

Project description:The aim of the project was to identify the tissue-specific DNA methylation patterns of selected horse tissues, derived from two germ layers, endodermal (liver and lung) and mesenchymal (cardiac striated muscle) origin. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique.

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Reduced Representation Bisulfite Sequencing analysis of human necrotizing enterocolitis

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Reduced representation bisulfite sequencing of cadmium-exposed mouse placentas

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Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

Project description:We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes.

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Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.

Project description:Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.

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Reduced Representation Bisulfite Sequencing from HD knock-in mouse model

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2020-07-02 | GSE147156 | GEO

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