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Mus musculus

ABSTRACT: Temporal DNA methylation analysis (RRBS) for differentiating mouse embryonic stem cells deficient for Zeb2

PROVIDER: PRJNA304746 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2969560_1.fastq.gz	Fastqsanger.gz
	SRR2969560_2.fastq.gz	Fastqsanger.gz
	SRR2969561_1.fastq.gz	Fastqsanger.gz
	SRR2969561_2.fastq.gz	Fastqsanger.gz
	SRR2969562_1.fastq.gz	Fastqsanger.gz

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Temporal DNA methylation analysis (RRBS) for differentiating mouse embryonic stem cells deficient for Zeb2

Project description:In this study we performed temporal profiling of DNA methylation by RRBseq of differentiating mouse embryonic stem cells using an embryoid body protocol. Analysis at d0, d4 and d6 revealed that Zeb2 deficient mESC lose their initially acquired DNA methylation at d6.

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Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

Project description:Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

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Project description:We report a time course of RNA-seq data from wild-type embryonic stem cells and embryonic stem cells in which the cardiogenic transcription factors ZNF503, ZEB2 and NKX2-5 are depleted with shRNAs differentiating along the cardiac lineage. Biological replicates of RNA-seq data from embryonic stem cells differentiating along the cardiac lineage.

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Ubiquitome analysis of UHRF1 and UHRF2-deficient mESCs

Project description:The E3 ligase UHRF1 is an essential epigenetic cofactor for DNMT1 dependent maintenance DNA methylation, which provides a binding platform for DNMT1 by both cooperative binding of histones and hemi-methylated DNA as well as by ubiquitinating histone H3. Here, we conduct a comprehensive screen to identify novel ubiquitination targets of UHRF1 and its paralogue UHRF2 by comparing the ubiquitome of wildtype (wt), UHRF1- and UHRF2-deficient mouse embryonic stem cells. With an antibody-dependent enrichment of ubiquitin remnant motif-containing peptides followed by isobaric-labeling based quantitative mass spectrometry, we find both known and novel E3 ligase substrates of UHRF1 involved in a variety of biological processes such as RNA processing, DNA methylation and DNA damage repair.

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Study of the impact of G9a on DNA methylation in mouse embryonic cells [seq]

Project description:We explored the role of the lysine-methyltrasferase G9a in the control of DNA methylation during mouse embryogenesis. We provide maps of cytosine methylation by MeDIP and RRBS in G9a-deficient mouse embryos and ES cells, as well as ChIP-Seq profiles for H3K9me2 in embryos and RNA-Seq expression profiles in G9a-deficient embryos.

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Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

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Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (RRBS)

Project description:In this study, we mapped modification of lysine 4 and lysine 27 of histone H3 genome-wide in a series of mouse embryonic stem cells (mESCs) varying in DNA methylation levels based on knock-out and reconstitution of DNA methyltransferases (DNMTs). We extend previous studies showing cross-talk between DNA methylation and histone modifications by examining a breadth of histone modifications, causal relationships, and direct effects. Our data shows a causal regulation of H3K27me3 at gene promoters as well as H3K27ac and H3K27me3 at tissue-specific enhancers. We also identify isoform differences between DNMT family members. This study provides a comprehensive resource for the study of the complex interplay between DNA methylation and histone modification landscape. Reduced representation bisulfite sequencing (RRBS) performed on wild-type, Dnmt triple knock-out (Dnmt1/3a/3b; TKO), Dnmt double knock-out (Dnmt3a/3b; DKO), and respective reconstitution mouse embryonic stem cell lines.

2016-08-02 | E-GEOD-84103 | biostudies-arrayexpress

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