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Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [MeDIP-seq]

ABSTRACT: Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [MeDIP-seq]

PROVIDER: PRJNA477584 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7415210_1.fastq.gz	Fastqsanger.gz
	SRR7415210_2.fastq.gz	Fastqsanger.gz
	SRR7415211_1.fastq.gz	Fastqsanger.gz
	SRR7415211_2.fastq.gz	Fastqsanger.gz
	SRR7415212_1.fastq.gz	Fastqsanger.gz

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Transcriptome and 5mC/5hmC of Trophoblast Stem Cells

Project description:Transcriptome and 5mC/5hmC of Trophoblast Stem Cells

| PRJNA477583 | ENA

Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [RNA-seq]

Project description:Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [RNA-seq]

| PRJNA477561 | ENA

Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [MeDIP-seq]

Project description:RNA-seq of WT, Tet2-het and Tet2-KO mTSCs in stem-state, RNA-seq of WT and Tet2-KO mTSCs in vitro differentiation, (h)MeDIP of WT and Tet2-KO mTSCs in stem-state

2020-06-15 | GSE116184 | GEO

MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum

Project description:Genomic DNA was prepared, fragmented, and immunoprecipitated with antibodies specific for 5mC or 5hmC prior to standard sequencing. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency. There are two groups, A-T and Control. For each group, cerebellar DNA samples were immunoprecipitated with anti-5mC (n=1) or anti-5hmC (n=3). There were also two replicates of input control for each group.

2015-10-30 | E-GEOD-61133 | biostudies-arrayexpress

MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum

2015-10-30 | GSE61133 | GEO

Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [RNA-seq]

Project description:RNA-seq of WT, Tet2-het and Tet2-KO mTSCs in stem-state, RNA-seq of WT and Tet2-KO mTSCs in vitro differentiation, (h)MeDIP of WT and Tet2-KO mTSCs in stem-state

2020-06-15 | GSE116181 | GEO

Change of 5hmC and 5mC landscapes in A2058-TET2WT cells cultured in high-g and normal-g

Project description:We report that high glucose can have a detrimental effect on the stability of TET2 protein, and thereby reduce the genome-wide 5hmC content. We use MeDIP and hMeDIP followed by sequencing to identify the change of 5hmC and 5mC landscapes in A2058-TET2WT over expressing cells cultured in high and normal glucose concentrations.

2018-07-15 | GSE86375 | GEO

Methylome of 5mC and 5hmC regulated by NEIL2

Project description:To elucidate the role of DNA glycosylase NEIL2 in regulation of DNA methylome, we performed genome sequencing of epigenetic marker 5mC and 5hmC in genome-wide using enyme-based library methods of TAPS and CAPS. The 5mC and 5hmC profile in CpG contect was further extracted and analysed.

2023-12-13 | GSE240177 | GEO

TET1 and 5-hydroxymethylation preserve the stem cell state of mouse trophoblast

Project description:Analysis of 5mC and 5hmC and associated transcription in trophoblast stem cells cultured and differentiated at 20% and 5% oxygen, integrated with previously published datasets

2020-04-23 | GSE139049 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

Project description:Oxidative modification of 5-methylcytosine (5mC) by TET DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here we present Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from the mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multi-modal single-cell data integration, enable accurate identification of neuronal subtypes, and uncover context-specific regulatory effects of cell-type-specific genes by TET enzymes.

2023-07-14 | GSE236776 | GEO

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