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RNA sequencing LSK cells after Cxxc5 knockdown

ABSTRACT: RNA sequencing LSK cells after Cxxc5 knockdown

PROVIDER: PRJNA606512 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11079931.fastq.gz	Fastqsanger.gz
	SRR11079932.fastq.gz	Fastqsanger.gz
	SRR11079933.fastq.gz	Fastqsanger.gz
	SRR11079934.fastq.gz	Fastqsanger.gz
	SRR11079935.fastq.gz	Fastqsanger.gz

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RNA sequencing LSK cells after Cxxc5 knockdown

Project description:To study the effect of knockdown of Cxxc5 on stem/progenitor cells, we used retrovirus to knockdown Cxxc5 expression in the LSK cells. We used this as a surrogate to study the function of Cxxc5 in mouse/stem progenitor cells.

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LSK cells after Cxxc5 knockdown

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LSK cells after Cxxc5 knockdown

Project description:This SuperSeries is composed of the SubSeries listed below.

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Gene expression profiling of control cohesin knockdown LSK cells

Project description:We performed RNA-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for Renilla, Smc1a or Stag2. RNA-sequencing control (Renilla) and cohesin (Smc1a and Stag2) knockdown cells.

2015-09-16 | E-GEOD-72369 | biostudies-arrayexpress

CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells [RNA-seq]

Project description:Mammalian genomes encode a family of 12 proteins that contain a CXXC zinc finger domain. These domains are known to bind to unmethylated DNA sequences rich in CpG dinucleotides. Most members of this family are large multi-domain proteins that function in the control of DNA methylation and histone methylation patterns. CXXC5 is a smaller member of the family, along with its closest homologue CXXC4. These two proteins lack known catalytic domains. Here we have characterized CXXC5 in mouse embryonic stem (ES) cells. We show that CXXC5 is a nuclear protein that interacts with 5-methylcytosine oxidases (TET proteins). Removal of CXXC5 from ES cells leads to very few changes in gene expression. CXXC5 extensively colocalizes with TET1 and TET2 at CpG islands. CXXC5 inactivation leads to a substantial reduction of DNA methylation levels that affects all genomic compartments including genic and intergenic regions and CpG island shores. No hypermethylation of CpG islands was observed. We propose a model in which CXXC5 serves as an anchor for TET proteins at CpG islands. In the absence of CXXC5, the 5-methylcytosine oxidases become dislodged from CpG islands and are enabled to induce genome-scale DNA demethylation. Thus, CXXC5 serves as a stabilizer of DNA methylation patterns.

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CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells [Bisulfite-Seq]

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CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells [ChIP-Seq]

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