Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of Dnmt3a/3b transient silencing in WT iPSCs and comparison with miR-203 tKI iPSCs

ABSTRACT: Effect of Dnmt3a/3b transient silencing in WT iPSCs and comparison with miR-203 tKI iPSCs

PROVIDER: PRJNA412165 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6076840.fastq.gz	Fastqsanger.gz
	SRR6076841.fastq.gz	Fastqsanger.gz
	SRR6076834.fastq.gz	Fastqsanger.gz
	SRR6076835.fastq.gz	Fastqsanger.gz
	SRR6076836.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Effect of Dnmt3a/3b transient silencing in WT iPSCs and comparison with miR-203 tKI iPSCs

Project description:The balance between pluripotency and differentiation is critical during development and regeneration. miR-203 is a microRNA previously involved in differentiation of different tissues as well as in tumor suppression in multiple malignancies. We have shown that miR-203 is able to promote differentiation of embryonic stem (ES) and induced pluripotent stem (iPS) cells without decreasing pluripotency. We have observed that transient expression of miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to inducing complex embryo-like structures when these pluripotent cells are injected in mice. Mechanistically, we have shown that miR-203 mediates such effects, at least in part, by modulating the levels of de novo DNA methyltransferases. In the present RNAseq we have transiently silenced the levels of DNMT3a/3b in order to compare their transcriptomic profile with that observed in PSCs transiently exponed to miR-203.

2020-07-05 | GSE104250 | GEO

Effect of miR-203 on the transcriptomic profile of IPSCs and IPSC-derived teratomas

Project description:The balance between pluripotency and differentiation is critical during development and regeneration. miR-203 is a microRNA previously involved in differentiation of different tissues as well as in tumor suppression in multiple malignancies. We have shown that miR-203 is able to promote differentiation of embryonic stem (ES) and induced pluripotent stem (iPS) cells without decreasing pluripotency. We have observed that transient expression of miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to inducing complex embryo-like structures when these pluripotent cells are injected in mice. In the present RNA seq, we intend to analyze the trascriptomic profile of WT IPSCs, compared to miR-203 KO IPSCs and miR-203 tKI IPSCs (in which we have induced a transient over-expression of miR-203). Moreover, we analyze the mRNA profiles of the teratomas derived from those IPSCs.

2020-07-05 | GSE81133 | GEO

Bulk RNA sequencing to characterize female hES cells with null DNMT3A/3B deletion

Project description:Bulk RNA sequencing to characterize female hES cells with null DNMT3A/3B deletion and WT cells.

2022-10-05 | GSE186124 | GEO

Targeted disruption of DNMT1, 3A and 3B in human embryonic stem cells [DNMT3A/3B DKO]

Project description:DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing. Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets. RRBS methylation profiling of DNMT3A/3B DKO human ES cells

2015-03-30 | E-GEOD-63280 | biostudies-arrayexpress

Time course of the miR-203 effect on the transcriptomic profile of IPSCs

Project description:The balance between pluripotency and differentiation is critical during development and regeneration. miR-203 is a microRNA previously involved in differentiation of different tissues as well as in tumor suppression in multiple malignancies. We have shown that miR-203 is able to promote differentiation of embryonic stem (ES) and induced pluripotent stem (iPS) cells without decreasing pluripotency. We have observed that transient expression of miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to inducing complex embryo-like structures when these pluripotent cells are injected in mice. In the present RNA seq, we intend to analyze the trascriptomic profile of WT IPSCs transiently treated with DOX to induce miR-203. We analyzed the transcriptomic profile at different time points before and after the induction.

2020-07-05 | GSE86794 | GEO

Reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines.

Project description:To better characterize the effects of USP7 on DNA methylation, we performed reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines. RRBS analysis showed increased DNA methylation in USK7-KO cells and loss of USP7 elevates DNA methylation on pre-existing sites and de novo methylation.

2020-09-07 | GSE136159 | GEO

TKI

Project description:TKI

| PRJEB37289 | ENA

Enhanced Pluripotent Cell Function through miR-203-mediated Control of DNA Methylation

Project description:Maintaining a full differentiation potential along self-renewal ability is a major property of stem cells during development and regeneration. miR-203 is a microRNA previously involved in skin differentiation and tumor suppression. We show here that transient expression of miR-203 enhances the potential of embryonic (ESC) and induced pluripotent stem cells (iPSC) in contributing to multiple lineages without decreasing their self-renewal properties. In fact, miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to improving the generation of complex teratomas and embryo-like structures in vivo. These effects are mediated by the direct miR-203-dependent repression of de novo DNA methyltransferases Dnmt3a and Dnmt3b, leading to genome-wide demethylation of pluripotent cells. Transient exposure to miR-203 improves functional differentiation and maturation of pluripotent cells into cardiomyocytes in a Dnmt3a/b-dependent manner, suggesting the possible therapeutic uses of this microRNA in regenerative medicine.

2020-07-05 | GSE86899 | GEO

Dnmt3a and Dnmt3b-mediated decommissioning of fetal enhancers linked to kidney disease

Project description:Cytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation. We generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells (Six2Cre Dnmt3a/3b) and kidney tubule cells (KspCre Dnmt3a/3b). We characterized KspCre Dnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing and RNA sequencing were performed on whole-kidney samples and isolated renal tubule cells. KspCre Dnmt3a/3b mice showed no obvious morphologic and functional alterations at baseline. Knockout animals exhibited increased resistance to cisplatin-induced kidney injury, but not to folic acid–induced fibrosis. Whole-genome bisulfite sequencing indicated that Dnmt3a and Dnmt3b play an important role in methylation of gene regulatory regions that act as fetal-specific enhancers in the developing kidney but are decommissioned in the mature kidney. Loss of Dnmt3a and Dnmt3b resulted in failure to silence developmental genes. We also found that fetal-enhancer regions methylated by Dnmt3a and Dnmt3b were enriched for kidney disease genetic risk loci. Methylation patterns of kidneys from patients with CKD showed defects similar to those in mice with Dnmt3a and Dnmt3b deletion. Our results indicate a potential locus-specific convergence of genetic, epigenetic, and developmental elements in kidney disease development.

2020-03-03 | GSE134267 | GEO

Transcriptome analysis in DNMT3A and 3B mutant female human pluriopotent stem cells.

Project description:Transcriptome analysis in DNMT3A and 3B mutant female human pluriopotent stem cells.

| PRJNA673224 | ENA