Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq in differentiating female FVBxCAST F1 ES cells with Smarcc1 gene knockdown [Female Smarcc1 RNA-seq]

ABSTRACT: Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test if X chromosome inactivation is altered upon Smarcc1 gene knockdown.

ORGANISM(S): Mus musculus

PROVIDER: GSE137160 | GEO | 2022/02/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

NOMe-seq in differentiating FVBxCAST F1 ES cells with Smarcc1 gene knockdown [NOMe-Seq]

Project description:Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test if nucleosome remodelling during X chromosome inactivation is altered upon Smarcc1 gene knockdown.

2022-02-02 | GSE137159 | GEO

RNA-seq in differentiating female FVBxCAST F1 ES cells with Smarca4 gene knockdown [Female Smarca4 RNA-seq]

Project description:Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test if X chromosome inactivation is altered upon Smarca4 gene knockdown.

2022-02-02 | GSE137162 | GEO

RNA-seq in differentiating Xmas cells ES cells [Xmas Differentiation RNA-seq]

Project description:Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test if Xmas ES cells are transcriptionally similar to published ES cell lines during differentiation.

2022-02-02 | GSE137156 | GEO

DNA-seq in male ES cells cultured by either standard ES cell culture or our improved culture conditions [Male DNA-seq]

Project description:Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test the effect of our improved ES culture conditions on the male ES cell karyotype.

2022-10-31 | GSE137158 | GEO

RNA-seq in male ES cells cultured by either standard ES cell culture or our improved culture conditions [Male RNA-seq]

Project description:Major complications with in vitro culture of female embryonic stem cells (ESC) have impeded study of sex-specific pluripotency; however, from the published work female pluripotency significantly differs to male. We report a replenishable female ESC system that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. To demonstrate the utility of the system, we screened for regulators of the female-specific process of X chromosome inactivation, revealing a new role for chromatin remodellers Smarcc1 and Smarca4 in establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation. This experiment is designed to test the effect of our improved ES culture conditions on the male ES cell transciptome.

2022-10-31 | GSE137157 | GEO

RNA-seq in differentiating female FVBxCAST F1 ES cells with Smarcc1 gene knockdown [Female Smarcc1 RNA-seq]

Project description:RNA-seq in differentiating female FVBxCAST F1 ES cells with Smarcc1 gene knockdown [Female Smarcc1 RNA-seq]

| PRJNA564681 | ENA

X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

Project description:During early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth and pluripotency exit largely independently of global DNA methylation. Our results uncover new insights into X-dosage in pluripotent stem cells, providing principles of how gene dosage modulates the epigenetic and genetic mechanisms regulating cell identity.

2018-03-31 | GSE110215 | GEO

XY female mice develop severe abdominal aortic aneurysms

Project description:Abdominal aortic aneurysms (AAAs) are a prevalent and deadly human pathology with strong sexual dimorphism. Research demonstrates that sex hormones influence, but do not fully explain, male versus female AAA pathology. In addition to sex hormones, the X and Y sex chromosomes, and their unique complements of genes, may contribute to sexually dimorphic AAA pathology. Here, for the first time, we defined the effect of female (XX) versus male (XY) chromosome complement on AAA formation and rupture in phenotypically female mice using an established murine model. Abdominal aortas from female mice bearing the XY chromosome selectively expressed Y chromosome genes, while genes known to escape X-inactivation were higher in XX females. The majority of gene differences in XY females fell within inflammatory pathways. When XY females were infused with AngII, AAA incidences doubled and aneurysms ruptured. AAAs from XY females exhibited significant inflammation. Moreover, infusion of AngII to XY females augmented aortic activity of matrix metalloproteinases. Finally, testosterone exposure applied chronically, or as a single bolus at postnatal day 1, markedly worsened AAA outcomes in XY compared to XX females. These results demonstrate that an XY sex chromosome complement profoundly influences aortic gene expression profiles and promotes AAA severity.

2016-11-07 | GSE81580 | GEO

RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of SWI/SNF complex

Project description:As one of the core components of the SWI/SNF complex, SMARCC1 (SAF155, SRG3) plays essential role in activation of the late inflammatory genes in response to microbial challenge. However, little is known about the mechanisms how SMARCC1 is regulated in innate response. Here, we identify for the first time that nuclear E3 ubiquitin ligase RNF138 acts as a critical negative regulator in inflammatory responses. RNF138 selectively interacts with SMARCC1 and mediates its K48-linked polyubiquitination at position Lys643 and proteasomal degradation. As a result, catalytic activity of RNF138 fine-tunes the kinetics of late inflammatory gene transcription by inhibiting persistent chromatin remodeling at SWI/SNF regulated gene loci. These results provide mechanistic insight into the interplay among nucleosome remodeling, inflammation and ubiquitylation, and underscore the critical role of the E3 ligases in controlling both extent and duration of inflammatory responses.

2023-02-11 | GSE207437 | GEO

RNA-seq in differentiating male C57/BL6 ES cells with Smarcc1 or Smarca4 gene knockdown [Male Smarc RNA-seq]

Project description:This experiment is designed to test if differentiation is altered upon depletion of either Smarcc1 or Smarca4

2022-02-02 | GSE137161 | GEO