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

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

ORGANISM(S): Mus musculus

PROVIDER: GSE137161 | GEO | 2022/02/02

REPOSITORIES: GEO

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

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

| PRJNA564683 | ENA

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

2022-02-02 | GSE137160 | GEO

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

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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 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]

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

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

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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

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

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

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

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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

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