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

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

PROVIDER: PRJNA564685 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10090669_1.fastq.gz	Fastqsanger.gz
	SRR10090669_2.fastq.gz	Fastqsanger.gz
	SRR10090670_1.fastq.gz	Fastqsanger.gz
	SRR10090670_2.fastq.gz	Fastqsanger.gz
	SRR10090671_1.fastq.gz	Fastqsanger.gz

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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 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

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

2022-02-02 | GSE137160 | GEO

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

Small RNAs in differentiating mouse ES cells

Project description:RNA-interference (RNAi) refers to a growing class of gene silencing phenomena defined by a requirement for small RNAs of 20-32 nt and the action of the Argonaute (Ago) family of ribonucleases. We have previously identified developmentally regulated small RNAs, using Northern blot analysis, that are expressed during X-chromosome inactivation in differentiating female mouse ES cels. We sought to identify these small RNAs using deep sequencing. We identified small RNAs that align to retrotransposon sequences and are enriched on the X-chromosome. LINE elements have been proposed to act as way stations during X-inactivation for the spreading of silencing along the entire chromosome, and our findings suggest that LINE elements found on the X-chromosome may be enriched for small RNAs relative to the genome. These results suggest that RNAi pathways are involved in regulating LINE elements during X-inactivation and ES cell differentiation. We size-fractionated total RNA from differentiating female mouse ES cells (day 4) into 18-24 nt and 25-45 nt populations and sequenced each fraction separately using the 454 platform. We used a karyotypically stable 40XX female ES cell line (EL16.7) with one X each of 129 and M. castaneus origins: 129 x (M.castaneus x 129).

2013-05-18 | E-GEOD-21888 | biostudies-arrayexpress

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

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

Project description:RNA-seq in differentiating Xmas cells ES cells [Xmas Differentiation RNA-seq]

| PRJNA564678 | ENA

Small RNAs in differentiating mouse ES cells

2013-05-18 | GSE21888 | 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

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