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

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

PROVIDER: PRJNA564680 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10090548.fastq.gz	Fastqsanger.gz
	SRR10090549.fastq.gz	Fastqsanger.gz
	SRR10090550.fastq.gz	Fastqsanger.gz
	SRR10090551.fastq.gz	Fastqsanger.gz
	SRR10090552.fastq.gz	Fastqsanger.gz

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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

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

2022-10-31 | GSE137158 | GEO

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

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

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Expression profile of MEFs, iPS, and ES in different culture condition

2010-10-27 | GSE24861 | 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

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

Effect of Tet1-knockdown on gene expression in mouse ES cells cultured in ES and TS cell culture conditions

Project description:TET-family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem (ES) cells. ES cells depleted of Tet1 by RNAi show diminished expression of the Nodal antagonist Lefty1, and display hyperactive Nodal signalling and skewed differentiation into the endoderm-mesoderm lineage in embryoid bodies in vitro. In Fgf4- and heparin-supplemented culture conditions that favor derivation of trophoblast stem (TS) cells, Tet1-depleted ES cells activate the trophoblast stem cell lineage determinant Elf5 and can colonize the placenta in mid-gestation embryo chimeras. Consistent with these findings, Tet1-depleted ES cells form aggressive hemorrhagic teratomas with increased endoderm, reduced neuroectoderm and ectopic appearance of trophoblastic giant cells. Thus Tet1 functions to regulate the lineage differentiation potential of ES cells. Here, we performed whole-genome transcriptome profiling of ES cells stably depleted of Tet1 by shRNA knockdown (Tet1-kd) cultured in either standard ES cell or in TS cell culture conditions. Gene expression changes in Tet1-kd ES cells were fairly modest compared to control (GFP-kd) cells, although gene ontology (GO) analysis of differentially expressed genes yielded many terms related to embryonic development and cell cycle regulation. In TS cell culture conditions, a core set of genes defining trophectodermal cell differentiation, including Cdx2, Eomes and Tead4, was enriched in Tet1-kd compared to GFP-kd cells.

2011-02-07 | GSE26900 | GEO

RNA-seq in Smchd1 wild-type and Smchd1 deleted differentiating male ES cells.

Project description:RNA-seq in Smchd1 wild-type and Smchd1 deleted differentiating male ES cells.

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Maintenance of undifferentiated mouse ES cells in suspension by the serum and feeder-free defined culture condition

Project description:Mouse embryonic stem (ES) cells are indispensable for gene targeting approaches to study gene functions and regulations, the production of animal models for human diseases, and in vitro cell differentiation studies. The proven pluripotency of ES cells is expected to allow their therapeutic use for regenerative medicine. We present here a novel suspension culture method that facilitates the proliferation of pluripotent ES cells without feeder cells. The culture medium is free of either animal-derived or synthetic serum, and contains very low amounts of peptidic or proteinaceous materials, which are favorable for therapeutic use. ES cells showed sustained proliferation in the suspension culture, and their undifferentiated state and pluripotency were experimentally verified. DNA microarray analyses showed a close relationship between the elevated expression of genes related to cell adhesions and activation of the WNT signaling pathway. We suggest that this suspension culture condition provides a better alternative to the conventional attached cell culture condition, especially for possible therapeutic use, by limiting the exposure of ES cells to feeder cells and animal products. Keywords: reference design,replicate design

2008-09-02 | GSE9022 | GEO

Expression profile of MEFs, iPS, and ES in different culture condition

Project description:MEFs can be reprograming to ES by defined reprogramming factors, the derived ES-like cells were termed iPSc. Completely reprogrammed iPSc have identifed gene expression profle with ES. Culture condition may influent the pluripotency of iPSCs.iPS/ES cultured in differient ES medium may have different gene expression profile. We preform an experiment to analyze the gene expression difference among MEFs cultured in FBS and iCD1,iPSc cultured in KSR medium and N2B27 supplementary with 2i medium , and ES cultured in N2B27 supplementary with 2i medium.

2010-10-27 | E-GEOD-24861 | biostudies-arrayexpress

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