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RNA-seq of mouse embryonic stem cells with Ronin/Thap11 knockout

ABSTRACT: RNA-seq of mouse embryonic stem cells with Ronin/Thap11 knockout

PROVIDER: PRJEB42573 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5165860.fastq.gz	Fastqsanger.gz
	ERR5165861.fastq.gz	Fastqsanger.gz
	ERR5165862.fastq.gz	Fastqsanger.gz
	ERR5165863.fastq.gz	Fastqsanger.gz
	ERR5165864.fastq.gz	Fastqsanger.gz

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RNA-seq of mouse embryonic stem cells with Ronin/Thap11 knockout

Project description:RNA-seq of Ronin/Thap11 knockout and heterozygous control mouse ES cells to assess the role of Ronin

2022-01-31 | E-MTAB-10024 | biostudies-arrayexpress

Genome-wide occupancy profiling of Ronin (Thap11) in retinal development

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Analysis of Ronin knockout related gene expression changes in mouse embryonic stem cells.

Project description:Ronin knockout is embryonic lethal and Ronin knockout ES cells are not viable. Here we used CreER2; Roninflox/flox mouse ES cells to induce Ronin knockout by tamoxfien treatment in comparison to control Roninflox/flox cells to study Ronin knockout related transcriptional changes.

2018-09-16 | GSE120008 | GEO

Gene expression profile in Ronin (Thap11) conditional knock out retina through RNA-sequencing

Project description:Conditional knockout of the transcription factor Ronin (Thap11) in retinal progenitor cells (RPCs) results in a profound failure cell proliferation resulting in a hypoplastic adult retina that also suffers from photoreceptor degeneration. The goal of this study was to determine which genes are deregulated in response to loss of Ronin transcription factor activity in the developing retina. We generated Ronin flox/flox (Control) and Chx10-Cre::GFP+/tg; Ronin flox/flox (CKO) mice, in which Ronin loss occurs specifically within RPCs, and performed RNA-Seq analysis of embryonic day E14.5 (E14.5) retinae. Three independent pools of control and Ronin CKO retinae were collected consisting of a minimum of 10 retinae per pool and total RNA was extracted followed by polyA selection, fractionation (200-500 nucleotide range) and generation of cDNA. The resulting DNA was then used for standard Illumina adaptor ligation and sequencing. This experiment revealed decreased expression of a large group of mitochondrial genes including components of the electron transport chain (ETC), which have been recently implicated as direct regulators of the cell cycle.

2016-01-19 | GSE74822 | GEO

Analysis of Ronin knockout related gene expression changes in mouse embryonic stem cells.

Project description:Analysis of Ronin knockout related gene expression changes in mouse embryonic stem cells.

| PRJNA491281 | ENA

Ronin governs early heart development by controlling core gene programs

Project description:Ronin (THAP11), an idiosyncratic DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence through which it controls a variety of developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions elsewhere in development. Here, we present evidence indicating that Ronin performs a novel function within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation through its control of a core set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me3 levels at specific target genes, suggesting the involvement of an epigenetic mechanism. On the strength of these findings, we propose that Ronin activity during cardiogenesis may offer a template that could be used to understand how important gene programs are sustained across different cell types within a developing organ, such as the heart.

2017-09-19 | GSE103959 | GEO