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Genome-wide transcriptome analysis of Esrrb wt and KO mouse embryonic stem cells, differentiated towards FS cells with AloXR protocol (Kinoshita et al., 2021)

ABSTRACT: Genome-wide transcriptome analysis of Esrrb wt and KO mouse embryonic stem cells, differentiated towards FS cells with AloXR protocol (Kinoshita et al., 2021)

PROVIDER: PRJNA860639 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20334800.fastq.gz	Fastqsanger.gz
	SRR20334801.fastq.gz	Fastqsanger.gz
	SRR20334802.fastq.gz	Fastqsanger.gz
	SRR20334803.fastq.gz	Fastqsanger.gz
	SRR20334804.fastq.gz	Fastqsanger.gz

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Genome-wide transcriptome analysis of Esrrb wt and KO mouse embryonic stem cells, differentiated towards FS cells with AloXR protocol (Kinoshita et al., 2021)

Project description:We report the application of genome-wide RNA-sequencing analysis for Esrrb WT and Esrrb KO mES cells after differentiation towards Formative Stem cells (FS cells). We find that expression of some formative genes was reduced in Esrrb KO cells compared to WT, and that lineage markers were significantly upregulated in Esrrb KO cells. This indicates that transition toward the formative state is impaired in Esrrb KO cells.

2023-01-25 | GSE208703 | GEO

Wound response in fs-THz-irradiated mouse skin

Project description:Terahertz (THz) technology has emerged for biomedical applications such as scanning, molecular spectroscopy, and medical imaging. However, the biological effect of THz radiation is not fully understood. Non-thermal effects of THz radiation were investigated by applying a femtosecond-terahertz (fs-THz) pulse to mouse skin. Analysis of the genome-wide expression profile in fs-THz-irradiated skin indicated that wound responses were predominantly through NF?B1- and Smad3/4-mediated transcriptional activation. Repeated fs-THz radiation delayed the closure of mouse skin punch wounds due to up-regulation of transforming growth factor-beta (TGF-?). These findings suggest that fs-THz radiation provokes a wound-like signal in skin with increased expression of TGF-? and activation of its downstream target genes, which perturbs the wound healing process in vivo. To identify non-thermally induced in vivo mode action of THz radiation, gene expression profile of fs-THz-irradiated skin (at post 24-hours after 1 hour exposure) was explored. Purified total RNAs from independent 3 mice of each sham and THz group were labeled and hybridized on the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA), according to manufacturer's standard protocol. Statistically filtered THz-responsive genes were examined for possible interactions with other molecules, canonical signaling pathways, and bio-functions.

2013-02-26 | E-GEOD-44671 | biostudies-arrayexpress

Wound response in fs-THz-irradiated mouse skin

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Issues with reporting and interpretation of Khan et al. 2021.

Project description: Not available

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Two isoforms of Fs(1)h ChIP-seq

Project description:ChIP-seq was performed using Drosophila Kc167 cells using antibodies against the two isoforms of Fs(1)h, the Brd4 homologue. Differences in binding patterns between the two isoforms are described. We examined the differences in Fs(1)h isoform binding across the genome and describe the short isoform to be correlated with transcription at enhancers and promoters. The long isoform is found predominately at insulator binding sites where multiple insulators are bound.

2012-11-15 | E-GEOD-42086 | biostudies-arrayexpress

Two isoforms of Fs(1)h ChIP-seq

2012-11-15 | GSE42086 | GEO

Reply to Soman et al, Alffenaar et al, Metcalfe et al, and Raoult.

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Global gene-expression analyses of the Esrrb knockdown cells

Project description:In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. These cells are also pluripotent and can differentiate in vitro and in vivo into the three major embryonic cell lineages. Furthermore, these cells contribute to mouse chimeras and are germline transmissible. In ES cells, Esrrb targets many genes involved in selfrenewal and pluripotency. This suggests that Esrrb may mediate reprogramming through the up-regulation of ES cell-specific genes. Our findings also indicate that it is possible to reprogram MEFs without exogenous Klf transcription factors and link a nuclear receptor to somatic cell reprogramming. Global gene expression effects of silencing the Esrrb gene. We used microarrays to detail the global programme of gene expression after silencing the Esrrb gene. Keywords: time-course Three biological replicates each for control GFP and Esrrb RNAi. The global gene expression profiles of the Esrrb knockdown cells were compared to control GFP knockdown cells for days 2, 4 and 6.

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UASB sludge FS sample

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Genome-wide transcriptome analysis of Esrrb WT and conditional Esrrb KO mouse embryonic stem cells

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2023-01-25 | GSE217802 | GEO

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