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Deep sequencing identifies PD0325901 modulated microRNAs in the J1 mESCs

ABSTRACT: PD0325901 is involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC). However, the knowledge about this small molecule regulating miRNAs in ESC was limited. To understand the role of miRNAs during PD03-induced ESC maintenance and gain an insight how PD0325901 regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. The data show the miRNAs regulated by PD0325901.

ORGANISM(S): Mus musculus

PROVIDER: GSE67570 | GEO | 2016/05/17

SECONDARY ACCESSION(S): PRJNA280279

REPOSITORIES: GEO

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Deep sequencing identifies PD0325901 modulated microRNAs in the J1 mESCs

Project description:PD0325901 is involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC). However, the knowledge about this small molecule regulating miRNAs in ESC was limited. To understand the role of miRNAs during PD03-induced ESC maintenance and gain an insight how PD0325901 regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. The data show the miRNAs regulated by PD0325901. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with PD0325901 for 24 hours, J1 treated with DMSO was set as control. Then total RNA was extracted for analysis.

2016-05-17 | E-GEOD-67570 | biostudies-arrayexpress

Deep sequencing identify small molecule modulated microRNAs in the J1 mESCs

Project description:Many small molecular compounds reported were involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC), including BIO, CHIR99021 (CHIR), and vitamin C et al. However, the knowledge about these small molecules regulating miRNAs in ESC was limited. To understand the role of miRNAs during small molecules induced ESC maintenance and gain an insight how these small molecules regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment.The data show the miRNAs regulated by SB431542

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Deep sequencing identifies small molecule modulated microRNAs in the J1 mESCs

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Identifying PD0325901-regulated genes in the J1 mESCs

Project description:It has been demonstrated that PD0325901 promotes self-renewal of mouse embryonic stem cells, however, the target genes of PD0325901 are not fully understood. To better understand the downstream target genes of PD0325901, we performed Microarray analyses to identify their downstream targets. The data show the genes regulated by PD0325901.

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Identifying PD0325901-regulated genes in the J1 mESCs

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Identifying SC1-regulated miRNAs in the J1 mESCs

Project description:It has been demonstrated that SC1 (Pluripotin) promotes self-renewal of mouse embryonic stem cells. To better understand miRNAs regulated by SC1 directly or indirectly in mouse embryonic stem cells, we performed next generation sequencing (NGS) to identify small RNAs with expression changes after SC1 treatment.

2017-10-23 | GSE103015 | GEO

Hatching is modulated by microRNA-378a-3p derived from extracellular vesicles secreted by blastocysts (miRNA)

Project description:The current study is focused on Isolating EVs and their cargo content (miRNAs) from culture medium conditioned by individual embryos that can differentiate between the blastocyst and non-blastocyst embryos. We were able to isolate EVs from both blastocyst and non-blastocyst group with size exclusion chromatography (Izon’s™ qEV single column) and characterize them with Western blotting, nanoparticle tracking analysis, and Transmission electron microscopy. Further, we could isolate total RNA (including small RNAs) from the blastocyst and non-blastocyst EVs for miRNA sequencing.

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Effect of PD0325901 on gene expression during inner ear organoids differentiation

Project description:To determine the mechanism through which PD0325901(PD) promotes inner ear hair cells generation, we cultured the inner ear organoids in 1 μM PD or the same volume of DMSO for 10 days, after which we used RNA-seq to establish a database to analyze differentially expressed genes .

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Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of Trophoblast Stem Cells

Project description:Derivation and maintenance of TS cells depends on the presence of Fgf signalling. Numerous gene knock-out experiments identified the mitogen activated kinase Mek/Erk branch of the Fgf signalling pathway as predominantly active in both TS cells and extraembryonic ectoderm. Therefore, we tested changes in expression of the key TS cell transcription factors (TFs) upon Mek/Erk inhibition using the Mek inhibitor PD0325901 (“PD03”). To obtain an unbiased genome-wide coverage of the immediate-early response genes of Mek inhibition in TS cells, we performed RNA-seq analysis after 3h and 24h of PD03 treatment. Notably, of the known TS cell TFs, this analysis confirmed Esrrb as the earliest, most rapidly silenced gene upon PD03 treatment. In order to gain first insights into which genes may be primary targets of Esrrb, we treated TS cells with the synthetic nonsteroidal estrogen diethylstilbestrol (DES), an estrogen-related receptor (Err) antagonist and also performed RNA-seq upon short (24h) and prolonged (4d) DES treatment. Finally, to obtain a comprehensive global overview of the binding sites of Esrrb in TS cells, and of its interaction with Lsd1 and Nr0b1 (Dax1), we performed chromatin immunoprecipitation (ChIP)-seq experiments on these factors.

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Palbociclib, PD0325901 and combination treatment induced gene expression in DLD1

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