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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

ABSTRACT: Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

PROVIDER: PRJNA603745 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10984944.fastq.gz	Fastqsanger.gz
	SRR10984945.fastq.gz	Fastqsanger.gz
	SRR10984946.fastq.gz	Fastqsanger.gz
	SRR10984947.fastq.gz	Fastqsanger.gz
	SRR10984948.fastq.gz	Fastqsanger.gz

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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

Project description:Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

Project description:Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

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Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation.

Project description:The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.

| S-EPMC7040006 | biostudies-literature

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]

Project description:Functional analysis of transcriptome (mRNA and microRNA) and proteome formation during treatment of cord-blood derived stem cell lines (USSC) with retinoic acid-containing XXL-medium to estimate the impact of microRNAs on final proteome.

2020-03-09 | GSE144465 | GEO

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

2020-03-09 | GSE144464 | GEO

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

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2020-03-09 | GSE144466 | GEO

Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process.

Project description:Plant regeneration via somatic embryogenesis is time-consuming and highly genotype-dependent. The plant somatic embryogenesis process provokes many epigenetics changes including DNA methylation and histone modification. Recently, an elite cotton Jin668, with an extremely high regeneration ability, was developed from its maternal inbred Y668 cultivar using a Successive Regeneration Acclimation (SRA) strategy. To reveal the underlying mechanism of SRA, we carried out a genome-wide single-base resolution methylation analysis for nonembryogenic calluses (NECs), ECs, somatic embryos (SEs) during the somatic embryogenesis procedure and the leaves of regenerated offspring plants. Jin668 (R4) regenerated plants were CHH hypomethylated compared with the R0 regenerated plants of SRA process. The increase in CHH methylation from NEC to EC was demonstrated to be associated with the RNA-dependent DNA methylation (RdDM) and the H3K9me2-dependent pathway. Intriguingly, the hypomethylated CHH differentially methylated regions (DMRs) of promoter activated some hormone-related and WUSCHEL-related homeobox genes during the somatic embryogenesis process. Inhibiting DNA methylation using zebularine treatment in NEC increased the number of embryos. Our multi-omics data provide new insights into the dynamics of DNA methylation during the plant tissue culture and regenerated offspring plants. This study also reveals that induced hypomethylation (SRA) may facilitate the higher plant regeneration ability and optimize maternal genetic cultivar.

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