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Alteration of miRNome and transcriptome by recombinant ncRNA agents

ABSTRACT: Alteration of miRNome and transcriptome by recombinant ncRNA agents

PROVIDER: PRJNA412644 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5995600.fastq.gz	Fastqsanger.gz
	SRR5995610.fastq.gz	Fastqsanger.gz
	SRR5995601.fastq.gz	Fastqsanger.gz
	SRR5995611.fastq.gz	Fastqsanger.gz
	SRR5995602.fastq.gz	Fastqsanger.gz

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Alteration of transcriptome by recombinant ncRNA agents

Project description:Alteration of transcriptome by recombinant ncRNA agents

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Alteration of miRNome by recombinant ncRNA agents

Project description:Purpose: Identify whether recombinant ncRNAs are recognized by mammalian cells and processed into mature microRNAs, thus leading to the alteration of downstream target genes. In addition, we also explored whether cleavage is Dicer dependent. Methods: HEK293T (Dicer-WT) and 424 (Dicer-KO) cell lines were treated with 20nM of control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-34a-3p in triplicate. Results: Read counts of known miRNAs were analyzed using a miRDeep module, and read counts derived from nCAR/miR-34a-5p or nCAR/miR-124a-3p transfection were obtained by mapping sequence reads by an in-house developed PERL script. EdgeR was used to analyze significant (P-value < 0.05 and log2CPM > 6) differentially expressed miRNAs and sRNAs. Conclusions: Upon transfection of recombinant RNA agents in mammalian cells, nCAR/miR-34a-5p became the most dominant miRNA and was processed in a Dicer dependent manner, while nCAR/miR-124a-3p become the 7th most abundant miRNA and displayed comparable levels with or without Dicer. In both cases, different isoforms of the mature miRNA sequence were generated.

2020-09-01 | GSE103349 | GEO

Alteration of transcriptome by recombinant ncRNA agents

Project description:Purpose: Identify whether recombinant ncRNAs are recognized by mammalian cells and processed into mature microRNAs, thus leading to the alteration of downstream target genes. In addition, we also explored whether the alteration of known or novel target genes are Dicer dependent. Methods: HEK293T (Dicer-WT) and 424 (Dicer-KO) cell lines were treated with 20nM of control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-34a-3p in triplicate. Results: Read counts of known mRNAs were analyzed using a RSEM-EdgeR workflow. Sequence reads were mapped to the human reference genome (hg19) by BWA, read counts for individual genes were computed using RSEM, and EdgeR was used to analyze significant (log2FC > 1.2 or log2FC < 0.8. P-value < 0.05 and log2CPM > 5) differentially expressed mRNAs. Conclusions: Upon transfection of recombinant RNA agents in mammalian cells, known and novel target genes were regulated in a Dicer dependent manner (nCAR/miR-34a-5p) and also in a Dicer independent manner (nCAR/miR-124a-3p).

2020-09-01 | GSE104442 | GEO

Homo sapiens

Project description:Alteration of miRNome by recombinant ncRNA agents

| PRJNA401884 | ENA

Alteration of miRNome and transcriptome by recombinant ncRNA agents

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-09-01 | GSE104445 | GEO

Microarray analysis of the wildtype and recombinant E. coli strain containing an ncRNA nfiS to H2O2 shock

Project description:The aim of this study was to investigate the expressional changes profiles of the wildtype and recombinant Escherichia coli strain which contains an non-coding RNA nfiS from the nitrogen-fixing Pseudomonas stutzeri A1501 after hydrogen peroxide shock, so as to lay a theoretical foundation for further clarifying the mechanism of this ncRNA to enhance the resistance ability of E.coli to oxidative stress. In our early research, an ncRNA named NfiS from the nitrogen fixing bacteria Pseudomonas stutzeri A1501 was identified to play an important role in the response to oxidative as well as osmotic stress. In this work, the nifS gene was transferred to E. coli Trans10. Heterologous expression of the nfiS in Trans10 enhanced its tolerance to salt stress and oxidative stress. To further study the effect of nfiS on gene expression in E. coli, microarray assay was performed to delineate the transcriptome difference between nfiS-expressing strain and wild type under H2O2 shock treatment.

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Healthy Antrum miRnome

Project description:Healthy Antrum miRnome

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Discovery of RUF6 ncRNA interacting proteins involved in P. falciparum immune evasion

Project description:RUF6 is a ncRNA gene family that is transcribed by RNA Polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connect to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including. Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique’s robustness for identifying ncRNA interactomes in P. falciparum. Our work identifies a RUF6 ncRNA protein complex that interacts with RNA Pol II to sustain var gene expression.

2022-11-15 | PXD036801 | Pride

Healing human gingiva miRNome

Project description:Healing human gingiva miRNome

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Genome-wide analysis of the circulating miRNome after cerebral ischemia reveals a reperfusion-induced microRNA cluster

Project description:Background and Purpose - Circulating microRNAs (miRNAs) are emerging biomarkers for stroke due to their high stability in the bloodstream and association with pathophysiologic conditions. However, the circulating whole-genome miRNAs (miRNome) has not been characterized comprehensively in the acute phase of stroke. Methods - We profiled the circulating miRNome in mouse models of acute ischemic and hemorrhagic stroke by next-generation sequencing (NGS). Stroke models were compared to sham-operated and naïve mice to identify deregulated circulating miRNAs. Top-ranked miRNAs were validated and further characterized by qRT-PCR. Results - We discovered 24 circulating miRNAs with an altered abundance in the circulation 3 hours following ischemia, whereas the circulating miRNome was not altered after intracerebral hemorrhage compared to sham-operated mice. Among the upregulated miRNA in ischemia, the top-listed miR-1264/1298/448 cluster was strongly dependent on reperfusion in different ischemia models. A time course experiment revealed that the miR-1264/1298/448 cluster peaked in the circulation around 3 hours after reperfusion and gradually decreased thereafter. Conclusions - Alteration of the miRNome in the circulation is associated with cerebral ischemia/reperfusion, but not hemorrhage, suggesting a potential to serve as biomarkers for reperfusion in the acute phase. The pathophysiological role of reperfusion-inducible miR-1264/1298/448 cluster, which is located on chromosome X within the introns of the serotonin receptor HTR2C, requires further investigation.

2016-12-31 | GSE84216 | GEO

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