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ShRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq]

ABSTRACT: shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq]

PROVIDER: PRJNA1007668 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25711970.fastq.gz	Fastqsanger.gz
	SRR25711971.fastq.gz	Fastqsanger.gz
	SRR25711972.fastq.gz	Fastqsanger.gz
	SRR25711973.fastq.gz	Fastqsanger.gz
	SRR25711974.fastq.gz	Fastqsanger.gz

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shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production

Project description:shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production

| PRJNA1007655 | ENA

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq PC-3]

Project description:shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq PC-3]

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shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [mRNA-seq]

Project description:shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [mRNA-seq]

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shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [DU-145 cells]

Project description:shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [DU-145 cells]

| PRJNA1041356 | ENA

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq]

Project description:miRNA overexpression strategy based on RNA Polymerase (Pol) III mediated expression of short hairpin RNA (shRNA) coding particular miRNA is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that extra \texttt{U} residues (up to five) added Pol III at the 3$'$-end of the transcribed shRNA associated with a shift in the Dicer cleavage position of the shRNA. This results in the undesirable formation of 5$'$-end miRNA isoforms (5$'$-isomiRs), which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. The predominant expression of 5$'$-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5$'$-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved.

2023-08-22 | GSE241301 | GEO

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [mRNA-seq]

2023-08-22 | GSE241300 | GEO

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq PC-3]

2024-04-17 | GSE264166 | GEO

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [DU-145 cells]

2023-11-17 | GSE247987 | GEO

shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production

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

2023-08-21 | GSE241303 | GEO

Effect of pre-miR-1307 overexpression on isomiR levels in MDA-MB-231 breast cancer cells

Project description:In the recent past, the impact of isomiR expression changes in cancer has gained increasing interest. Here, we stably overexpress pre-miR-1307, a pre-miRNA which is frequently upregulated in cancer, and assess the effect on isomiR expression. While we see robust and significant upregulation of the canonical form miR-1307-3p|0 and its abundant 5'isomiR miR-1307-3p|1, as well as of the canonical miR from the 5p arm (miR-1307-5p|0), the overexpression of pre-miR-1307 did not lead to global alterations in isomiR expression patterns. These data validate the suitability of our model cell line for the analysis of the effects of joint upregulation of miR-1307-3p|0, -3p|1 and -5p|0.

2024-01-11 | GSE227354 | GEO

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