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HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [RNA-Seq]

ABSTRACT: HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [RNA-Seq]

PROVIDER: PRJNA790825 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17278650_1.fastq.gz	Fastqsanger.gz
	SRR17278650_2.fastq.gz	Fastqsanger.gz
	SRR17278651_1.fastq.gz	Fastqsanger.gz
	SRR17278651_2.fastq.gz	Fastqsanger.gz
	SRR17278652_1.fastq.gz	Fastqsanger.gz

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HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [miRNA-Seq]

Project description:Purpose: To explore the potential integrated molecular network by long non-coding RNA HOXA11-AS in keloid fibroblast Methods: Using primary cultured keloid-derived fibroblasts (sample 0), small interfering RNAs were designed and transfected into two keloid fibroblast samples (samples 1 and 2) to knockdown HOXA11-AS. One nonspecific transfection control (sample 3) and one blank control (sample 4) were used to remove nonspecific overlap from the studied group. The lncRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs) of five samples were sequenced to identify differentially expressed (DE) profiles in HOXA11-AS-knockdown keloid fibroblasts in samples 1 and 2, which facilitated removal of overlap with the nonspecific controls (samples 3 and 4). Using stepwise bioinformatic analysis, DE lncRNA and mRNAs characterized by close and natural antisense relationship were constructed into an interactive network by bioinformatic analysis. Based on this network, a lncRNA–mRNA–protein interaction network was extended by integration of the human protein–protein interaction (PPI) network. The Page Rank algorithm was used to score each mRNA in the extended LMN network to reveal significant functioning genes. Next, screened genes were validated by real-time PCR and western blot ting. Validated genes were used to construct a competing endogenous network based on DE miRNA profiles. Results: SNED1, NIPAL3, and VTN were detected significantly changed in HOXA11-AS-knockdown keloid fibroblasts. Only NIPAL3 was predicted to be involved in an intergated network for HOXA11-AS via three competing endogenous miRNAs (hsa-miRNA-19a-3p, hsa-miR-141-3p, and hsa-miR-140- 5p). Conclusion: An interactive molecular network of HOXA11-AS–three miRNAs–NIPAL3 was predicted in keloid fibroblasts

2021-12-22 | GSE191266 | GEO

HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [RNA-Seq]

2021-12-22 | GSE191265 | GEO

HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network

Project description:HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network

| PRJNA790821 | ENA

HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [miRNA-Seq]

Project description:HOXA11-AS regulates NIPAL3 via hsa-miRNA-19a-3p, hsa-miR-141-3p and hsa-miR-140-5p in keloid fibroblast: stepwise bioinformatical screen for an integrated molecular network [miRNA-Seq]

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Transcript expression levels of neonatal mouse cardiomyocytes mock-transfected, or transfected with cel-miR-67, hsa-miR-590-3p or hsa-miR-199a-3p

Project description:To identify the relevant targets of the selected miRNAs, we assessed global transcriptome changes by deep-sequencing total neonatal mouse cardiomyocyte RNA after transfection with hsa-miR-590-3p or hsa-miR-199a-3p Four condition experiment; one replicate per condition; mouse neonatal cardiomyocytes transfected with cel-miR-67, hsa-miR-590-3p and hsa-miR-199a-3p; samples collected 72 hours after transfection

2012-10-13 | E-GEOD-41538 | biostudies-arrayexpress

Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells

Project description:We report the application of transcriptome sequencing for investigating of the hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes. JAR, JEG-3 and BeWo choriocarcinoma cells were transfected with hsa-miR-371a-5p or hsa-miR-518a-3p inhibitors or control inhibitors. Totally, 237, 132 and 277 genes with > 2 folds change and adjusted P < 0.05 were upregulated in JAR, JEG-3 and BeWo cells respectively after hsa-miR-371a-5p knockdown. Meanwhile, 229, 269 and 191 genes were upregulated in JAR, JEG-3 and BeWo cells respectively after hsa-miR-518a-3p knockdown. The top upregulated genes included many oncogenes or oncogenesis associated ones. Enrichment analysis showed hsa-miR-371a-5p and hsa-miR-518a-3p regulated diverse pathways related to tumorigenesis and metastasis. Our results would be helpful for the searching of early molecular biomarkers and therapeutic targets for gestational trophoblastic neoplasia.

2018-11-01 | GSE106394 | GEO

Transcript expression levels of neonatal mouse cardiomyocytes mock-transfected, or transfected with cel-miR-67, hsa-miR-590-3p or hsa-miR-199a-3p

2012-10-13 | GSE41538 | GEO

Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells

Project description:Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells

| PRJNA416704 | ENA

Identify the effects of miR-19a-3p miRNA mimic overexpression in mouse calvarial osteoblast primary cultures

Project description:We used a primary calvarial osteoblast cell line (CalOB) to transfect either a negative control or miR-19a-3p miRNA mimic to understand the effects on global gene expression using bulk RNA-seq.

2023-06-14 | GSE226402 | GEO

Epigenetic downregulation of hsa-miR-193b-3p increases Cyclin D1 expression level and cell proliferation in human meningiomas

Project description:Meningiomas are common intracranial tumors in adults. Abnormal miRNA expression plays a role in their pathogenesis. Change in miRNA expression level can be caused by impaired epigenetic regulation of miRNA-encoding genes. We found genomic region covering MIR193B gene as DNA hypermethylated in meningiomas based on analysis of genome-wide methylation (HM450k Illumina arrays). Hypermethylation of MIR193B was as also confirmed by bisulfite pyrosequencing. Both hsa-miR-193b-3p and hsa-miR-193b-5p are downregulated in meningiomas as found with qRT-PCR. Lower expression of hsa-miR-193b-3p and higher MIR193b methylation was observed in WHO GII/GIII as compared to GI meningiomas. 3’UTR of CCND1 mRNA was identified as target of hsa-miR-193b-3p as further validated with luciferase reporter assay in IOMM-Lee meningioma cells. IOMM-Lee cells transfected with hsa-miR-193b-3p mimic showed decreased cyclin D1 level and lower cell viability and proliferation, confirming suppressive nature of this miRNA. Cyclin D1 protein expression (immunoreactivity) was higher in atypical than in benign meningiomas, accordingly to observation of lower hsa-miR-193b-3p level in GII tumors. The commonly observed hypermethylation of MIR193B in meningiomas apparently contributes to downregulation of hsa-miR-193b-3p. Since hsa-miR-193b-3p regulates proliferation of meningioma cells through negative regulation of cyclin D1 expression, it seems to be an important tumor suppressor in meningiomas.

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