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Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

ABSTRACT: Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

PROVIDER: PRJNA773487 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16525306.fastq.gz	Fastqsanger.gz
	SRR16525307.fastq.gz	Fastqsanger.gz
	SRR16525308.fastq.gz	Fastqsanger.gz
	SRR16525309.fastq.gz	Fastqsanger.gz
	SRR19546547.fastq.gz	Fastqsanger.gz

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Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

Quantitative profiling of differentially expressed miRNAs in exosomes of siCTL- and siPRDX3-transfected HCT 116 cells

Project description:Quantitative profiling of differentially expressed miRNAs in exosomes of siCTL- and siPRDX3-transfected HCT 116 cells

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Quantitative profiling of differentially expressed miRNAs in exosomes of siCTL- and siPRDX3-transfected HCT 116 cells

Project description:Purpose: The goal of this study is to compare exosomal small RNA transcriptome of HCT116 cells to identify the target of PRDX3 under basal or knock down conditions by utilizing miRNA-seq. Methods: miRNA profilies of siCTL or siPRDX3 transfected HCT 116 exosoems were generated by illumina sequencing method, in triplicate. After sequencing, the raw sequence reads are filtered based on quality.Sequence reads were mapped with the bowtie2 software tool, which yielded bam files. Mature miRNA sequences were used as references for mapping. Read counts mapped to a mature miRNA sequence were extracted from the alignment file using bedtools v2.25.0 and Bioconductor, which use the R statistical programming language. Read counts were used to determine the expression level of miRNAs. The CPM+TMM normalization method was used for between-sample comparison. Results: We identified known miRNA in species (miRDeep2) in the HCT116 exosome transfected with siCTL or siPRDX3. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of HCT116 exosomal miRNA profiles affected by PRDX3 knockdown with biologic replicates.

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Differentially expressed miRNAs in colorectal cancer

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High-throughput sequencing analyze the differentially expressed miRNA of HUVECs after lncRNA uc003pxg.1 knockdown by siRNA compared with NC group

Project description:Sequencing of relevant miRNAs was performed in si-uc003pxg.1-transfected HUVECs and control HUVECs. Fourteen upregulated and 5 downregulated miRNAs were selected based on P-values and fold change values. And cell experiments also showed that miR-25-5p was significantly upregulated in HUVECs compared to normal samples following uc003Pxg.1 knockdown. The luciferase activities of the miR-25-5p mimic + uc003pxg.1 wt group were significantly decreased compared with those of the miR-25-5p mimic + uc003pxg.1 mut group, while there was no significant difference in the luciferase activities between the miR-25-5p mimic and NC samples in the mutant group. This result indicated that uc003pxg.1 interacts with miR-25-5p. This study provides a theoretical basis for the study of the molecular mechanism of uc003pxg.1 in HUVECs.

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Differentially expressed miRNAs in SW1990 and PANC-1 cells following GLI1 cDNA transfection.

Project description:Screening of differentially expressed miRNAs in SW1990 and PANC-1 cells following GLI1 cDNA transfection. We independently transfected SW1990 and Panc-1 cells with Gli1 cDNA for mRNA and miRNA microarray analysis. The results unveiled significant differential expression patterns, with numerous miRNAs and mRNAs showing changes post-Gli1 transfection. Remarkably, miR-301a exhibited high expression in both SW1990 and Panc-1 cells transfected with Gli1 cDNA.

2025-01-29 | GSE281315 | GEO

Differentially expressed miRNAs identified in various influenza virus infection

Project description:Differentially expressed miRNAs identified in various influenza virus infection

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Transcriptomic profiles of OASL knockdown HUVECs under basal or activated condition

Project description:Purpose: The goal of this study is to compare endothelial transcriptome affected by OASL knockdown under basal or stimulated conditions by utilizing RNA-seq. Methods: Endothelial mRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. Following an optimized data analysis workflow, RNA sequence reads were counted using StringTie-2.1.3b and used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs treated with or without TNFα and IFNγ. Results: DESeq2 was used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs under basal or stimulated conditions. Genes showing <10 read counts total were pre-filtered. Conclusions: Our study represents the first analysis of endothelial mRNA affected by OASL knockdown with biologic replicates, generated by RNA-seq.

2022-09-06 | GSE186352 | GEO

RNA-Seq of inflammatory stimulated HUVECs transfected with microRNA-125a-5p or negative control.

Project description:Purpose: In recent years, research has revealed the role of microRNAs (miRs) as important regulators of endothelial function. Notably, miR-125a is upregulated in the blood of patients with acute vascular diseases. Since miRNAs act out their function in networks, we aimed at investigating the presence of a miR-125a-related network regulating the endothelial barrier. Method: We investigated transcriptional changes of human umbilical cord endothelial cells (HUVEC) after miR-125a overexpression in an acute inflammatory in-vitro setting using Next Generation Sequencing. Briefly, primary HUVECs from five different donors were transfected either with hsa-miR-125a-5p or negative control (NC). After transfection HUVECs were cultivated for 18 hours and stimulated with TNF (25 ng/ml) for additional 6 hours. We compared the following groups: NC (18047-0001, 18047-0002, 18047-0003, 18047-0004, 18047-0005) versus miR125a: (18047-0006, 18047-0007, 18047-0008, 18047-0009, 18047-0010) Results: MiR-125a overexpression in inflammatory activated HUVECs significantly altered gene expression of 468 genes (FC: +1.25 to -1.25 p<0.01). We found eight potential miR-125a direct target genes involved in endothelial barrier function.

2022-02-07 | GSE196161 | GEO

Dynamics of intercellular and extracellular miRNAs in HUVECs co-cultured with K562 cells

Project description:MicroRNAs (miRNAs) are small (18-22 nucleotides), non-coding RNAs that suppress the translation of target mRNAs by binding to their 3` untranslated region, and regulate gene networks, helping to control cell function and phenotype. Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication. The goals of this study were to elucidate whether or not miRNAs secreted from neoplastic cells transfer into endothelial cells and works functionally active in the recipient cells. In the present study, we investigated the interaction of a leukemia cell line (K562) and human umbilical vein endothelial cells (HUVECs) using a non-contact co-culture system, and assess the expression profiles of intercellular and extracellular miRNAs in HUVECs and K562 cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). We compared the miRNA expression profiles between 1) K562 cells or HUVECs; 2) intercellular and extracellular; 3) mono-culture medium and co-culture medium.

2012-06-12 | GSE31114 | GEO

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