The change of mRNA expression in SKOV3 cells after treated with placental extracellular vesicles
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE243543 | GEO | 2023/11/01
REPOSITORIES: GEO
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Project description:Purpose: The goals of this study is to compare and profile the transcriptome of the placenta in preeclamptic and normal patients using RNA sequencing. Methods: Placental and Placental vesicles (STB-EVs) mRNA profiles of normal and preeclamptic patients were generated by deep sequencing using Illumina HISEQ. The sequence reads that passed quality filters were analyzed at the gene level HISAT2 followed by featureCounts. Quantitative PCR validation was performed using TaqMan gene expression assays Results: This contains a set of three parallel mRNA sequencing experiments involving placenta tissue, medium/large STB-EVs and small STB-EVs. Comparison between PE and normal pregnancy placental tissue revealed 18,070 genes from which 580 were upregulated and 563 were downregulated (p-value of <0.05 ) while in medium/large STB-EVs, revealed 14,216 genes from which 1,128 were upregulated and 833 were downregulated. In small STB-EVs, out of 23,322 genes, 232 were upregulated and 106 were downregulated) (adjusted P-value of <0.05) We identified a number of mechanistic and biomarker targets, which were validated with qRT–PCR and confirmed to be signifficantly DE. The differentially expressed analysis identified potential yet undescribed genes that may contribute to the pathogenesis of preeclampsia or/and may act as biomarkers of the disease. Conclusions: Our study represents the first detailed analysis of combined Placenta and placental extracellular vesicles (STB-EVs) transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results have identified potential STB-EV based small RNA biomarkers in preeclampsia.
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Project description:Purpose: The goals of this study is to compare and profile the smallRNA transcriptome of the placenta in preeclamptic and normal patients using RNA sequencing. Methods: Placental and Placental vesicles (STB-EVs) smallRNA profiles of normal and preeclamptic patients were generated by deep sequencing using Illumina HISEQ. FASTq.gz files were compressed with OASIS compressor and alignment was done with OASIS 2.0 ( by trimmimng with trimmomatic, aligning using default OASIS 2.0 aligning papameters). Quantitative PCR validation was performed using TaqMan gene expression assays Results: This contains a set of three parallel smallRNA sequencing experiments involving placenta tissue, medium/large STB-EVs and small STB-EVs. Comparison between PE and normal pregnancy placental tissue revealed 134 (p-value of <0.05 ) while in medium/large STB-EVs, 101 and in small STB-EVs, 16 (adjusted P-value of <0.05) differentially expressed small RNA We identified a number of mechanistic and biomarker targets, which were validated with qRT–PCR and confirmed to be signifficantly DE. The differentially expressed analysis identified potential yet undescribed small RNAs that may contribute to the pathogenesis of preeclampsia or/and may act as biomarkers of the disease. Conclusions: Our study represents the first combined analysis of placenta, medium/large and small STB-EV transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results identified potential Placenta EV small RNA biomarkers that can help diagnose the preeclampsia
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