RNAseq data of VP
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PROVIDER: PRJEB57782 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goals of this study are to compare VEGF-treated HUVECs with or without Verteporfin (VP) pretreatment transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: After serum-starving for 12 hours, HUVECs were divided into two group: VEGF and VEGF+VP. Cells from VEGF+VP group were pretreated with VP (4 μM) for 2 hours and then all cells were treated with VEGF (200 ng/mL) for another 24 hours. Subsequently, total RNA from HUVECs were prepared using Trizol reagent and mRNA library was constructed. RNA-sequencing: RNA-sequencing was carried out by BGI (Beijing Genomic Institute, ShenZhen, China). SOAPnuke software (v1.5.2) was used to filter the data for RNA-sequencing and then these data were mapped to the reference genome using HISAT2 software (v2.0.4). The clean reads were aligned to the gene set by Bowtie2 (v2.2.5). The expression level of genes was then measured by RSEM software (v1.2.12). The heatmap of top 40 different expression genes was drawn according to the gene expression with FPKM (fragment per kilobase of transcript per million). Reactome (https://www.reactome.org/) enrichment analysis of different expression genes was undertaken and the significant levels of terms and pathways were corrected by Q value. Results: The statistical results of significant DEGS confirmed that approximately 7204 genes of the transcripts showed differential expression between the VEGF group and VEGF+VP group, with a fold change ≥1.5 and p value <0.05. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to angiogenesis. Data analysis with GO analysis and GSEA analysis revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed transcriptomic analysis of VEGF treated HUVECs with or without VP treatment, 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.
2022-04-06 | GSE181880 | GEO
Project description:Atherosclerosis, characterized by the buildup of plaque in arteries, is a major cause of cardiovascular mortality worldwide, as there is no efficient strategy for targeted therapy. However, we have developed a new drug delivery platform called MoNP, which is loaded with VP, a potent inhibitor of YAP/TAZ signaling. To investigate the MoNP-VP treatment effect, EC were pretreated with MoNP or MoNP-VP then induced the inflammation by TNFalpha. After TNFalpha treatment, the cells were collected and extracted the RNA for RNA sequencing (RNA-Seq). The results showed that MoNP-VP significantly decreased the expression of YAP/TAZ-targeted genes and inflammatory markers while upregulating atheroprotective genes. Overall, these findings suggest that MoNP-VP has the potential to serve as an effective drug delivery platform for atherosclerosis.
2024-10-23 | GSE229918 | GEO
Project description:Verteporfin (trade name Visudyne) is a medication used as a photosensitizer for photodynamic therapy to eliminate the abnormal blood vessels in the eye associated with conditions such as the wet form of macular degeneration. Verteporfin accumulates in these abnormal blood vessels and, when stimulated by nonthermal red light with a wavelength of 689 nm[1] in the presence of oxygen, produces highly reactive short-lived singlet oxygen and other reactive oxygen radicals, resulting in local damage to the endothelium and blockage of the vessels. Recently, it was reported that VP has chemotherapeutic effect in cancer. To identify the gene expression profile in gastric cancer cells by VP, we performed microarray.
2017-12-26 | GSE77982 | GEO
Project description:PRR5 transcription factor acts in the circadian clock system. To elucidate regulated genes by PRR5, Chimeric protein PRR5-VP, which activates direct target genes of PRR5, was over-expressed in Col-0. Microarray analsysis was performed using these plants with Affymetrix ATH1 genechip. PRR5-VP expressing plants and its parental plants (accession Col-0, described as Wild) were grown under 12 hr light / 12 hr dark conditions, and harvested at ZT6(6 hr after light on), ZT12, and ZT18
2012-09-20 | E-GEOD-36360 | biostudies-arrayexpress
Project description:Human hepatocellular carcinoma RNAseq data
| PRJNA760521 | ENA
Project description:Vibrio parahaemolyticus strain:vp-HL-202005 Genome sequencing
| PRJNA910996 | ENA
Project description:PRR5 transcription factor acts in the circadian clock system. To elucidate regulated genes by PRR5, Chimeric protein PRR5-VP, which activates direct target genes of PRR5, was over-expressed in Col-0. Microarray analsysis was performed using these plants with Affymetrix ATH1 genechip.
2012-09-20 | GSE36360 | GEO
Project description:Mesenchymal stem cell (MSC) transplantation is a promising therapy for regenerative medicine. However, MSCs cultured in two-dimensional (2D) culture conditions are significantly different from the cell shape in the body, down-regulation of stemness genes and the secretion of paracrine factors. Here, we evaluated the effect of 3D culture using Cellhesion VP, a water-insoluble material composing of chitin-based polysaccharide fibers, on the characteristics of human Wharton’s jelly-derived MSCs (hWJ-MSCs). Cellhesion VP significantly increased the cell proliferation after retrieval. Transcriptome analysis revealed that genes involved in cell stemness, migration ability, and extracellular vesicle (EV) production appeared to be enhanced by 3D culture. Subsequent biochemical analyses showed that the expression levels of stemness genes including OCT4, NANOG, and SSEA4 were up-regulated, and migration capacity was elevated in 3D cultured hWJ-MSCs. In addition, the EV production was significantly increased in 3D cells, which contained a distinct protein profile from 2D cells. Gene and drug connectivity analysis revealed that the 2D and 3D EVs had similar functions as immunomodulators; however, 3D EVs had completely distinct therapeutic profiles on various infectious and metabolic diseases by activating the disease-associated signaling pathways. Therefore, EVs from Cellhesion VP-primed hWJ-MSCs appear as a new treatment for immune and metabolic diseases.
2021-06-30 | GSE152507 | GEO
Project description:We used RNAseq to evaluate baseline expression of NPAS+ VP translatomes in comparison to bulk VP translatomes.
2022-11-28 | GSE218580 | GEO
Project description:We report that ~300 mature miRNAs were detected in these cells. 73 miRNAs were overexpressed (fold change > 2; adjusted P-value < 0.05) and 14 were underexpressed (fold change > 2; adjusted P-value < 0.05) in K/VP.5 compared to K562 cells.
2020-01-31 | GSE141687 | GEO