Journal: Frontiers in Pharmacology

Article Title: Phosphodiesterase 7: a potential novel therapeutic target in ovarian cancer

doi: 10.3389/fphar.2025.1566330

Figure Lengend Snippet: Validation of gene expression by RT-qPCR. (A-I) The relative expression of genes in seven fallopian tube samples and seven samples from HGSC patients, as determined by RNA sequencing data, was validated using RT-qPCR.

Article Snippet: Amongst the first twenty genes from the high-throughput RNA sequencing data (data gently provided by Dr. Shih from Johns Hopkins University), we designed primers for nine of them.

Techniques: Biomarker Discovery, Gene Expression, Quantitative RT-PCR, Expressing, RNA Sequencing

Journal: EBioMedicine

Article Title: Potential clinical value of circular RNAs as peripheral biomarkers for the diagnosis and treatment of major depressive disorder

doi: 10.1016/j.ebiom.2021.103337

Figure Lengend Snippet: Bioinformatics analysis of circFKBP8 and circMBNL1. (a) Possible binding of miRNAs and mRNAs to circFKBP8 and circMBNL1. Circles indicate circRNA, triangles indicate miRNA and squares indicate mRNA. Nodes highlighted in red and blue represent upregulation and downregulation, respectively. (b) The biological process of 10 mRNAs of ceRNA networks, identified from the Gene Ontology enrichment analysis of all significantly different mRNAs of the RNA sequencing. The above panel indicates up-regulated biological process in MDD and the bottom panel indicates down-regulated biological process in MDD. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: We thank extremely Shanghai Genesky Biotechnology Company and Mr. Lingbin Sun for their help in RNA high-throughput sequencing.

Techniques: Binding Assay, RNA Sequencing

Journal: BMC Cancer

Article Title: Overcoming acquired resistance to HSP90 inhibition by targeting JAK-STAT signalling in triple-negative breast cancer

doi: 10.1186/s12885-019-5295-z

Figure Lengend Snippet: Differential RNA expression in HSP90i-resistant clones compared to parental Hs578T cells. RNA samples from DMSO-treated and ganetespib-treated Hs578T, CR2 and CR3 cells were analysed for whole transcriptome profiling with RNA-sequencing. Differential gene expression analyses were performed between DMSO-treated parental Hs578T cells with either DMSO-treated CR2 or CR3 and the significantly upregulated genes observed in these clones were mostly overlapping. Pathway enrichment analysis using Metacore™ was performed on the significantly upregulated overlapping genes. The graph represents the top 20 most significantly upregulated pathways in the HSP90i-resistant clones, with FDR (false discovery rate) value < 0.05. Pathways highlighted in blue are linked to JAK-STAT signalling

Article Snippet: Duplicate samples (1 μg RNA in 30 μl) were subjected to RNA Sequencing (RNA-seq) analysis (Oxford Gene Technology) and gene expression was quantified using their analysis pipeline [ ].

Techniques: RNA Expression, Clone Assay, RNA Sequencing, Gene Expression

Journal: Frontiers in Immunology

Article Title: Altered circular RNA expressions in extracellular vesicles from bronchoalveolar lavage fluids in mice after bacterial infections

doi: 10.3389/fimmu.2024.1354676

Figure Lengend Snippet: Validation of individual circRNAs detected in microarray profiling using RT-qPCR. WT mice were exposed to Acid (0.1 N HCl) or LPS (1µg) for 1 day. BALF EVs and cells were collected and circRNAs were evaluated using qPCR (normalized to β-actin or GAPDH). (A) To validate the specific circRNAs using RT-qPCR, we first designed the specific primers targeting the BSJ region to detect circular forms of RNAs, as illustrated here (left panel). The specific sequence of each specific circRNAs is listed on the right panel. (B) Validation of specific circRNAs using RT-qPCR in BALF EVs. We selected five circRNAs that were highly altered in the BALF EVs using microarray profiling. Next, we validated the expression and alteration of each circRNA using RT-qPCR in BALF EVs. *p<0.05. (C) To confirm that the specific primers used to detect circRNAs fail to detect the linear form host RNA. Using circ30884 as an example, we confirmed that using the primer listed above, we failed to detect its host linear RNA XDH. The figures shown here represent repeats from three independent experiments. *p<0.05. (D) AMs and neutrophils were separately isolated from LPS-exposed mouse lung as the above. Circular RNAs were then detected using RT-qPCR. *p<0.05, ns, not significant.

Article Snippet: We first used the high-throughput RNA-sequencing microarray screening by Arraystar.

Techniques: Biomarker Discovery, Microarray, Quantitative RT-PCR, Sequencing, Expressing, Isolation