Journal: Biology Direct

Article Title: hsa_circ_0020093 suppresses ovarian cancer progression by modulating LRPPRC activity and miR-107/LATS2 signaling

doi: 10.1186/s13062-024-00520-y

Figure Lengend Snippet: hsa_circ_0020093 acts as miR-107 sponge to regulate LATS2 expression. A AGO2 RIP assay was executed in SKOV3 cells. B Venn diagram of the predicted target miRNAs of hsa_circ_0020093 identified from GSE47481, TargetScan, RegRNA and Starbase. C Differential expression of overlapped miRNAs across normal and high-grade serous ovarian cancer (HGSOC) samples in GSE47841. D Schematic illustration of hsa_circ_0020093-WT and hsa_circ_0020093-MUT luciferase reporter vectors. E-F The relative luciferase activities were detected in 293 T cells after co-transfection with hsa_circ_0020093-WT or hsa_circ_0020093-MUT and mimics or miRNC, respectively. G Venn diagram of the predicted target genes of miR-107 identified from RNA-seq data and three tools (TargetScan, miRTarbase, miRDB). H RT-qPCR detection of the expression of upregulated mRNAs in hsa_circ_0020093-overexpressed OC cells. I Western blot analysis of LATS2 protein level after hsa_circ_0020093 overexpression in OC cells. J Western blot analysis of LATS2 protein level after co-transfection of hsa_circ_0020093 or control and miR-107 or miRNC, respectively, in OC cells. P values were calculated by two-tailed Student’s t test. ns, not significant; * P < 0.05; ** P < 0.01; *** P < 0.001

Article Snippet: The miRNA microarray dataset GSE47841 was applied to analyze differentially expressed miRNAs between OC tissues and normal ovary tissues using dbDEMC database ( https://www.biosino.org/dbDEMC/index ).

Techniques: Expressing, Quantitative Proteomics, Luciferase, Cotransfection, RNA Sequencing, Quantitative RT-PCR, Western Blot, Over Expression, Control, Two Tailed Test

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Study design flowchart. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure. DEcircRNAs, differentially expressed circRNAs; DEmiRNAs, differentially expressed miRNAs; DEmRNAs, differentially expressed mRNAs

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of mRNAs for GSE103465. (A) Boxplot of GSE103465. (B) Volcano plots of DEmRNAs based on GSE103465. (C) Venn diagram of mRNAs for GeneCards and GSE103465, where the intersection section is predicted DEmRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of miRNAs for GSE121219. (A) Boxplot of GSE121219. (B) Volcano plots of DEmiRNAs based on GSE121219. (C) Venn diagram of miRNAs for miRDIP and GSE121219, where the intersection section is predicted DEmiRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Boxplots, volcano plots and Venn diagram of circRNAs for GSE147442. (A) Boxplot of GSE147442 after standardization. (B) Volcano plots of DEcircRNAs based on GSE147442. (C) Venn diagram of miRNAs for starBase 2.0 and GSE147442, where the intersection section is predicted DEcircRNAs asscociated with angiogenesis in RIF. circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: Figure 5 CircRNA-miRNA-mRNA regulatory network, which consists of 8 DEcircRNAs, 10 DEmiRNAs and 45 DERNAs. DEcircRNA, differentially expressed circular RNA; DEmiRNA, differentially expressed micro RNA; DERNA, differentially expressed RNA. Arrow-shape nodes: circRNAs, triangle nodes: miRNAs, ellipse-shaped nodes: mRNAs

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: BMC Medical Genomics

Article Title: Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

doi: 10.1186/s12920-024-01944-1

Figure Lengend Snippet: A PPI network and circRNA–miRNA–hub gene regulatory subnetwork. (A) A PPI network of the fifty-five target genes associated with angiogenesis in RIF. (B) Six hub genes extracted by cytoHubba plug-in. (C) CircRNA–miRNA–hub gene regulatory subnetwork, consisting of 3 circRNAs, 3 miRNAs, and 3 mRNAs. PPI, protein–protein interaction; circRNA, circular RNA; miRNA, microRNA; RIF, recurrent implantation failure

Article Snippet: CircRNA, miRNA and mRNA microarray expression profile datasets were selected from the National Center of Biotechnology Information Gene Expression Omnibus (NCBI) GEO ( https://www.ncbi.nlm.nih.gov/geo/ ).

Techniques:

Journal: Computational and Mathematical Methods in Medicine

Article Title: Integrative Bioinformatics Analysis Reveals That miR-524-5p/MEF2C Regulates Bone Metastasis in Prostate Cancer and Breast Cancer

doi: 10.1155/2022/5211329

Figure Lengend Snippet: Identification of DE-miRNAs and DEGs related to cancer bone metastasis. (a) Clustered heat map of 1555 DEGs in GSE137842. Red: significantly upregulated genes; blue: significantly downregulated genes. (b) Differentially expressed volcano plots in GSE137842. Red dots: significantly upregulated; green dots: significantly downregulated; and black dots: no significant differences. (c) Clustered heat map of 833 DEGs in GSE32269. Red: significantly upregulated genes; blue: significantly downregulated genes. (d) Differentially expressed volcano plots in GSE32269. Red dots: significantly upregulated; green dots: significantly downregulated; and black dots: no significant differences. (e) Clustered heat map of 88 DE-miRNAs in GSE26964. Red: upregulated genes; blue: downregulated genes. (f) Differentially expressed volcano plots in GSE26964. Red dots: significantly upregulated; green dots: significantly downregulated; and black dots: no significant differences. (g) The common DEGs from GSE32269 and GSE137842 involved in prostate cancer bone metastasis and breast cancer bone metastasis by Venny 2.1.0. (h) List of the common DEGs from GSE32269 and GSE137842.

Article Snippet: The miRNA microarray dataset GSE26964 [ ] was composed of 6 primary prostate cancer samples and 7 prostate cancer bone metastatic samples (platform: Capitalbio mammal microRNA V3.0).

Techniques:

Journal: Frontiers in Cell and Developmental Biology

Article Title: Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease

doi: 10.3389/fcell.2021.622021

Figure Lengend Snippet: Details of miRNA and mRNA datasets of patients with SSc-ILD.

Article Snippet: A total of one miRNA microarray dataset GSE81293 ( ) and three mRNA microarray datasets GSE81292 , GSE48149 ( ; ), and GSE76808 ( ) from lung biopsy tissues of SSc-ILD patients and controls were downloaded from the National Center for Biotechnology Information (NCBI) GEO database .

Techniques: Expressing

Journal: BMC Nephrology

Article Title: PTGER3 and MMP-2 play potential roles in diabetic nephropathy via competing endogenous RNA mechanisms

doi: 10.1186/s12882-020-02194-w

Figure Lengend Snippet: The summary of differentially expressed miRNAs (DEmiRNAs) and genes (DEGs) in diabetic nephropathy (DN) samples versus control samples. a and b , the Volcano plot of the DEmiRNAs (GSE51674) and DEGs (GSE111154) between DN and control samples, respectively. c and d , the heatmap presenting the expression profiles of the DEmiRNAs (GSE51674) and DEGs (GSE111154) between DN and control samples, respectively

Article Snippet: The human miRNA microarray dataset GSE51674 and gene expression dataset GSE111154 are available at the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ).

Techniques: Control, Expressing

Journal: Aging (Albany NY)

Article Title: Inhibition of circulating exosomal microRNA-15a-3p accelerates diabetic wound repair

doi: 10.18632/aging.103143

Figure Lengend Snippet: Dia-Exos were enriched with miR-15a-3p, which altered HUVEC function. ( A , B ) An miRNA microarray dataset of non-diabetic foot wound patients and DFU patients retrieved from NCBI GEO (accession number: GSE80178) indicated that miR-15a-3p was upregulated in foot skin from diabetic patients. ( C , D ) MiR-15a-3p overexpression was found in serum and exosomes from the diabetic group; n = 10 per group. ( E ) Effects of the two kinds of exosomes on miR-15a-3p levels in the skin tissues of mice treated with Dia-Exos. ( F ) qRT-PCR indicated that antagomiR-15a-3p could partially counteract the overexpression of miR-15a-3p in HUVECs. ( G ) A CCK-8 assay was used to assess the effects of antagomiR-15a-3p on HUVEC proliferation. ( H , I ) Flow cytometry was used to quantify the cell cycle distribution. ( J ) qRT-PCR analysis indicated that antagomiR-15a-3p could restore the mRNA levels of Cyclin D1 and Cyclin D3 . ( K ) The effects of antagomiR-15a-3p on the apoptosis-related genes Bcl-2 and Bax were measured using qRT-PCR. ( L , M ) A Transwell migration assay was used to measure the effects of miR-15a-3p on HUVEC migration; scale bar: 100 μm. ( N – P ) A tube formation assay was used to assess the effects of miR-15a-3p on HUVEC angiogenesis; scale bar: 200 μm. ( Q , R ) The scratch assay results of the three groups; scale bar: 250 μm. Data are the means ± SDs of three independent experiments. *p < 0.05, **p < 0.01, ***p < 0.001.

Article Snippet: We retrieved an miRNA microarray dataset of foot skin samples from non-diabetic foot wound patients and DFU patients from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI; accession number: GSE80178), which also indicated that miR-15a-3p was upregulated in diabetic patients ( and ).

Techniques: Microarray, Over Expression, Quantitative RT-PCR, CCK-8 Assay, Flow Cytometry, Transwell Migration Assay, Migration, Tube Formation Assay, Wound Healing Assay