Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Differentially expressed circRNAs in MS patients versus HCs, circRNA array analysis. ( A ) Volcano plots, used to visualize up- and downregulated genes across MS samples as compared to HCs. The red (up) and green (down) dots in the plot represent the significative differentially expressed circRNAs. ( B ) Clustered heatmap of the differentially expressed circRNAs showing the relationships among the expression levels of samples. Upregulation is shown in red, and downregulation is in green. ( C ) Table showing the list of circRNAs differentially expressed, depicting the top 7 upregulated and 10 downregulated.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Expressing

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Characteristics of the circRNAs identified in PBMCs of MS patients versus HCs. ( A ) Distribution of significantly upregulated circRNAs according to the chromosomal location. ( B ) Class distribution of upregulated circRNAs based on the genomic origins. ( C ) Distribution of significantly downregulated circRNAs according to the chromosomal location. ( D ) Class distribution of downregulated circRNAs based on the genomic origins.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques:

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Validation of the circRNAs identified in PBMCs of MS patients versus HCs. Expression levels in PBMCs of five upregulated and four downregulated circRNAs ( A ) and the corresponding cognate linear mRNAs ( B ) were measured by qPCR analysis. The levels of circRNAs and mRNAs were normalized to GAPDH mRNA levels. Data are the means and standard deviation (+SD) from at least three independent experiments. ** p < 0.01, *** p < 0.001.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Biomarker Discovery, Expressing, Standard Deviation

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Validation of the circRNAs in serum of MS patients versus HCs. The levels in serum of five upregulated and four downregulated circRNAs ( A ) and the corresponding mRNAs ( B ) were measured by qPCR analysis. The levels of circRNAs and mRNAs were normalized to GAPDH mRNA levels. Data are the means and standard deviation (+SD) from at least three independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Biomarker Discovery, Standard Deviation

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Identification of the miRNAs and RBP Targets. ( A ) Schematic representation of circRNAs with putative miRNA binding site (MRE) and RNA-binding protein binding site (RBP-bs). ( B , C ) Tables showing list of human circRNA identified from our studies and target miRNAs and interacting RNA-binding proteins as determined by analysis performed using miRanda and circInteractome, respectively.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Binding Assay, RNA Binding Assay, Protein Binding

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Network of circRNA-miRNA-mRNA for MS-associated genes. ( A ) Network of upregulated circRNAs and ( B ) downregulated circRNAs. CircRNAs are represented as red or green diamonds, miRNAs as red or green circles, and mRNAs as light red or light green rectangles. Red represents network generated from upregulated circRNAs and green from downregulated circRNAs.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Generated

Journal: Cells

Article Title: Identification of hsa_circ_0018905 as a New Potential Biomarker for Multiple Sclerosis

doi: 10.3390/cells13191668

Figure Lengend Snippet: Validation of the circRNA expression in PBMCs and correlation with disease severity. ( A ) Expression levels in PBMCs of five upregulated and three downregulated circRNAs in MS with different disease severity measured by RT-qPCR analysis. The levels of circRNAs were normalized to GAPDH mRNA levels. ( B ) Receiver operating characteristic (ROC) curve of differentially expressed circRNAs in MS vs. HCs. Green line, hsa_circ_0003445 and blue line, hsa_circ_0018905. Data are represented as the means and standard deviation (+SD) from at least three independent experiments. ** p < 0.01, *** p < 0.001.

Article Snippet: The Arraystar circRNAs Array was designed to identify 13,617 circRNAs, which were analyzed using the Agilent Feature Extraction software.

Techniques: Biomarker Discovery, Expressing, Quantitative RT-PCR, Standard Deviation

Journal: Cell Death & Disease

Article Title: Angiotensin II inhibits apoptosis of mouse aortic smooth muscle cells through regulating the circNRG-1/miR-193b-5p/NRG-1 axis

doi: 10.1038/s41419-019-1590-5

Figure Lengend Snippet: a Scatter plots were used to evaluate the difference in the expression of circRNAs between Ang II and control groups. The values plotted on X and Y axes are the averaged normalized signal values of each group (log2 scaled). The circRNAs above the top green line and below the bottom green line indicate >1.5-fold change between the two groups. b Hierarchical clustering analysis showed the differentially expressed circRNAs over 2.0-fold change. Red color indicates high expression level, and blue color indicates low expression level. c Divergent and convergent primers were used to verify whether circNRG-1 was a circRNA. Convergent primers were used to detect NRG-1 mRNA. Divergent primers amplified circNRG-1 in cDNA but not gDNA. GAPDH served as linear control and size marker in base pairs. d Sanger sequencing confirmed head-to-tail junction of circNRG-1. e RNA fluorescence in situ hybridization for circNRG-1 was detected. Nuclei were stained with DAPI. Scale bars = 50 μm. f qRT-PCR detected circNRG-1 expression in MASMCs treated with Ang II (10 −7 M) for the different times. Data represent the means ± SEM of three independent experiments. * P < 0.05, *** P < 0.001 vs . Ang II for 0 h

Article Snippet: Circular RNA expression profiling was performed using Arraystar Mouse circRNA Array V2 analysis (Arraystar, USA).

Techniques: Expressing, Control, Amplification, Marker, Sequencing, Fluorescence, In Situ Hybridization, Staining, Quantitative RT-PCR

Journal: Cell Death & Disease

Article Title: Angiotensin II inhibits apoptosis of mouse aortic smooth muscle cells through regulating the circNRG-1/miR-193b-5p/NRG-1 axis

doi: 10.1038/s41419-019-1590-5

Figure Lengend Snippet: The orange, purple and green nodes represent circRNA, miRNA and mRNA respectively. Markers highlighting staining showed circNRG-1-miR-193b-5p-NRG-1 interactions

Article Snippet: Circular RNA expression profiling was performed using Arraystar Mouse circRNA Array V2 analysis (Arraystar, USA).

Techniques: Staining

Journal: Molecular Therapy. Nucleic Acids

Article Title: The circular RNA Ataxia Telangiectasia Mutated regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms

doi: 10.1016/j.omtn.2023.08.017

Figure Lengend Snippet: Circular RNAs are deregulated in human abdominal aortic aneurysm (A) Volcano plot depicting downregulated (51, blue) and upregulated (40, red). Circular RNAs (circRNAs) in human elective human abdominal aortic aneurysm (eAAA, n = 11) vs . control (CTRL, n = 6) aorta specimens, as resulted by array experiments. Log2 fold change and -log10 p value are plotted on the x and y axes, respectively. IDs of circRNAs meant for a first round of validation are highlighted. Statistics: unpaired t test; p values <0.05 are considered significant. (B) Pie chart illustrating the proportion of exonic (89.8%), intronic (5.7%), sense overlapping (3.4%), and antisense (1.1%) array-identified differentially expressed circRNAs. Absolute numbers are further indicated for each group. (C) Real-time quantitative PCR (qPCR) validation of hsa_circ_0005660 (c NFIX ), hsa_circ_0003641 (c ATM ), hsa_circ0042103 (c MYOCD ), hsa_circ003218 (c BMPR2 ), hsa_circ0004771 (c NRIP1 ), and hsa_circ0005615 (c NFATC3 ) differential expression in human eAAA (N = 8) and CTRL (N = 4) aortas. 2 –ddCT was calculated by normalizing on RPLPO . Data are represented as mean ± SEM. Statistics: unpaired t test; p values <0.05 are considered significant. NS, not significant; eAAA, elective AAA.

Article Snippet: The resulting labeled cDNA was then purified and 1 μg was fragmented, heated, and subsequently hybridized with an 8 × 15k commercially available array chip displaying 13,617 human circRNAs (Arraystar, no. AS-S-CR-H-V2.0) for 17 h at 65°C in an Agilent Hybridization Oven.

Techniques: Control, Biomarker Discovery, Real-time Polymerase Chain Reaction, Quantitative Proteomics

Journal: Medicine

Article Title: Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients

doi: 10.1097/MD.0000000000016072

Figure Lengend Snippet: CircRNA expression profiles of CD patients (n = 5) in comparison with HCs (n = 5) screened by microarray analysis. A, Boxplot view showed the distribution of normalized intensity values for CD patients (T12, T40, T49, and T51) and HCs (C1, C2, C3, C4, and C5). B, Scatter plot indicated the variation of circRNA expression between groups. Dots outside the green lines represented circRNAs with logarithmized expression changes greater than 2-fold between groups. C, Volcano plots showed the values of FC and P of the microarray data. Red dots indicated significantly dysregulated circRNAs. D, Hierarchical clustering revealed circRNA expression profiles of CD and HCs. Red color strip represented relatively high expression, while green color one indicated relatively low expression. circRNA = circular RNA, CD = Crohn disease, FC = fold-change, HCs = health controls.

Article Snippet: The microarray hybridization of all the RNA samples was undertaken as previously described by Ouyang et al. [ ] Human circRNA Arrays (Arraystar Inc., Rockville, MD) was used for screening differentially expressed circRNAs.

Techniques: Expressing, Comparison, Microarray, Stripping Membranes

Journal: Medicine

Article Title: Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients

doi: 10.1097/MD.0000000000016072

Figure Lengend Snippet: Verification of the relatively expression level of 5 up-regulated circRNAs (092520, 102610, 004662, 103124, and 103546) by RT-PCR and qPCR. PBMCs from 52 CD patients and 38 HCs were used for initial verification. CircRNA_004662 was further validated in 87 CD patients and 55 HCs and 50 UC patients. The statistical significance between CD, UC, and HCs was calculated by Student t test or one-way ANOVA. A, The relative expression of circRNA_09250. B, The relative expression of circRNA_102610. C, The relative expression of circRNA_004662. D, The relative expression of circRNA_103124. E, The relative expression of circRNA_103546. P < .05 was considered as statistically significant. ∗ P = .01; ∗∗ P < .001. ANOVA = analysis of variance, CD = Crohn disease,circRNA = circular RNA, HCs = health controls, qPCR = quantitative polymerase chain reaction, RT-PCR = reverse transcription polymerase chain reaction, PBMCs = peripheral blood mononuclear cells, UC = ulcerative colitis.

Article Snippet: The microarray hybridization of all the RNA samples was undertaken as previously described by Ouyang et al. [ ] Human circRNA Arrays (Arraystar Inc., Rockville, MD) was used for screening differentially expressed circRNAs.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Reverse Transcription, Polymerase Chain Reaction

Journal: Medicine

Article Title: Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients

doi: 10.1097/MD.0000000000016072

Figure Lengend Snippet: ROC curve analysis to evaluate diagnostic value of validated circRNAs. Four up-regulated circRNAs (103124, 004662, 102610, and 092520) verified were analyzed. AUC = area under curve, circRNA = circular RNA, CI = confidence interval, ROC = receiver operating characteristic, SEM = standard error of mean.

Article Snippet: The microarray hybridization of all the RNA samples was undertaken as previously described by Ouyang et al. [ ] Human circRNA Arrays (Arraystar Inc., Rockville, MD) was used for screening differentially expressed circRNAs.

Techniques: Diagnostic Assay

Journal: Medicine

Article Title: Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients

doi: 10.1097/MD.0000000000016072

Figure Lengend Snippet: CircRNA_004662 and the 5 most potential target miRNAs predicted. miRNAs that may bind to circRNA were predicted by TargetScan and miRanda. circRNA = circular RNA, miRNA = microRNA.

Article Snippet: The microarray hybridization of all the RNA samples was undertaken as previously described by Ouyang et al. [ ] Human circRNA Arrays (Arraystar Inc., Rockville, MD) was used for screening differentially expressed circRNAs.

Techniques:

Journal: Medicine

Article Title: Circular RNA expression profile in peripheral blood mononuclear cells from Crohn disease patients

doi: 10.1097/MD.0000000000016072

Figure Lengend Snippet: Network of circRNA_004662-miRNA-mRNA. circRNA = circular RNA, miRNA = microRNA.

Article Snippet: The microarray hybridization of all the RNA samples was undertaken as previously described by Ouyang et al. [ ] Human circRNA Arrays (Arraystar Inc., Rockville, MD) was used for screening differentially expressed circRNAs.

Techniques: