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: 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