Journal: Frontiers in Neuroscience

Article Title: Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

doi: 10.3389/fnins.2020.00081

Figure Lengend Snippet: Characterization of the expression profile of circular RNAs in blood samples of MCAO-treated mice. (A) Normalized intensities of all circular RNAs expressed in the blood in sham and 5 min, 3-h, and 24-h MCAO-treated mice; n = 3 per group. (B) The scatter plots show the differentially expressed circRNAs in the 5-min, 3-h, and 24-h MCAO groups compared with sham. circRNAs in the scatter plot above and below the diagonal line indicate upregulation and downregulation, respectively. (C) Volcano plots show circRNA expression profiles in the 5-min, 3-h, and 24-h MCAO groups compared with sham control. Red dots represent differentially expressed circRNAs ( p < 0.05 and fold-change ≥ 2.0). (D) Distribution of different types of differentially expressed circRNAs, including those consisting of exon, intron, intergenic region, sense, and antisense sequences. (E) Venn diagram shows the overlapping differentially expressed circRNA probes among the three groups compared with sham control. The total numbers of probes exhibiting differential expression in 5 min, 3 h, and 24 h are 1051, 782, and 2721, respectively.

Article Snippet: Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled on the circRNA expression microarray slide [Arraystar Mouse circRNA Array v2 (8 × 15K, Arraystar)].

Techniques: Expressing, Control, Quantitative Proteomics

Journal: Frontiers in Neuroscience

Article Title: Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

doi: 10.3389/fnins.2020.00081

Figure Lengend Snippet: RT-qPCR verification of the microarray data from mouse blood. Representative circRNAs with significant differential expression at 5 min (upper panel), 3 h (middle panel), and 24 h of MCAO (lower panel) were verified by RT-qPCR. Left and right panels show the circRNAs with upregulation and downregulation, respectively. Values are mean ± SEM ( n = 3 per group). ∗ p < 0.05, ∗∗ p < 0.05, and ∗∗∗ p < 0.001 compared with sham (independent samples t -test, single-tailed).

Article Snippet: Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled on the circRNA expression microarray slide [Arraystar Mouse circRNA Array v2 (8 × 15K, Arraystar)].

Techniques: Quantitative RT-PCR, Microarray, Quantitative Proteomics

Journal: Frontiers in Neuroscience

Article Title: Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

doi: 10.3389/fnins.2020.00081

Figure Lengend Snippet: circRNA-miRNA interaction. Diagrams show the predicted miRNAs (square boxes) that bind to the verified differentially expressed circRNAs (round circles) at the 5-min (A) , 3-h (B) , and 24-h (C) time points of MCAO in mice. Blue lines represent upregulation; red lines represent downregulation.

Article Snippet: Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled on the circRNA expression microarray slide [Arraystar Mouse circRNA Array v2 (8 × 15K, Arraystar)].

Techniques:

Journal: Frontiers in Neuroscience

Article Title: Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

doi: 10.3389/fnins.2020.00081

Figure Lengend Snippet: Gene ontology analysis. Gene ontology classifications of the circRNA-miRNA target genes at the (A) 5-min, (B) 3-h, and (C) 24-h time points of MCAO. Color key represents log( p -value).

Article Snippet: Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled on the circRNA expression microarray slide [Arraystar Mouse circRNA Array v2 (8 × 15K, Arraystar)].

Techniques:

Journal: Frontiers in Neuroscience

Article Title: Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke

doi: 10.3389/fnins.2020.00081

Figure Lengend Snippet: KEGG pathway analysis of circRNA-miRNA target genes. (A) KEGG pathway analysis of the circRNA-miRNA target genes at the (A) 5-min, (B) 3-h and (C) 24-h time points of MCAO. Color key represents log( p value).

Article Snippet: Fifty microliters of hybridization solution was dispensed into the gasket slide and assembled on the circRNA expression microarray slide [Arraystar Mouse circRNA Array v2 (8 × 15K, Arraystar)].

Techniques:

Journal: Aging (Albany NY)

Article Title: Comprehensive analysis of differentially expressed profiles of Alzheimer’s disease associated circular RNAs in an Alzheimer’s disease mouse model

doi: 10.18632/aging.101387

Figure Lengend Snippet: The hierarchical cluster, scatter plot and volcano plot of differential expression of circRNAs in 10-month-old SAMP8 versus age-matched SAMR1 and 10-month-old SAMP8 versus 5-month-old SAMP8. ( A ) Hierarchical cluster of differentially expressed circRNAs. “green” indicates low intensity, “black” indicates medium intensity and “red” indicates strong intensity. ( B ) Scatter plot of circRNA signal values. The values of X and Y axes represents the normalized signal values of the samples (log2 scaled) and the averaged normalized signal values of samples (log2 scaled) respectively. The green lines are fold change lines. The CircRNAs above the top green line and below the bottom green line demonstrates more than 1.5-fold change of circRNAs between the two compared samples. ( C ) Volcano plot of differential expression of circRNAs. The vertical lines correspond to 1.5-fold up and down, respectively. The horizontal line represents a P -value of 0.05, and the red point in the plot represents the differentially expressed circRNAs with statistical significance.

Article Snippet: Three hippocampal tissues of SAMP8 and SAMR1 were used for microarray assay to determine differentially expressed circRNAs using the circRNAs chip (Arraystar mouse circRNAs chip, AraryStar) containing 14,236 probes specific for mouse circular RNAs splicing sites.

Techniques: Quantitative Proteomics

Journal: Aging (Albany NY)

Article Title: Comprehensive analysis of differentially expressed profiles of Alzheimer’s disease associated circular RNAs in an Alzheimer’s disease mouse model

doi: 10.18632/aging.101387

Figure Lengend Snippet: The expression levels of candidate circRNAs for validation by real-time qPCR in 15 10-month-old SAMR1 and SAMP8 hippocampal tissues. Statistically differences were calculated by t -test using SPSS 13.0 software. * P <0.05, ** P <0.01 versus SAMP8 group.

Article Snippet: Three hippocampal tissues of SAMP8 and SAMR1 were used for microarray assay to determine differentially expressed circRNAs using the circRNAs chip (Arraystar mouse circRNAs chip, AraryStar) containing 14,236 probes specific for mouse circular RNAs splicing sites.

Techniques: Expressing, Biomarker Discovery, Software

Journal: Aging (Albany NY)

Article Title: Comprehensive analysis of differentially expressed profiles of Alzheimer’s disease associated circular RNAs in an Alzheimer’s disease mouse model

doi: 10.18632/aging.101387

Figure Lengend Snippet: The expression levels of candidate circRNAs for validation by real-time qPCR in 15 10-month-old SAMP8 and 5-month-old SAMP8 hippocampal tissues. Statistically differences were calculated by t -test using SPSS 13.0 software. ** P <0.01 versus 5-month-old SAMP8 group.

Article Snippet: Three hippocampal tissues of SAMP8 and SAMR1 were used for microarray assay to determine differentially expressed circRNAs using the circRNAs chip (Arraystar mouse circRNAs chip, AraryStar) containing 14,236 probes specific for mouse circular RNAs splicing sites.

Techniques: Expressing, Biomarker Discovery, Software

Journal: Life sciences

Article Title: Role of circular RNA cdr1as in modulation of macrophage phenotype

doi: 10.1016/j.lfs.2022.121003

Figure Lengend Snippet: Microarray analysis of differentially expressed circular RNAs in bone marrow derived macrophages. (A) The BMDMs were sorted based on the following cell surface markers: pro-inflammatory- F4/80+, CD86+, CD11c+, CD206−; anti-inflammatory- F4/80+, CD86−, CD11c−, CD206+. Total RNA was isolated. (B) Heat map revealing differential circular RNA expression profiles between pro-inflammatory and anti-inflammatory macrophages. The red color indicates a higher FC value; green indicates a smaller FC value. (C) Volcano plot comparing significantly expressed circular RNA between pro-inflammatory and anti-inflammatory macrophages. The circular RNA expression log 2- transformed FC values (x-axis) were plotted against the log10 P values (on the y-axis). The red dots represent the circular RNAs having an FC value ≥1.5 and P < 0.05 comparing between pro-inflammatory and anti-inflammatory macrophages. (D) Box plot visualizing the distribution of a dataset for the circRNAs profiles. The distributions were nearly the same after normalization. (E) Scatter plot demonstrating the distributions of circular RNAs that are differentially expressed between pro-inflammatory and anti-inflammatory macrophages. The values of the x- and y-axes in the scatter plot were averaged to the normalized signal values of the group. FC, fold change; circRNA, circular RNA; N, naïve; P, pro-inflammatory; A-anti-inflammatory macrophages.

Article Snippet: Then, the enriched circular RNAs samples were then amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar) and hybridized onto the Arraystar Mouse circRNA Array V2 (8×15K, Arraystar).

Techniques: Microarray, Derivative Assay, Isolation, RNA Expression, Transformation Assay