Journal: Stroke

Article Title: Circular RNA expression Profiles Alter Significantly in Mouse Brain after Transient Focal Ischemia

doi: 10.1161/STROKEAHA.117.017469

Figure Lengend Snippet: Majority (~80%) of the circRNAs altered after stroke are exonic (A). The circRNAs altered after stroke were transcribed from all 20 chromosomes (B). Real-time PCR confirmed the microarray data for 6 circRNAs (3 upregulated and 3 downregulated) at 6h reperfusion compared to sham (C). Values are mean ± SD (n =3/group). Real-time PCR analysis was conducted in triplicate. *p<0.05 compared to sham (Student’s T-test).

Article Snippet: The fluorophore-labeled cRNAs were purified (RNeasy Mini Kit; Qiagen USA) and 1 μg sample of each labeled cRNA was fragmented (60°C for 30 min in fragmentation buffer/blocking buffer; Arraystar USA), suspended in hybridization buffer and hybridized to a mouse circRNA microarray (8×15K, Arraystar USA).

Techniques: Real-time Polymerase Chain Reaction, Microarray

Journal: Genes

Article Title: Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

doi: 10.3390/genes13122258

Figure Lengend Snippet: Alterations of tsRNA expression profiles induced by septic cardiomyopathy. ( A ) Comparison of CK-MB in myocardial tissue of CLP group versus SHAM group. * p < 0.05. ( B ) Comparison of LDH in myocardial tissue of CLP group versus SHAM group. * p < 0.05. ( C ) Comparison of myocardial HE staining between CLP Group and SHAM group. ( D ) Septic cardiomyopathy-related tsRNAs were shown in the heat map. The colors in the panel indicate the relative expression levels (log2 transformation). The color bar graph on the top panel shows the sample group at the top. ( E ) The scatter plot showed that there were 158 significantly altered tsRNAs between CLP and SHAM groups ( p < 0.05, FC ≥ 1.5). ( F ) The volcano plot showed that there were 158 significantly altered tSNAs between CLP and SHAM groups ( p < 0.05, FC ≥ 1.5). Red showed up-regulated tsRNAs and blue showed down-regulated tsRNAs. Data were presented as the mean ± standard deviation ( n = 3). ( G ) Venn diagram indicates the relationship between up- and down-regulated expression groups and tsRNAs that have been studied in tRFdb. CLP: Cecal ligation and puncture; tRF: tRNA fragments; tiRNA: tRNA halves; tsRNA: tRNA-derived small RNA.

Article Snippet: We then hybridized on a mouse tsRNA microarray (8 × 15K, Arraystar) containing a 1767 tsRNA probe.

Techniques: Expressing, Comparison, Staining, Transformation Assay, Standard Deviation, Ligation, Derivative Assay

Journal: Genes

Article Title: Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

doi: 10.3390/genes13122258

Figure Lengend Snippet: Preliminary analysis of microarray results. ( A – C ) Pie chart of the distribution of tiRNA and tRF subtypes. The color represents the tiRNA and tRF subtypes. ( D , E ) Pie chart of the distribution of tsRNA-precursors. The color represents the tsRNA-precursors. tRF: tRNA fragments; tiRNA: tRNA halves; tsRNA: tRNA-derived small RNA.

Article Snippet: We then hybridized on a mouse tsRNA microarray (8 × 15K, Arraystar) containing a 1767 tsRNA probe.

Techniques: Microarray, Derivative Assay

Journal: Genes

Article Title: Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

doi: 10.3390/genes13122258

Figure Lengend Snippet: Identification of septic cardiomyopathy-related tsRNAs and qPCR verification. ( A – H ) The qPCR results confirmed that 5′tiRNA-34-AspGTC-2 ( n = 4 in SHAM group, n = 7 in CLP 12 h group, n = 3 in CLP 24 h group), 5′tiRNA-33-CysACA-1 ( n = 4 in SHAM group, n = 3 in CLP 12 h group, n = 3 in CLP 24 h group), 5′tiRNA-33-ProTGG-1 ( n = 3 in SHAM group, n = 4 in CLP 12 h group, n = 4 in CLP 24 h group), 5′tiRNA-32-LysCTT-11 ( n = 4 in SHAM group, n = 6 in CLP 12 h group, n = 4 in CLP 24 h group), 5′tiRNA-33-AlaTGC-7 ( n = 4 in SHAM group, n = 7 in CLP 12 h group, n = 4 in CLP 24 h group), 5′tiRNA-36-ArgTCT-1 ( n = 4 in SHAM group, n = 4 in CLP 12 h group, n = 4 in CLP 24 h group), 5′tiRNA-35-LeuCAG-4 ( n = 3 in SHAM group, n = 5 in CLP 12 h group, n = 4 in CLP 24 h group) and tRF5-18-ArgCCT-3 ( n = 4 in SHAM group, n = 5 in CLP 12 h group, n = 5 in CLP 24 h group) were consistent with tsRNA microarray data. Data were presented as mean ± standard deviation. * p < 0.05; ** p < 0.01; *** p < 0.001 compared with the SHAM group. CLP: Cecal ligation and puncture; qPCR: Quantitative real-time PCR; tRF: tRNA fragments; tiRNA: tRNA halves; tsRNA: tRNA-derived small RNA.

Article Snippet: We then hybridized on a mouse tsRNA microarray (8 × 15K, Arraystar) containing a 1767 tsRNA probe.

Techniques: Microarray, Standard Deviation, Ligation, Real-time Polymerase Chain Reaction, Derivative Assay

Journal: Genes

Article Title: Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

doi: 10.3390/genes13122258

Figure Lengend Snippet: Targets of septic cardiomyopathy-related tsRNAs. ( A – F ) The targets of 5′tiRNA-33-AlaTGC-7, 5′tiRNA-36-ArgTCT-1, 5′tiRNA-33-CysACA-1, 5′tiRNA-34-GlnCTG-5 and 3′tiRNA-41-ProTGG-4 are shown. tiRNA: tRNA halves; tsRNA: tRNA-derived small RNA.

Article Snippet: We then hybridized on a mouse tsRNA microarray (8 × 15K, Arraystar) containing a 1767 tsRNA probe.

Techniques: Derivative Assay

Journal: Genes

Article Title: Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

doi: 10.3390/genes13122258

Figure Lengend Snippet: Function detection of septic cardiomyopathy-related tsRNAs after ANG interference. ( A ) The effect of ANG interference is detected by qPCR ( n = 3 in NC group, n = 3 in si-ANG group) ( B ) The qPCR results confirmed that the expression of 5′tiRNA-33-CysACA-1 ( n = 4 in NC group, n = 3 in si-ANG group) changed after ANG was interfered. Data were presented as mean ± WB standard deviation. * p < 0.05 compared with the NC group. ( C ) The effect of si-ANG on cell viability after 24 h of LPS + TNF-α treatment ** p < 0.01; *** p < 0.001 compared with the Control group. ( D ) The effect of si-ANG on the release of LDH (cell death) after 24 h of LPS + TNF-α treatment ** p < 0.01; *** p < 0.001 compared with the Control group. si-ANG: ANG-specific siRNA; NC: negative control; qPCR: Quantitative real-time PCR; tRF: tRNA fragments; tiRNA: tRNA halves; tsRNA: tRNA-derived small RNA.

Article Snippet: We then hybridized on a mouse tsRNA microarray (8 × 15K, Arraystar) containing a 1767 tsRNA probe.

Techniques: Expressing, Standard Deviation, Control, Negative Control, Real-time Polymerase Chain Reaction, Derivative Assay

Journal: Frontiers in Genetics

Article Title: Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions

doi: 10.3389/fgene.2024.1356558

Figure Lengend Snippet: Predicted association of dysregulated lncRNAs to altered mRNA expression . (A) POVPC vs. DMSO treatment groups (effect of POVPC in wild type SMC), (B) siOCT4-DMSO vs. siNT-DMSO groups (effect of OCT4 inactivation), (C) siOCT4-POVPC vs. siOCT4-DMSO groups (effect of POVPC in OCT4 deficient SMC). Table lists microarray details of selected top lncRNA/mRNA predicted associations along with (i); KEGG pathway enrichment for mRNAs associated with lncRNAs based on the genomic proximity (<300 kbp) from IPA analysis (ii).

Article Snippet: The labeled RNA was hybridized onto Arraystar Mouse small RNA Microarray (8 × 15K, Arraystar).

Techniques: Expressing, Microarray

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: bioRxiv

Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

doi: 10.1101/2025.07.10.663777

Figure Lengend Snippet: Volcano plots showing the mature miRNAs differentially expressed in the TraxE126A mutants compared to wildtype littermates as identified by (A) miRNA sequencing and (B) miRNA microarray. Volcano plots showing the differentially expressed small RNA species identified using microarray analysis including (C) Precursor miRNAs (pre-miRNAs), (D) Small nucleolar RNAs (snoRNAs), (E) mature tRNAs and (F) tRNA-derived small RNAs (tsRNAs). In all the plots, the upregulated and downregulated miRNAs (false discovery rate, FDR <0.050 and log 2 fold change ≥0.200) are highlighted in red and blue, respectively. (TraxE126A, n=4; WT, n=5, all males). Largest changes were seen in tsRNA levels (majority are 5’-fragments) and mature miRNAs.

Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

Techniques: Sequencing, Microarray, Derivative Assay

Journal: bioRxiv

Article Title: Genetic inactivation of the Translin/Trax RNase activity alters small RNAs including miRNAs, disrupts gene expression and impairs distinct forms of hippocampal synaptic plasticity and memory

doi: 10.1101/2025.07.10.663777

Figure Lengend Snippet: (A) Venn diagram showing the overlap between mature miRNAs identified using miRNA sequencing and microarray analysis (with FDR<0.050 and log 2 fold change ≥0.200). A total of 12 miRNAs (10 upregulated and 2 downregulated) were found to be common and were used for target prediction using miRDB database. (B) An upset plot showing the shared and unique predicted mRNA target profiles in the miRDB database for the 12 common miRNAs. Only targets with miRDB Target Score ≥60 are included. (C) Top 15 KEGG pathways and (D) Gene Ontology (GO) Biological Process terms from the functional enrichment analysis of the predicted targets of the 12 common miRNAs performed using DAVID database.

Article Snippet: The labeled RNA species are then hybridized onto Arraystar Small RNA Expression Microarray (8×15K format), scanned by an Agilent G2505C scanner followed by data processing and analysis.

Techniques: Sequencing, Microarray, Functional Assay

Journal: Advances in drug and alcohol research

Article Title: Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes

doi: 10.3389/adar.2022.10831

Figure Lengend Snippet: Schematic diagram detailing the experimental pipeline utilized to generate the list of top novel ethanol-responsive hub lncRNA candidates to target for ethanol-related functional interrogation. Male mice were given a priming injection of either ethanol and pyrazole or saline and pyrazole and placed in either an ethanol- or room-air vapor champers for 16 hours/day, 4 days/week, for 7 weeks, respectively. Hippocampi were dissected 24 hours after the final vapor exposure and then subject to mRNA, lncRNA, circRNA, and miRNA microarray analysis. These data sets were then used to generate ceRNA networks of ethanol-responsive RNA genes.

Article Snippet: For circRNA analysis, Arraystar Inc. isolated total RNA, digested with RNase R (Epicentre, Inc.), fluorescently labeled (Arraystar Super RNA Labeling Kit), and subsequently hybridized to Arraystar Mouse circRNA Array V2 (8×15K).

Techniques: Functional Assay, Injection, Saline, Microarray

Journal: Advances in drug and alcohol research

Article Title: Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes

doi: 10.3389/adar.2022.10831

Figure Lengend Snippet: Volcano plots showing differential RNA expression based on log2 fold-change in expression (x-axis) and log10 p-value (y-axis) for (A) protein-coding RNA (mRNA), (B) long non-coding RNA (lncRNA), (C) circular RNA (circRNA), and (D) microRNA (miRNA). Each point indicates an individual non-duplicated probe on the microarray with blue = significantly down-regulated, red = significantly up-regulated, and black = non-significant. Significance is defined by p < 0.05.

Article Snippet: For circRNA analysis, Arraystar Inc. isolated total RNA, digested with RNase R (Epicentre, Inc.), fluorescently labeled (Arraystar Super RNA Labeling Kit), and subsequently hybridized to Arraystar Mouse circRNA Array V2 (8×15K).

Techniques: RNA Expression, Expressing, Microarray