Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: CircRNA_103827 and circRNA_104816 expressions in granulosa cells according to patients’ clinical characteristics.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Biomarker Discovery

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: CircRNA_103827 and circRNA_104816 expression levels in granulosa cells according to ART outcomes.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: The top 10 significantly differentially expressed circRNAs between young and older women ranked by fold change.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques:

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: Comparison of candidate circRNAs (circRNA_103829, circRNA_10827, circRNA_104816, circRNA_101889, circRNA_103828, circRNA_100833, circRNA_104852, circRNA_103611) expression levels in granulosa cells from additional young (n = 20) and older (n = 20) women by qRT-PCR. YA, women with young age (≤ 30 years); AA, women with advanced age (≥ 38 years). P values were calculated by Mann-Whitney U test. Relative expressions were analyzed by 2 -ΔΔCt method which was normalized to GAPDH. For each box plotting, the central mark represents the median, the edges of the box represent the 25 th and 75 th percentiles, and the whiskers are the most extreme data points not considered outliers.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Comparison, Expressing, Quantitative RT-PCR, MANN-WHITNEY

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: ( A-E ) circRNA_103827 expression levels in granulosa cells according to (A) serum AMH levels, (B) AFC, (C) retrieved oocytes, (D) top quality embryos and (E) top quality embryo percentage. ( F-J ) circRNA_104816 expression levels in granulosa cells according to (F) serum AMH levels, (G) AFC, (H) retrieved oocytes, (I) top quality embryos and (J) top quality embryo percentage.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: ROC analysis to evaluate predictive performance of circRNA_103827, circRNA_104816 expressions in granulosa cells and top quality embryo proportion for ( A-C ) clinical pregnancy outcomes, as well as for ( D-F ) live births. AUC, area under the ROC curve.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques:

Journal: PLoS ONE

Article Title: Circular RNA expression profiling of human granulosa cells during maternal aging reveals novel transcripts associated with assisted reproductive technology outcomes

doi: 10.1371/journal.pone.0177888

Figure Lengend Snippet: (A) CircRNA_103827/circRNA_104816 targeted “Top 5” miRNA-gene network was portrayed based on sequence-pairing prediction. A pink round node represents a gene, a blue square represents miRNA, and a yellow diamond represents a circRNA. Overlapping genes of both circRNAs in this interactive network were ANKRD20A9P , XIST and KCNQ1OT1 . (B) GO and (C) KEGG pathway analysis of circRNA_103827 and circRNA_104816 predicted target genes. The top 10 significantly enriched activities and their scores (negative logarithm of P value) were listed in the X-axis and the Y-axis, respectively.

Article Snippet: In stage 1, GCs samples from women of advanced age (AA, ≥ 38 years, n = 3) and young age (YA, ≤ 30 years, n = 3) were analyzed by a human circRNA microarray (8×15K, Arraystar Inc.).

Techniques: Sequencing

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