Journal: Experimental and Therapeutic Medicine

Article Title: Differential expression profile study and gene function analysis of maternal foetal-derived circRNA for screening for Down's syndrome

doi: 10.3892/etm.2019.8288

Figure Lengend Snippet: Results of target prediction and sequence analysis of miRNA response elements. miR/miRNA, microRNA; circRNA, circular RNA.

Article Snippet: To identify circRNAs acting as miRNA sponges, the circRNA/miRNA interactions were predicted using a miRNA target prediction software (cat. no. AS-S-CR-H-V2.0; Arraystar, Inc.) based on TargetScan ( ) and miRanda , and the differentially expressed circRNAs were annotated with the circRNA/miRNA interaction information.

Techniques: Sequencing

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: Boxplots of circRNA expression levels, normalized to MS2 RNA, in healthy subjects, BAG3 -related DCM, idiopathic DCM, ischemic DCM, and LMNA -related DCM. The analysis was carried out using qRT-PCR. Data are present in log 2 . Data represent the mean ± SEM. * p < 0.05. Abbreviations: BAG3, BCL2-associated athanogene 3; CT, healthy cohort; circRNA, circular RNA; DCM, dilated cardiomyopathy; LMNA , lamin A/C; LMNA Ph − , LMNA carrier of the pathogenic variant; LMNA Ph+ , LMNA carrier phenotype positive

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques: Expressing, Quantitative RT-PCR, Variant Assay

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: Comparisons of single circRNA as predictors of DCM

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques:

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: Correlation between the echocardiographic variables and individual circRNA for the LMNA cohort

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques:

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: CircRNA-centered regulatory network established among the selected circRNAs. The depicted interactions are based on data extracted from the circInteractome database and include miRNAs and RBPs. CircRNAs are represented as squares, RBPs as circles and miRNAs as triangles. The size of each symbol is proportional to the number of interactions established. The edge thickness is also proportional to the number of targets for each interacting partner as included in the circInteractome database. The regulatory network was prepared with Navigator software . Abbreviations: DCM, dilated cardiomyopathy; LMNA , lamin A/C gene; miRNA, microRNA; RBP, RNA-binding protein

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques: Software, RNA Binding Assay

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: Differentially expressed circRNA potentially interact with RBP and miRNAs

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques:

Journal: Journal of Molecular Medicine (Berlin, Germany)

Article Title: Circulating circRNA as biomarkers for dilated cardiomyopathy etiology

doi: 10.1007/s00109-021-02119-6

Figure Lengend Snippet: Peripheral circRNA levels in the study groups

Article Snippet: The labelled cDNAs were hybridized onto the Arraystar Human circRNA Array V2.0 (Arraystar, Inc.).

Techniques:

Journal: Cell Death & Disease

Article Title: Long intergenic non-coding RNA APOC1P1-3 inhibits apoptosis by decreasing α -tubulin acetylation in breast cancer

doi: 10.1038/cddis.2016.142

Figure Lengend Snippet: LncRNA microarray screening and qPCR validation for differentially expressed lncRNAs in breast cancer. The microarray results in five pairs of fresh breast cancer tissues and corresponding para-cancer normal tissues were shown in ( a , b , and c ). ( a ) Quality assessment of lncRNA data after filtering using box plot. The box plot is a convenient way to quickly visualize the distributions of a data set. It is commonly used for comparing the distributions of the intensities from all samples. After normalization, the distributions of log2 ratios among all tested samples are nearly the same. Red bars indicate abnormal values. Blue boxes, the bottom and top of the box are the first and third quartiles, and the band inside the box is the median. ( b ) The scatter plot for assessing the lncRNA expression variation between cancer and para-cancer tissues. The values of X and Y axes in the scatter plot are the normalized signal values of the samples (log2 scaled) or the averaged normalized signal values of groups of samples (log2 scaled). The green lines are fold change lines (the default fold change value given is 1.5). The lncRNAs above the top green line and below the bottom green line indicated >1.5-fold change of lncRNAs between the two compared samples or the two compared groups of samples. ( c ) Hierarchical clustering for ‘differentially expressed lncRNAs for cancer versus para-cancer'. ‘Red' indicates high relative expression, and ‘blue' indicates low relative expression. The result from hierarchical clustering shows a distinguishable lncRNA expression profiling among samples. ( d ) qPCR detection showed all breast cancer cell lines bear higher expression level of APOC1P1-3 than non-tumoral mammary epithelial cell line MCF10A. Data are shown as the mean±S.D. Error bars indicate S.D. ** P <0.01 versus control (MCF10A). ( e ) qPCR detection in 25 pairs of fresh tissues showed APOC1P1-3 was highly expressed in breast cancer tissues. ΔΔCt=ΔCt (cancer)−ΔCt (normal), ΔCt=Ct ( APOC1P1-3 )−Ct ( GAPDH )

Article Snippet: After hybridization, using Human LncRNA Microarray v2.0 (Arraystar, Rockville, MD, USA), slides were scanned with the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) and analyzed with Agilent Feature Extraction software v. 11.5.1.1.

Techniques: Microarray, Biomarker Discovery, Expressing, Control

Journal: Gastroenterology

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells

doi: 10.1053/j.gastro.2019.07.029

Figure Lengend Snippet: Mecp2 regulates the transcripts controlling myofibroblast DNA replication, cell cycle and integrity, metabolism, and fibrogenesis. ( A ) Western blot for Mecp2 in HSCs from WT or Mecp2 –/y mice. Schematic showing the samples used for lncRNA microarray and RNA microarray. ( B ) Volcano plot and heatmap displaying results of mRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. ( C ) Representation of the groups with 2-fold or greater change in gene expression after the KEGG pathway enrichment analysis. ( D ) Top significantly enriched canonical pathway identified by IPA, showing cell cycle control of chromosomal replication. Blue nodes signify down-regulated gene Mecp2 –/y fibroblasts; red signifies up-regulation. Symbol shapes signify the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set.

Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven.

Techniques: Western Blot, Microarray, Isolation, Control, Gene Expression

Journal: Gastroenterology

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells

doi: 10.1053/j.gastro.2019.07.029

Figure Lengend Snippet: Mecp2 is a regulator of the noncoding transcriptome. ( A ) Volcano plot and heatmap displaying results of lncRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. ( B ) Schematic showing the lncRNAs classified according with their genomic location. ( C ) Schematic showing the lncRNAs according to their association with known and unknown protein coding genes. ( D ) Heatmap displaying results of lncRNA microarray performed on activated HSCs isolated from 3 control and 3 Mecp2 –/y mice. The top 50 most up-regulated and down-regulated lncRNAs are shown. Blue are down-regulated; red, up-regulated; white, unchanged. ( E ) IPA was used to form a network of focus genes that are downstream targets of differentially expressed lncRNAs. Blue nodes show down-regulated genes in Mecp2 –/y myofibroblasts, red nodes are up-regulated. Symbol shape signifies the nature of the encoded protein, and unshaded symbols signify genes relevant to the pathway but not differentially expressed in our data set.

Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven.

Techniques: Microarray, Isolation, Control

Journal: Gastroenterology

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells

doi: 10.1053/j.gastro.2019.07.029

Figure Lengend Snippet: Identification/representation of the down-regulated transcript uc008hgf as in close physical association with the ACTA2 (α-SMA) locus. mRNA levels of uc008hgf.1 and α-SMA quantified by qRT-PCR to validate the results of microarray. Predicted RNA secondary structures from uc008hgf.1 lncRNA obtained with CentroidFold software using the CONTRAfold model. Error bars in relevant panels represent mean ± SEM. Statistical significance was determined by Student t test; * P < .05.

Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven.

Techniques: Quantitative RT-PCR, Microarray, Software

Journal: Gastroenterology

Article Title: Fibrogenic Activity of MECP2 Is Regulated by Phosphorylation in Hepatic Stellate Cells

doi: 10.1053/j.gastro.2019.07.029

Figure Lengend Snippet: Graphical view of differentially expressed coding-noncoding gene coexpression network analysis represents similar patterns of expression and interconnectivity of the most representative Gene Ontology terms (cell cycle, DNA metabolic process, innate immunity, and protein activation cascades). The interaction network was produced in Cytoscape, where nodes correspond to mRNA ( triangles in purple ) or lncRNA ( circles in green ), and the edges are the coexpression links.

Article Snippet: The labeled complementary RNAs were purified, and 1 μg of each labeled complementary RNA was hybridized onto the Mouse LncRNA Array v2.0 (8 × 60,000, Arraystar) for 17 hours at 65°C in an Agilent (Santa Clara, CA) Hybridization Oven.

Techniques: Expressing, Activation Assay, Produced