Journal: Experimental and Therapeutic Medicine

Article Title: Microarray analysis of long non-coding RNA expression profiles in Marfan syndrome

doi: 10.3892/etm.2020.9093

Figure Lengend Snippet: Microarray profiling of lncRNAs in the MFS and NA tissue specimens. (A) Volcano plots, (B) scatter plots and (C) hierarchical clustering showing the lncRNA expression profiling (P<0.05 and fold change ≥1.5). Upregulated lncRNAs are denoted in red and downregulated in green. lncRNA, long noncoding RNA; MFS, Marfan syndrome; NA, normal aorta.

Article Snippet: An Arraystar Human Microarray lncRNA v3.0 (array format: 8 x 60K; Arraystar, Inc.), which can probe more than 30,000 lncRNAs, covering all lncRNAs from authoritative databases RefSeq ( http://www.ncbi.nlm.nih.gov/projects/RefSeq ) , UCSC Known Genes ( http://genome.ucsc.edu ) , LNCipedia ( http://www.lncipedia.org ) , NONCODEv4 ( http://www.noncode.org ) ( ) and Ensembl ( https://asia.ensembl.org ) ( ) and their coding proteins, were used for microarray analysis.

Techniques: Microarray, Expressing

Journal: Experimental and Therapeutic Medicine

Article Title: Microarray analysis of long non-coding RNA expression profiles in Marfan syndrome

doi: 10.3892/etm.2020.9093

Figure Lengend Snippet: The lncRNAs and mRNA co-expression network. The interaction network of differentially expressed genes (lncRNA: uc003jka.1, uc003jox.1, XIST, linc-LPA-1, linc-PPWD1). Round nodes represent protein-coding genes and square nodes represent lncRNAs. Blue nodes represent upregulated genes or lncRNAs, red nodes represent downregulated genes or lncRNAs. The node size represents the connectivity, with larger node showing that more genes or lncRNAs are co-expressed with this gene or lncRNA. Solid lines represent positive correlation and dotted lines negative correlation. lncRNA, long noncoding RNA; XIST, X-inactive specific transcript; linc-LPA-1, linc-lysophosphatidic acid receptor 1; linc-PPWD1, linc-peptidylprolyl isomerase domain and wd repeat containing 1.

Article Snippet: An Arraystar Human Microarray lncRNA v3.0 (array format: 8 x 60K; Arraystar, Inc.), which can probe more than 30,000 lncRNAs, covering all lncRNAs from authoritative databases RefSeq ( http://www.ncbi.nlm.nih.gov/projects/RefSeq ) , UCSC Known Genes ( http://genome.ucsc.edu ) , LNCipedia ( http://www.lncipedia.org ) , NONCODEv4 ( http://www.noncode.org ) ( ) and Ensembl ( https://asia.ensembl.org ) ( ) and their coding proteins, were used for microarray analysis.

Techniques: Expressing

Journal: Experimental and Therapeutic Medicine

Article Title: Microarray analysis of long non-coding RNA expression profiles in Marfan syndrome

doi: 10.3892/etm.2020.9093

Figure Lengend Snippet: Reverse transcription-quantitative PCR validation. Compared to healthy controls, 5 long noncoding RNAs (uc003jka.1, uc003jox.1, XIST, linc-LPA-1, linc-PPWD1) with highest degree were selected. Results were consistent with the findings obtained from the microarray chip analysis (n=6). Data are presented as the mean ± standard deviation. * P<0.05, ** P<0.01 vs. NA samples. MFS, Marfan syndrome; NA, normal aorta; XIST, X-inactive specific transcript; linc-LPA-1, linc-lysophosphatidic acid receptor 1; linc-PPWD1, linc-peptidylprolyl isomerase domain and WD repeat containing 1.

Article Snippet: An Arraystar Human Microarray lncRNA v3.0 (array format: 8 x 60K; Arraystar, Inc.), which can probe more than 30,000 lncRNAs, covering all lncRNAs from authoritative databases RefSeq ( http://www.ncbi.nlm.nih.gov/projects/RefSeq ) , UCSC Known Genes ( http://genome.ucsc.edu ) , LNCipedia ( http://www.lncipedia.org ) , NONCODEv4 ( http://www.noncode.org ) ( ) and Ensembl ( https://asia.ensembl.org ) ( ) and their coding proteins, were used for microarray analysis.

Techniques: Reverse Transcription, Real-time Polymerase Chain Reaction, Biomarker Discovery, Microarray, Standard Deviation

Journal: Journal of Cellular and Molecular Medicine

Article Title: A novel antisense lncRNA NT5E promotes progression by modulating the expression of SYNCRIP and predicts a poor prognosis in pancreatic cancer

doi: 10.1111/jcmm.15718

Figure Lengend Snippet: LncNT5E is up‐regulated in pancreatic cancer (PC) tissues and cell lines. A, The heat map from our previous lncRNA microarray reflected the differentially expressed lncRNAs in PC and normal tissues. T represents PC tissue, and N represents normal pancreatic tissue. ENST00000421594 indicates lncNT5E. B, Relative expression of lncNT5E in 45 paired PC and adjacent normal tissues. LncNT5E expression from all tissues was normalized to 18S expression (ΔCT) and then compared with adjacent normal tissues and converted to the fold change (2 −ΔΔCT ). C, Relative expression of lncNT5E in different cell lines. Data are shown as fold change (2 −ΔΔCT ). * P < .05, ** P < .01, *** P < .001

Article Snippet: We used microarray detection (H1602063, Arraystar Human LncRNA 8 × 60 k v3.0 1‐color) to study lncRNAs in three pairs of PC and adjacent normal tissues.

Techniques: Microarray, Expressing

Journal: Experimental Hematology & Oncology

Article Title: METTL3 modulates m6A modification of CDC25B and promotes head and neck squamous cell carcinoma malignant progression

doi: 10.1186/s40164-022-00256-3

Figure Lengend Snippet: METTL3 high expression is associated with poor prognosis of HNSCC patients. A Dot blot assay was conducted with mRNA extracted from HNSCC tissues and paired paracancerous normal tissues using an anti-m6A antibody, and MB (methylene blue) staining served as the loading control (representative images in left panel). The relative m6A contents on mRNA in HNSCC tissues and paired normal normal tissues were calculated (right panel, n = 7). B TCGA data showed that METTL3 expression was significantly upregulated in HNSCC (n = 520) than normal tissue (n = 44). C Disease-free survival (RFS) of HNSCC patients based on METTL3 expression obtained from GEPIA website ( http://gepia.cancer-pku.cn/ ). D The levels of METTL3 expression in HNSCC and paired normal tissues were measured by qRT-PCR (n = 10). E METTL3 protein levels were measured in HNSCC tissues and paired normal tissues by western blotting (n = 7). F METTL3 expression was significantly upregulated in HNSCC compared with the paired paracancerous normal tissue by IHC staining (n = 5, scale bars = 100 μm). G Kaplan–Meier OS analysis of HNSCC patients based on METTL3 expression measured by IHC of tissue microarray (n = 100). H Univariate Cox regression analysis was conducted in HNSCC patients (n = 100). All bars correspond to 95% confidence intervals. I Multivariate Cox regression analysis was conducted in HNSCC patients (n = 100). J The time-dependent receiver operating characteristic (ROC) analysis for the clinical risk score (TNM stage), the METTL3 risk score, and the combined METTL3 and clinical risk scores in HNSCC cohort

Article Snippet: After hybridizing these cRNAs onto a Arraystar Epitranscriptomic Microarray slide (8 × 60 K, Arraystar) and washing it, an Agilent Scanner G2505C was used to scan the array.

Techniques: Expressing, Dot Blot, Staining, Quantitative RT-PCR, Western Blot, Immunohistochemistry, Microarray

Journal: Experimental Hematology & Oncology

Article Title: METTL3 modulates m6A modification of CDC25B and promotes head and neck squamous cell carcinoma malignant progression

doi: 10.1186/s40164-022-00256-3

Figure Lengend Snippet: METTL3 mediates the m6A modification on CDC25B mRNA in HNSCC. A m6A-mRNA epitranscriptomic microarray showed signal pathways in which most differentially expressed gene enriched in METTL3 knockdown cells (SAS), DE represents differentially expressed. B m6A-mRNA epitranscriptomic microarray showed signal pathways in which most differentially methylated genes enriched in METTL3 knockdown cells (SAS), DM represents differentially methylated. C m6A-mRNA epitranscriptomic microarray showed an overlap of the total differentially expressed gene, total differentially methylated gene, and differentially expressed and methylated gene enriched in the cell cycle pathway. D Genes selected from the overlap were used for qRT-PCR in METTL3 knockdown and their corresponding control cells, and CDC25B was the most significantly downregulated gene upon knockdown of METTL3. E , F CDC25B mRNA expression was confirmed by qRT-PCR in METTL3 knockdown (FaDu) and METTL3 overexpression (Hep2) cells. G CDC25B protein level was measured by western blot assay in METTL3 knockdown SAS cells. H CDC25B protein level was measured by western blot assay in METTL3 knockdown FaDu cells. I CDC25B protein level was measured by western blot assay in METTL3 overexpressed Hep2 cells. J MeRIP-qPCR was conducted to detect the m6A level of CDC25B mRNA in METTL3 knockdown (SAS) cells. K MeRIP-qPCR was conducted to detect the m6A level of CDC25B mRNA in METTL3 knockdown (FaDu) cells. L , M The levels of CDC25B expression in METTL3 knockdown and their corresponding control cells treated with actinomycin D (5 μg/mL) at the indicated time points were detected by qRT-PCR. The data are the means ± SD of three independent experiments. */# p < 0.05; **/## p < 0.01; ***/### p < 0.001; ****/#### p < 0.0001

Article Snippet: After hybridizing these cRNAs onto a Arraystar Epitranscriptomic Microarray slide (8 × 60 K, Arraystar) and washing it, an Agilent Scanner G2505C was used to scan the array.

Techniques: Modification, Microarray, Methylation, Quantitative RT-PCR, Expressing, Over Expression, Western Blot