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: ALKBH5‐mediated m6A modification of lncRNA KCNQ1OT1 triggers the development of LSCC via upregulation of HOXA9

doi: 10.1111/jcmm.17091

Figure Lengend Snippet: Results of the m6A‐lncRNA expression profiles in LSCC. (A) Hierarchical clustering for lncRNAs with differential ‘m6A quantity’. The red‐green gradient colour scheme indicates the high and low m6A methylation relative quantity as referenced in the Color Key. The top dendrogram shows the tightness between the samples. Sample group members are represented by colour bars above the heat map. (B) Volcano plot. X‐axis: log2 (fold change); Y‐axis: ‐log10 ( P ‐value). The vertical green lines correspond to 1.2‐fold up and down, and the horizontal green line represents 0.05 p ‐value. The red dot in the figure represents the high m6A methylation lncRNAs, and the green dot represents the low m6A methylation lncRNAs. (C) Pie chart shows 33 high m6A methylation lncRNAs and 9 low m6A methylation lncRNAs

Article Snippet: The cRNAs were combined together and hybridized onto Arraystar Human lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

Techniques: Expressing, Methylation

Journal: Cancer Science

Article Title: Adoptive cell therapy using tumor‐infiltrating lymphocytes for melanoma refractory to immune‐checkpoint inhibitors

doi: 10.1111/cas.15009

Figure Lengend Snippet: Total mutation burden, transcriptome signature (ssGSEA score), and quantitative real‐time polymerase chain reaction analysis of pretreatment melanoma cells and expanded TILs. A, To evaluate their mutation status, exome sequencing was performed on the melanoma cells used for TIL manufacturing. The numbers of mutations and the mutated genes in each tumor are shown in the upper columns. Transcriptome signatures based on single‐sample gene set enrichment analysis (ssGSEA) of the tumor cells are shown in the lower columns. B, ssGSEA scores of gene sets related to tumor phenotype (based on microarray data) in the tumors of the three melanoma patients. The cut‐off score was set at 4,000. C, D, Quantitative RT‐PCR analysis of the expression levels of chemokines in the primary tumors (C) and of cytotoxic factors in the expanded TIL products (D). The results are fold‐changes in gene expression normalized to the endogenous reference gene; error bars are standard deviations

Article Snippet: Total RNA from isolated melanoma cells was subjected to microarray analysis using an Agilent SurePrint G3 Human GE v3 8x60K Microarray (DNA Chip Research Inc.).

Techniques: Mutagenesis, Real-time Polymerase Chain Reaction, Sequencing, Microarray, Quantitative RT-PCR, Expressing

Journal: PLoS ONE

Article Title: Adenomatous polyposis coli-binding protein end-binding 1 promotes hepatocellular carcinoma growth and metastasis

doi: 10.1371/journal.pone.0239462

Figure Lengend Snippet: (a and b) RNA microarray analysis to identify genes differentially expressed in the presence of EB1. Comparison of gene expression levels in EB1-KO HuH7 cells infected with control and EB1-expressing lentiviruses identified a number of genes upregulated by EB1 re-expression.

Article Snippet: After properly converting the extracted RNA to the cRNA labeled with Cy3 as recommended by the manufacturers, 0.6 μg of the cRNA was fragmented and hybridized at 65°C for 17 h to an Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID: 072363) containing a total of 58,201 probes excluding control probes.

Techniques: Microarray, Expressing, Infection

Journal: Frontiers in Immunology

Article Title: Identification of potential biomarkers and immune infiltration characteristics in recurrent implantation failure using bioinformatics analysis

doi: 10.3389/fimmu.2023.992765

Figure Lengend Snippet: Baseline Characteristics.

Article Snippet: Techniques , GPL16043 platform , Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 , GPL15789 platform , 10X Genomics Chromium platform.

Techniques: Microarray, Control