Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Microarray analysis was applied to detect the lncRNAs and mRNAs in glioma compared to normal peritumoral tissue. A – Differentially expressed lncRNAs were detected in gliomas. A, B – Differentially expressed mRNAs were detected in gliomas. C – Clustering data of lncRNAs in gliomas were analyzed. D – Clustering data of mRNAs in gliomas were analyzed

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Summary of data from microarray for three pairs of glioma and adjacent normal tissues

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray, RNA Expression

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: LncRNA-mRNA co-expression network: nodes with red cycle represent lncRNAs, nodes without cycle represent mRNAs, straight lines represent interactions between genes, purple represents increased expression, and blue represents decreased expression. The size of the node represents the degree; the higher the degree, the more genes interact with the particular node in the network

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Expressing

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Degree was used to assess interactions in the lncRNA/mRNA network. This table is a collection of a series of key lncRNA/mRNAs

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques:

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Comparison of microarray data and qPCR results. A – qPCR was used to verify expression of lncRNAs ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc003qmb.2. B – Distribution of lncRNA expression levels were provided. All six lncRNAs of ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc- 003qmb.2 were validated by qPCR analysis in the 40 paired glioma and peritumoral tissues. Each histogram represents the average fold change (T/N) with logarithmic conversion. Error bars are indicative of standard deviation. Distribution of lncRNA expression

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Comparison, Microarray, Expressing, Standard Deviation

Journal: Clinical and Translational Medicine

Article Title: Androgen receptor decreases the renal cell carcinoma bone metastases via suppressing the osteolytic formation through altering a novel circEXOC7 regulatory axis

doi: 10.1002/ctm2.353

Figure Lengend Snippet: CircRNA microarray and screening process. Results from circRNA microarray and bioinformatics analysis from five paired human RCC vs. RBM tissues were summarized in (A‐D). (A) Box plot demonstrated no significant differences in the distribution of intensity across 10 clinical samples. (B) Scatter plot displayed circRNAs expression correlation between RCC and RBM group. (C) Heat map generated from circRNAs microarray data reflecting circRNAs expression values in RCC and RBM groups. (D) Volcano plot showing DERs data. The red points indicate points‐of‐interest that display both large magnitude fold‐changes (x‐axis) and high statistical significance (‐log10 of p ‐value, y‐axis). The green line shows points above the line having p < 0.05 and points below the line having p > 0.05. This plot is colored such that those points having a fold‐change less than 2 (log2 = 1) are shown in gray. (E) The qRT‐PCR was performed to show 32 selected candidate circRNAs expression levels in cells. (F) The qRT‐PCR was performed on SW839 cells to show effects of manipulating efficiency of selected candidate circRNAs, ciR4#, ciR6#, ciR19#, and ciR26#. (G‐J) Interruption assays revealed that suppressing (G) ciR‐4# (hsa_circ_0001275), (H) ciR‐6# (hsa_circRNA_405974), expression cannot reverse/block the knocked‐down AR‐increased osteolytic formation in SW839 cells (scale bars, 200 μm), increasing (I) ciR‐19# (hsa_circ_0091743) expression, and (J) increasing ciR‐26# hsa_circ_0075303 expression cannot reverse/block the AR‐suppressed osteolytic formation in SW839 cell line (scale bars, 200 μm). For (E‐J), quantitation is at the right, and data are presented as Mean ± SD, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Abbreviation: N.S., not significant

Article Snippet: In the current study, five human RCC and five RCC bone metastasis tissues were deeply sequenced using Arraystar human circRNA V2.0 microarray.

Techniques: Microarray, Expressing, Generated, Quantitative RT-PCR, Blocking Assay, Quantitation Assay

Journal: Clinical and Translational Medicine

Article Title: Androgen receptor decreases the renal cell carcinoma bone metastases via suppressing the osteolytic formation through altering a novel circEXOC7 regulatory axis

doi: 10.1002/ctm2.353

Figure Lengend Snippet: The expression of circEXOC7 is regulated by DHX9. (A) The qRT‐PCR was performed on SW839 and OS‐RC‐2 cell lines to show correlation between AR and four genes related to circRNA biogenesis. Among them, ADAR2 and DHX9 have a positive correlation with AR mRNA expression. (B and C) The qRT‐qPCR was performed to show (B) knocking down DHX9, and not (C) ADAR2 gene, led to increased circEXOC7 expression in SW839 cells. (D) WB was performed on SW839 and OS‐RC‐2 cells to show that modulated AR expression also altered DHX9 expression. (E) Predicted AR binding sites on the DHX9 promoter region using website http://jaspar.genereg.net/ . (F) ChIP assay showing AR could bind to the No. 2 potential ARE on the DHX9 5′‐promoter region. (G) The wild type and mutant pGL3‐DHX9 promoter reporter constructs. (H and I) Luciferase activity after transfection of wild type or mutant DHX9 promoter reporter constructs in OS‐RC‐2 cells (H) transfected with AR‐cDNA or pWPI and SW839 cells (I) transfected with AR‐shRNA or pLKO. For (B and C), (H and I), data are presented as Mean ± SD, * p < 0.05, ** p < 0.01, *** p < 0.001. Abbreviation: N.S., not significant

Article Snippet: In the current study, five human RCC and five RCC bone metastasis tissues were deeply sequenced using Arraystar human circRNA V2.0 microarray.

Techniques: Expressing, Quantitative RT-PCR, Binding Assay, Mutagenesis, Construct, Luciferase, Activity Assay, Transfection, shRNA

Journal: Redox Report : Communications in Free Radical Research

Article Title: LncRNA Fendrr: involvement in the protective role of nucleolin against H 2 O 2 -induced injury in cardiomyocytes

doi: 10.1080/13510002.2023.2168626

Figure Lengend Snippet: lncRNAs regulated by nucleolin in cardiomyocytes. (A) Heatmap profile of lncRNA microarray analysis. Green to red colors indicate low to high transcriptional levels. The lncRNAs differentially expressed between the two groups were identified through paired t-test P ≤ 0.05 and a fold change (FC) ≥ 2.5; n = 3 independent biological samples for each group. (B) The expression of 15 selected lncRNAs in chip test, where 10 differentially expressed up-regulated lncRNAs (up) and 5 differentially expressed down-regulated lncRNAs (down) were selected. (C) The interactions between nucleolin and lncRNAs were confirmed by RIP and identified via qRT-PCR. *, P < 0.05, vs. IgG group, n = 3. pcDNA3.1, the empty vector served as negative control; pcDNA3.1-Nuc, overexpression nucleolin group. (D) Bioinformatics website predicted Fendrr binding elements with nucleolin.

Article Snippet: Using the Aglient Rat lncRNA microarray V2.0 (Arraystar, Rockville, MD, USA), three sample pairs were prepared for lncRNA microarray analysis in the nucleolin-overexpressing rat cardiomyocyte cell line and control group.

Techniques: Microarray, Expressing, Quantitative RT-PCR, Plasmid Preparation, Negative Control, Over Expression, Binding Assay