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: bioRxiv

Article Title: Noncoding RNA’s competing endogenous gene pair as motif in serous ovarian cancer

doi: 10.1101/2022.04.04.486923

Figure Lengend Snippet: Functional analysis of the cceGPs. A) The 18 cceGPs or gene pair-circRNA motifs in SOC. B) Heatmap illustrating the expression abundance of circRNAs. C) Enriched functions of the 18 cceGPs in Reactome. D) Enriched functions of the 18 cceGPs in GO. Yellow node denotes functional category while grey node represents gene. E, F) Expression abundance of PRC1 and BBS4 in normal controls and SOCs. G, H) Correlations between circHUNK and PRC1 (BBS4 ) in SOCs. I) PRC1 -circHUNK- BBS4 as an example of cceGPs relationship in SOC progress.

Article Snippet: We performed Arraystar Human LncRNA Microarray V2.0 and Arraystar Human circRNA Array V2.0 analyses on all 16 samples.

Techniques: Functional Assay, Expressing

Journal: Frontiers in Pharmacology

Article Title: Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach

doi: 10.3389/fphar.2020.00927

Figure Lengend Snippet: Transcriptomic data information for Noonan syndrome, LEOPARD syndrome, and hypertrophic cardiomyopathy (HCM).

Article Snippet: GSE68316 , Human myocardial tissues , CapitalBio Human LncRNA Microarray v2.0 , • 7 patient samples: 7 HCM patients • 5 Control samples: 5 disease-free individuals.

Techniques: Expressing, Mutagenesis, Control, Microarray

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: A Summary of Publicly Accessible Biological Databases, their Inherent Data Types, Species Diversity, and Statistics of Raw Sequences Related to Different Genomic and Proteomic Data.

Article Snippet: LncRNADisease v2.0 , 2018 , lncRNAs, circRNAs , Animal, Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus , _ , 19,166 lncRNAs, 823 circRNAs, 529 diseases, 205,959 lncRNA-disease associations, 1004 circRNA-disease associations , .xlsx.

Techniques: Immunopeptidomics, Mutagenesis, Binding Assay, RNA modification, Functional Assay, Quantitative Proteomics, Virus, Bacteria, Next-Generation Sequencing

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Summary of Uniquely Pre-trained Language Models along with pre-training Data for RNA Sequence Analysis Tasks.

Article Snippet: LncRNADisease v2.0 , 2018 , lncRNAs, circRNAs , Animal, Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus , _ , 19,166 lncRNAs, 823 circRNAs, 529 diseases, 205,959 lncRNA-disease associations, 1004 circRNA-disease associations , .xlsx.

Techniques: Sequencing, Virus, Derivative Assay

Journal: Heliyon

Article Title: RNA sequence analysis landscape: A comprehensive review of task types, databases, datasets, word embedding methods, and language models

doi: 10.1016/j.heliyon.2024.e41488

Figure Lengend Snippet: Non-coding RNA target prediction related 4 distinct RNA sequence analysis tasks predictive pipelines performance.

Article Snippet: LncRNADisease v2.0 , 2018 , lncRNAs, circRNAs , Animal, Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus , _ , 19,166 lncRNAs, 823 circRNAs, 529 diseases, 205,959 lncRNA-disease associations, 1004 circRNA-disease associations , .xlsx.

Techniques: Sequencing, Control, Small Interfering RNA

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Screen of miRNAs and Targeting mRNAs Reveals the Negatively Regulatory Effect of miR-130b-3p on PTEN by PI3K and Integrin β1 Signaling Pathways in Bladder Carcinoma

doi: 10.3390/ijms18010078

Figure Lengend Snippet: Heat maps show expression profiles of miRNAs and co-expressed target mRNAs. Each row represents a sample and each column represents a miRNAs or mRNA. The red strip represents high relative expression and the green strip represents low relative expression. T represents the bladder cancer group, and N represents the normal control group. Each group contains four different samples. ( A ) Heat map of differentially expressed miRNAs (fold change ≥ 1.5 and p -value < 0.05); and ( B ) Heat map of co-expressed target mRNAs from the two most up- and the three most down-regulated miRNAs.

Article Snippet: The microarray hybridization was performed according to the manufacturer’s standard protocols (Agilent Technology, Shanghai, China) including purifying RNA, transcribing into fluorescent cDNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar, Shanghai, China) and the Human miRNA Array v2.0 (Arraystar).

Techniques: Expressing, Stripping Membranes, Control

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Screen of miRNAs and Targeting mRNAs Reveals the Negatively Regulatory Effect of miR-130b-3p on PTEN by PI3K and Integrin β1 Signaling Pathways in Bladder Carcinoma

doi: 10.3390/ijms18010078

Figure Lengend Snippet: The co-expression network is constructed with representative miRNAs and their target genes. Solid lines mean negative correlations between five representative miRNAs and their targets (the absolute value of Pearson correlation coefficient (PCC) ≥ 0.90, p -value < 0.01 and false positive rate (FDR) < 0.01).

Article Snippet: The microarray hybridization was performed according to the manufacturer’s standard protocols (Agilent Technology, Shanghai, China) including purifying RNA, transcribing into fluorescent cDNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar, Shanghai, China) and the Human miRNA Array v2.0 (Arraystar).

Techniques: Expressing, Construct

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Screen of miRNAs and Targeting mRNAs Reveals the Negatively Regulatory Effect of miR-130b-3p on PTEN by PI3K and Integrin β1 Signaling Pathways in Bladder Carcinoma

doi: 10.3390/ijms18010078

Figure Lengend Snippet: The differentially expressed miRNAs are validated in bladder carcinoma by quantitative RT-PCR. ( A , B ) The relative expression levels of the five miRNAs are shown in thirty pairs of tumor tissues (T) and normal tissues (N). Data are shown as mean ± SEM. * p < 0.05, ** p < 0.01, n = 30; and ( C ) The comparison between qPCR results and microarray data. The heights of the columns represent the fold changes (log2 transformed) computed from qPCR and microarray data respectively.

Article Snippet: The microarray hybridization was performed according to the manufacturer’s standard protocols (Agilent Technology, Shanghai, China) including purifying RNA, transcribing into fluorescent cDNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar, Shanghai, China) and the Human miRNA Array v2.0 (Arraystar).

Techniques: Quantitative RT-PCR, Expressing, Comparison, Microarray, Transformation Assay

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Screen of miRNAs and Targeting mRNAs Reveals the Negatively Regulatory Effect of miR-130b-3p on PTEN by PI3K and Integrin β1 Signaling Pathways in Bladder Carcinoma

doi: 10.3390/ijms18010078

Figure Lengend Snippet: Pathways of target genes for the five representative miRNAs are analyzed. ( A ) KEGG pathway enrichment analysis with a top ten Enrichment score; ( B ) Hierarchical clustering of miRNA related pathways. The heatmap of the miRNAs merged pathway reveals significance by p -value (log scaled). Red represents high significance; and ( C ) DAVID analysis of target genes of miR-130b-3p.

Article Snippet: The microarray hybridization was performed according to the manufacturer’s standard protocols (Agilent Technology, Shanghai, China) including purifying RNA, transcribing into fluorescent cDNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar, Shanghai, China) and the Human miRNA Array v2.0 (Arraystar).

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Screen of miRNAs and Targeting mRNAs Reveals the Negatively Regulatory Effect of miR-130b-3p on PTEN by PI3K and Integrin β1 Signaling Pathways in Bladder Carcinoma

doi: 10.3390/ijms18010078

Figure Lengend Snippet: miR-130b-3p affects the expression of PTEN and modulates PI3K/AKT and integrin β1/FAK signaling pathways. ( A , B ) The relative expression levels of miRNA miR-130b and mRNA PTEN in cells transfected with miR-130b mimics, the scramble control, anti-130b or anti-con by qRT-PCR; ( C , D ) Western blot analysis; and ( E , F ) Quantitative analysis of relative protein levels. Data are expressed as mean ± SD ( n = 3), * p < 0.05, ** p < 0.01.

Article Snippet: The microarray hybridization was performed according to the manufacturer’s standard protocols (Agilent Technology, Shanghai, China) including purifying RNA, transcribing into fluorescent cDNA, and then hybridizing onto the Human lncRNA Array v3.0 (Arraystar, Shanghai, China) and the Human miRNA Array v2.0 (Arraystar).

Techniques: Expressing, Protein-Protein interactions, Transfection, Control, Quantitative RT-PCR, Western Blot