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: Journal of Diabetes

Article Title: CircMAP3K5 promotes cardiomyocyte apoptosis in diabetic cardiomyopathy by regulating miR ‐22‐3p/ DAPK2 Axis

doi: 10.1111/1753-0407.13471

Figure Lengend Snippet: Differential expression of circRNA by A, scatter plot, B, volcanic map, and C, cluster analysis in normal group and diabetic cardiomyopathy (DCM) group. circRNA, circular RNA.

Article Snippet: These circRNAs were amplified and transcribed into fluorescent cRNA using a random primer method (Arraystar Super RNA Labeling Kit; Arraystar). labeled cRNAs that were hybridized to Arraystar Rat circRNA Array V2.0 (8 × 15 K) with a total of 14 145 circRNA probes on the chip.

Techniques: Quantitative Proteomics

Journal: Journal of Diabetes

Article Title: CircMAP3K5 promotes cardiomyocyte apoptosis in diabetic cardiomyopathy by regulating miR ‐22‐3p/ DAPK2 Axis

doi: 10.1111/1753-0407.13471

Figure Lengend Snippet: Depletion of circRNA Mitogen‐activated protein kinase kinase kinase 5 (circMAP3K5) attenuates cardiomyocyte apoptosis in a diabetic cardiomyopathy (DCM) cell model. A, quantitative real‐time polymerase chain reaction results show expression levels of circMAP3K5 in samples of DCM ( n = 3) and control ( n = 3) cells. B, Western blots showing expression levels of Bcl‐2, Bax, and cleaved caspase‐3 proteins in the samples. C, Flow cytometry results depict the rate of apoptosis. Statistically significant difference: * p < .05 ( n = 3). circRNA, circular RNA; HG, high glucose.

Article Snippet: These circRNAs were amplified and transcribed into fluorescent cRNA using a random primer method (Arraystar Super RNA Labeling Kit; Arraystar). labeled cRNAs that were hybridized to Arraystar Rat circRNA Array V2.0 (8 × 15 K) with a total of 14 145 circRNA probes on the chip.

Techniques: Real-time Polymerase Chain Reaction, Expressing, Control, Western Blot, Flow Cytometry