Journal: iScience

Article Title: Mild hypothermia promotes neuronal differentiation of human neural stem cells via RBM3-SOX11 signaling pathway

doi: 10.1016/j.isci.2024.109435

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Article Snippet: The protein concentration was determined using the BCA protein assay kit (Sangon, C503021), and an equal amount of protein was loaded and separated using SDS-PAGE Bis-Tris Protein Gel (Vazyme, E304/305) with SDS running buffer.

Techniques: Virus, Recombinant, Protease Inhibitor, Bicinchoninic Acid Protein Assay, cDNA Synthesis, Reporter Assay, RNA Sequencing, Sequencing, Software

Journal: Scientific Reports

Article Title: Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients

doi: 10.1038/s41598-020-67742-8

Figure Lengend Snippet: ( a ) Schematic overview of the strategy used to study pathways associated with clinically relevant lncRNAs and its potential regulated genes. LncRNA and mRNA expression profile are performed on HCC tumor tissues and adjacent non-tumor tissues. Clinical phenotypes of HCC tumor tissues are used for clinical association studies. Only differentially expressed (DE) and clinically relevant lncRNAs are included for further analysis. DEmRNAs that are correlated with clinically relevant DElncRNAs are included for further analysis. Clinical association of DEmRNAs are also identified. Two different analysis are carried out on clinically relevant lncRNAs-mRNAs pairs. Among correlated pairs, lncRNAs that are associated with only 1 clinical phenotype are selected for pathway analysis to identify potential prognostic markers. LncRNAs that are associated with more than 1 clinical phenotypes are selected for network analysis, followed by pathway analysis. Clinical association of DEmRNAs are also considered in the network analysis. Colored circles represent 5 groups of clinical phenotypes in this study: Tumor properties in orange, Tumor capsule in yellow, Tumor grade in blue, Tumor invasion in green, Patient overall survival in purple. ( b ) Differentially expressed lncRNAs and mRNAs between tumor (T) and non-tumor (NT) samples. Top: Workflow shows the number of lncRNAs/mRNAs at different stages of the workflow. Bottom: heatmap of the differentially expressed lncRNAs/mRNAs in T and NT samples. Each column in the heatmap represent the patient tissues samples types: red in column: T; blue in column: NT. Each row in the heatmap represents lncRNA/mRNA: red: Upregulation; green: Downregulation.

Article Snippet: A total of 40,173 lncRNAs and 20,730 mRNAs were interrogated using the Arraystar Human LncRNA Array V4.0.

Techniques: Expressing

Journal: Scientific Reports

Article Title: Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients

doi: 10.1038/s41598-020-67742-8

Figure Lengend Snippet: ( a ) Figure shows the strategy used to identify deregulated genes of lncRNA-GSE and lncRNA-CTD in L02 cells. LncRNA-GSE and lncRNA-CTD were transfected into L02 cells respectively. RNA sequencing was then performed on lncRNA-GSE overexpressing cells and lncRNA-CTD overexpressing cells to identify genes deregulated by lncRNA-GSE and lncRNA-CTD. Genes that are differentially expressed by |FC|≥ 2 in lncRNA-GSE overexpressing cells versus control or lncRNA-CTD overexpressing cells versus control were selected for further analysis. The differentially expressed genes that are correlated with lncRNA-GSE/lncRNA-CTD (|PCC|≥ 0.6) in the same direction in patient microarray dataset were included for pathway analysis. Red arrow: upregulated mRNAs; green arrow: Downregulated mRNAs. ( b ) Pathways of genes upregulated by lncRNA-GSE are mainly related to epigenetic mechanism, RNA polymerase I activity, cell division stage and regulation of rRNA expression. ( c ) Pathways of genes upregulated by lncRNA-CTD are involved in epigenetic mechanism, RNA polymerase I activity, Nonhomologous end joining, rRNA regulation, packaging of telomere ends and E3 ubiquitin ligases. Each line represents the common genes shared between the pathways. ( d ) Pathways of genes downregulated by lncRNA-GSE are related to carboxylic acid metabolism, proteoglycan metabolism, aclyglycerol biosynthetic process, regulation of cellular carbohydrates and serine-type endopeptidase. ( e ) Pathways of genes downregulated by lncRNA-CTD are mainly involved in amino acids, starch and sucrose, fatty acids and drug metabolism.

Article Snippet: A total of 40,173 lncRNAs and 20,730 mRNAs were interrogated using the Arraystar Human LncRNA Array V4.0.

Techniques: Transfection, RNA Sequencing, Control, Microarray, Activity Assay, Expressing, Ubiquitin Proteomics, Starch