Journal: iScience

Article Title: Screening and molecular mechanism research on bile microRNAs associated with chemotherapy efficacy in perihilar cholangiocarcinoma

doi: 10.1016/j.isci.2024.111437

Figure Lengend Snippet: High-throughput sequencing results (A–C) Sequencing and qPCR validation of bile miRNAs. (D) Sequencing of bile mRNAs. (E and F) KEGG pathway analysis of the upregulated mRNAs in the bile of patients with dismal prognosis (E) and better prognosis (F). Data are represented as mean ± SD. n = 4, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ns: no significance, miRNAs microRNAs, qPCR quantitative polymerase chain reaction, KEGG Kyoto Encyclopedia of Genes and Genomes.

Article Snippet: • miRNA sequencing data have been deposited at Mendeley data. mRNA sequencing data have been deposited in the Gene Expression Omnibus (GEO). miRNA and mRNA sequencing data are publicly available as of the date of publication.

Techniques: Next-Generation Sequencing, Sequencing, Biomarker Discovery, Real-time Polymerase Chain Reaction

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia before irradiation vs. healthy donors. a Volcano plot; X axis: log2 transformed fold change; Y axis: −log10 transformed p -values. b Heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia. d Top 10 significant Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways affected by upregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p value, with the most significant pathway on the top. e Top 10 significant KEGG pathways affected by downregulated miRNAs of patients with leukaemia vs. healthy donors, ordered from top to bottom by p -value

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation, Transformation Assay

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 23) and downregulated ( n = 16) miRNAs in EVs from serum of patients with leukaemia vs. healthy volunteers

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Differentially expressed miRNAs of EVs derived from serum of patients with leukaemia after whole-body irradiation vs. before irradiation. a Volcano plot, b heatmap of upregulated and c heatmap of downregulated miRNAs in EVs from serum of patients with leukaemia after and before irradiation. d Top 10 KEGG pathways affected by upregulated miRNAs or e downregulated miRNAs from irradiated vs. non-irradiated patients with leukaemia

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques: Derivative Assay, Irradiation

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Significantly up- ( n = 11) and downregulated ( n = 15) miRNAs in EVs from serum of patients with leukaemia after irradiation

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Strahlentherapie Und Onkologie

Article Title: Irradiation alters extracellular vesicle microRNA load in the serum of patients with leukaemia

doi: 10.1007/s00066-024-02307-6

Figure Lengend Snippet: Venn diagram analyses (program InteractiVenn, www.interactivenn.net ) of ( a ) upregulated or ( b ) downregulated miRNAs in AML, ALL and combined (AML+ALL = leukaemia) patients and of miRNAs ( c ) upregulated and ( d ) downregulated following TBI in AML, ALL and combined cohort patients (leukaemia)

Article Snippet: Workflow of miRNA sequencing data analysis (ArrayStar Inc.).

Techniques:

Journal: Briefings in Bioinformatics

Article Title: Exploring miRNA–target gene pair detection in disease with coRmiT

doi: 10.1093/bib/bbae060

Figure Lengend Snippet: General overview of the coRmiT methodology. Sequencing data for miRNA and gene expression are processed to generate all possible pairs of expressed genes/miRNAs. Correlation between these pairs is computed using different strategies that combine individual gene/miRNA expression and co-expression module expression. Odds ratios are computed for each strategy (Overall odds ratio) and each miRNA (Specific odds ratio) based on overlap with mTPs obtained from databases. The selection-integration method ranks, for each miRNA, the strategies based on their specific odds ratio and selects the top strategy. The integrated mTPs are those detected with the selected strategy for each miRNA. DEGs and DEMs represent the differentially expressed genes and miRNAs, respectively. CPM is the expression matrix normalized to show counts per million mapped reads for each gene/miRNA. Eigengene and hub are the representative profiles for each co-expression module. mTPs are the miRNA–target gene pairs. STRAT N represents an example correlation strategy and miR-N represents an example miRNA.

Article Snippet: For each experiment, data were generated in the form of miRNA and mRNA sequence data (fastq files) using Illumina technology.

Techniques: Sequencing, Gene Expression, Expressing, Selection