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: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Significantly regulated miRNAs in rat brain after exposure to RDX.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques:

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Hierarchical clustering of differentially expressed miRNAs induced by RDX . Nine differentially expressed miRNAs (horizontal axis) were used for a Two-Way hierarchical clustering across all the control and RDX treated samples (vertical axis). A Pearson correlation algorithm was applied to calculate the distances between transcripts or between conditions. The relative level of gene expression is indicated by the color scale at the right side.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques: Control, Gene Expression

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Most significantly physiological processes (A) and canonical pathways (B) of the putative target genes of RDX regulated miRNAs . Top ten physiological processes (A) and pathways (B) were selected to present. The putative target genes of RDX regulated miRNAs in rat brain tissues were used to run the Ingenuity pathway tool. The bigger the -log(p-value) of a pathway is, the more significantly the physiological process or pathway is regulated. The threshold lines represent a p value with 0.05.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques:

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Gene network of the putative target genes of RDX regulated miRNAs . The putative target genes of RDX induced differentially expressed miRNAS were used to run the IPA tool for gene network analysis. The orange highlighted genes are involved in nervous system development function. The networks score described in Materials and Methods for the network is 39. The solid lines connecting molecules here represents a direct relation and dotted lines an indirect relation.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques:

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Comparison of canonical pathways based on the putative target genes of RDX regulated miRNAs and differentiated mRNA genes . Overlapped all mapped pathways (A) or significant pathways (B) based on the putative target genes of RDX regulated miRNAs and differentiated mRNA genes, are presented in the Venn diagrams. The IPA tool was used for the pathway analyses. A pathway enrichment p value less than 0.05 was considered as significant. The overlapped significant pathway names and their significance are depicted too (C).

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques: Comparison

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Gene network using immune and inflammation response genes from both the putative target genes of RDX regulated miRNAs and differentiated mRNA genes . The network indicates that RDX could first modulate miRNA expression and then trigger an immune and inflammation gene network by indirectly regulating some immune and inflammation response genes. The network was built using the IPA tool. Nodes colored in red or green denote up-regulated and down-regulated genes respectively.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques: Expressing

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: Verification of miRNA microarray responses using real time QRT-PCR . The fold changes represent the expression values of the miRNAs of the RDX-treated versus control samples. Values refer to the mean ± SD of three independent samples, each run in triplicate.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques: Microarray, Quantitative RT-PCR, Expressing, Control

Journal: BMC Genomics

Article Title: MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity

doi: 10.1186/1471-2164-15-S11-S1

Figure Lengend Snippet: A hypothetical model to explain the molecular mechanisms of RDX-induced neurological disorder and neurotoxicity . RDX could first up-regulate the expression of miR-71, miR-27ab, miR-98, and miR-135a, then reduce the expression of the gens POLE4, C5ORF13, SULF1 and ROCK2, and eventually induce neurotoxicity. Over-expression of miR-27ab, or reduction of the expression of unknown miRNAs by RDX, could up-regulate HMGCR expression to cause neurotoxicity too.

Article Snippet: The miRNA micro-array analysis was performed by LC Sciences (Houston, TX) as described previously [ ].

Techniques: Expressing, Over Expression

Journal: Saudi Journal of Biological Sciences

Article Title: Legume genomics and transcriptomics: From classic breeding to modern technologies

doi: 10.1016/j.sjbs.2019.11.018

Figure Lengend Snippet: Bioinformatics software packages and workbenches available for transcriptome data analysis.

Article Snippet: , miRPlant , miRNA analysis , https://sourceforge.net/projects/mirplant/.

Techniques: Software, Gene Expression, Control, Sequencing, Amplification, Expressing

Journal: Biomedicines

Article Title: Therapeutic Efficacy of Interferon-Gamma and Hypoxia-Primed Mesenchymal Stromal Cells and Their Extracellular Vesicles: Underlying Mechanisms and Potentials in Clinical Translation

doi: 10.3390/biomedicines12061369

Figure Lengend Snippet: Pre-clinical studies reported priming with IFN-γ as a strategy for enhancing the therapeutic efficacy of MSC therapies.

Article Snippet: 100 ng/mL IFN-γ, 48 h , Human AT-MSCs , Carbon tetrachloride (CCl 4 )-induced liver cirrhosis mouse model; immunocompetent mice , 2 μg or 5 μg EVs , Intravenous injection , Proteomics (nano-LC-MS) and miRNA content analysis (DNAFORM) of EVs , Macrophage polarity-mRNA expression of genes encoding pro- and anti-inflammatory factors (qPCR), motility and phagocytosis (immunofluorescent) assays , Ameliorate fibrosis and inflammation, promote tissue repair , Via the induction of anti-inflammatory macrophages with higher motility and phagocytic ability, increasing regulatory T cell counts , IFN-γ priming resulted in enhanced efficacy of MSC-derived EVs. , Takeuchi et al., 2021 [ ] .

Techniques: Drug discovery, Concentration Assay, In Vitro, Functional Assay, Recombinant, Injection, Enzyme-linked Immunosorbent Assay, Expressing, Derivative Assay, Histopathology, Gene Expression, Microarray, Inhibition, Flow Cytometry, Activity Assay, In Vivo, Comparison, Luminex, Activation Assay, Sequencing, Western Blot, Biomarker Discovery, Cytometry, Bacteria, Quantitation Assay, Cell Differentiation, Generated, BrdU Incorporation Assay, Protein Array, Immunohistochemistry

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: Hierarchical clustering and heatmap of 101 significantly distributed miRNAs in synaptosome and cytosol in UC samples. Red color intensity showed the miRNAs upregulation and blue color intensity showed the miRNAs downregulation.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques:

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: (A) Volcano plot depicting differentially expressed miRNAs in UC synaptosome vs UC cytosol. Red dot showed the miRNAs upregulation, blue dot showed the miRNAs downregulation, and gray dot showed no difference. Significantly upregulated and downregulated miRNAs are highlighted, illustrating distinct expression profiles between the two cellular compartments. (B) Correlation plot comparing miRNA expression levels between UC synaptosome and UC cytosol. Each dot corresponds to an individual miRNA, with the diagonal line indicating equal expression between the two compartments. Deviations from the diagonal reflect differential distribution of miRNAs between the synaptosome and cytosol with red color intensity indicating level of significance. (C) Venn diagram illustrating the distribution of miRNAs between UC synaptosome and UC cytosol with significant overlap between the two compartments shaded in deep green color, and compartment specific expression of miRNAs, shaded in light green color for synaptosome and shaded in red color for cytosol. (D) Bar chart depicting the top 20 cellular component localization of miRNAs showing differential enrichment of miRNAs across cellular regions.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques: Expressing

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: Hierarchical clustering and heatmap of 101 significantly distributed miRNAs synaptosome and cytosol in PD samples. Red color intensity showed the miRNAs upregulation and blue color intensity showed the miRNAs downregulation.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques:

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: (A) Volcano plot depicting differentially expressed miRNAs in PD synaptosome vs PD cytosol. Red dots show miRNAs upregulation, blue dots show miRNAs downregulation, and gray dots show no significant difference. Significantly upregulated and downregulated microRNAs are highlighted, illustrating distinct expression profiles between the two cellular compartments. (B) Correlation plot comparing miRNA expression levels between PD synaptosome and PD cytosol. Each dot corresponds to an individual miRNA, with the diagonal line indicating equal expression between the two compartments. Deviations from the diagonal reflect differential distribution of miRNAs between the synaptosome and cytosol with red color intensity indicating level of significance. (C) Venn diagram illustrating the distribution of miRNAs between PD synaptosome and PD cytosol with significant overlap between the two compartments shaded in deep green color, and compartment specific expression of miRNAs, shaded in light green color for synaptosome and shaded in red color for cytosol. (D) Bar chart depicting the top 20 molecular function enrichment of miRNAs showing differential enrichment of miRNAs across molecular functions.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques: Expressing

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: Hierarchical clustering and heatmap of 32 significantly distributed miRNAs in cytosol in PD vs UC samples. Red color intensity showed the miRNAs upregulation and blue color intensity showed the miRNAs downregulation.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques:

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: (A) Volcano plot depicting differentially expressed miRNAs in PD cytosol vs UC cytosol. Red dot showed the miRNAs upregulation, blue dot showed the miRNAs downregulation, and gray dot showed no difference. Significantly upregulated and downregulated miRNAs are highlighted. (B) Correlation plot comparing miRNA expression levels between PD cytosol and UC cytosol. Each dot corresponds to an individual miRNA, with the diagonal line indicating equal expression between the two cohorts. Deviations from the diagonal reflect differential distribution of miRNAs between the PD and UC samples with red color intensity indicating level of significance. (C) Venn diagram illustrating the distribution of miRNAs between PD cytosol and PD cytosol with significant overlap between the two cohorts shaded in deep green color, and cohort specific expression of miRNAs, shaded in light green color for PD cytosol and shaded in red color for UC cytosol. (D) Bar chart depicting the top 20 molecular function enrichment of miRNAs showing differential enrichment of miRNAs across molecular functions.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques: Expressing

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: Hierarchical clustering and heatmap of 49 significantly distributed miRNAs in synaptosomes in PD vs UC samples. Red color intensity showed the miRNAs upregulation and blue color intensity showed the miRNAs downregulation.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques:

Journal: bioRxiv

Article Title: MicroRNAs alteration and unique distribution in the soma and synapses of substantia nigra in Parkinson’s disease

doi: 10.1101/2025.03.12.642888

Figure Lengend Snippet: (A) Volcano plot depicting differentially expressed microRNAs in PD synaptosome vs UC synaptosome. Red dot showed the miRNAs upregulation, blue dot showed the miRNAs downregulation, and gray dot showed no difference. Significantly upregulated and downregulated microRNAs are highlighted. (B) Correlation plot comparing miRNA expression levels between PD synaptosome and UC synaptosome. Each dot corresponds to an individual microRNA, with the diagonal line indicating equal expression between the two cohorts. Deviations from the diagonal reflect differential distribution of miRNAs between the PD and UC samples with red color intensity indicating level of significance. (C) Venn diagram illustrating the distribution of miRNAs between PD synaptosome and PD synaptosome with significant overlap between the two cohorts shaded in deep green color, and cohort specific expression of miRNAs, shaded in light green color for PD synaptosome and shaded in red color for UC synaptosome. (D) Bar chart depicting the top 20 cellular component localization of miRNAs showing differential enrichment of miRNAs across cellular regions.

Article Snippet: The miRNAs HiSeq analysis were performed commercially at LC Sciences Houston, Texas following our previous lab publications ( ; ).

Techniques: Expressing