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NanoString Technologies Inc ncounter pancancer progression panel
Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the <t>nCounter</t> Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter <t>PanCancer</t> Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).
Ncounter Pancancer Progression Panel, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/ncounter pancancer progression panel/product/NanoString Technologies Inc
Average 90 stars, based on 32 article reviews
Price from $9.99 to $1999.99
ncounter pancancer progression panel - by Bioz Stars, 2022-09
90/100 stars

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1) Product Images from "Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19"

Article Title: Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19

Journal: The New England journal of medicine

doi: 10.1056/NEJMoa2015432

Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the nCounter Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter PanCancer Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).
Figure Legend Snippet: Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the nCounter Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter PanCancer Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).

Techniques Used: Expressing, Isolation, Immunohistochemistry, RNA Extraction, Labeling, Negative Control, Positive Control, Software

2) Product Images from "Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures"

Article Title: Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

Journal: The European Respiratory Journal

doi: 10.1183/13993003.01881-2021

Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC (waterfall plot). The genesets visualised are custom genesets for “angiogenesis response”, “blood coagulation”, “hypoxia” responses based on nanoString's nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see table 2 ), MSigDB Hallmark gene set for IFN-α and IFN-γ and MSigDB Gene Ontology (GO) gene sets for “Regulation of response to cytokine stimulus’ and “Positive regulation of cytokine production involved in immune response’. Genesets ordered by gene counts. Refer to comprehensive list in table 1 . GSEA conducted using limma-fry with FDR
Figure Legend Snippet: Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC (waterfall plot). The genesets visualised are custom genesets for “angiogenesis response”, “blood coagulation”, “hypoxia” responses based on nanoString's nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see table 2 ), MSigDB Hallmark gene set for IFN-α and IFN-γ and MSigDB Gene Ontology (GO) gene sets for “Regulation of response to cytokine stimulus’ and “Positive regulation of cytokine production involved in immune response’. Genesets ordered by gene counts. Refer to comprehensive list in table 1 . GSEA conducted using limma-fry with FDR

Techniques Used: Infection, Coagulation

3) Product Images from "Spatial Profiling of Lung SARS-CoV-2 and Influenza Virus Infection Dissects Virus-Specific Host Responses and Gene Signatures"

Article Title: Spatial Profiling of Lung SARS-CoV-2 and Influenza Virus Infection Dissects Virus-Specific Host Responses and Gene Signatures

Journal: medRxiv

doi: 10.1101/2020.11.04.20225557

Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC. The genesets are custom genesets for ( a ) angiogenesis response, ( b ) blood coagulation ( g ) hypoxia responses based on nanoString’s nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see Table 2). ( e, f ) MSigDB Hallmark gene set for IFN-α and IFN-γ. ( c, d ) MSigDB Gene Ontology (GO), biological processes (BP) collection identified by GSEA for cytokine regulation and responses. Refer to comprehensive list in Table 1 . GSEA conducted using limma-fry with FDR
Figure Legend Snippet: Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC. The genesets are custom genesets for ( a ) angiogenesis response, ( b ) blood coagulation ( g ) hypoxia responses based on nanoString’s nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see Table 2). ( e, f ) MSigDB Hallmark gene set for IFN-α and IFN-γ. ( c, d ) MSigDB Gene Ontology (GO), biological processes (BP) collection identified by GSEA for cytokine regulation and responses. Refer to comprehensive list in Table 1 . GSEA conducted using limma-fry with FDR

Techniques Used: Infection, Coagulation

4) Product Images from "The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis"

Article Title: The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis

Journal: Nature Communications

doi: 10.1038/s41467-018-07922-3

Knocking out TOP1MT restrains cell proliferation and sensitizes cells to glucose starvation. a Representative Ki67 immunofluorescence staining of WT and TOP1MT -KO xenograft tumors. Scale bar, 50 μm. b , c Quantification of the fraction of Ki67-positive cells ( b ) and nuclei count per field ( c ) measured by ZEN software (6 images per animal, 5 animals per genotype). d Heat map showing significant changes in gene expression profiles analyzed with the nCounter PanCancer Progression panel in four TOP1MT -deficient vs. four WT tumors (89 genes, p
Figure Legend Snippet: Knocking out TOP1MT restrains cell proliferation and sensitizes cells to glucose starvation. a Representative Ki67 immunofluorescence staining of WT and TOP1MT -KO xenograft tumors. Scale bar, 50 μm. b , c Quantification of the fraction of Ki67-positive cells ( b ) and nuclei count per field ( c ) measured by ZEN software (6 images per animal, 5 animals per genotype). d Heat map showing significant changes in gene expression profiles analyzed with the nCounter PanCancer Progression panel in four TOP1MT -deficient vs. four WT tumors (89 genes, p

Techniques Used: Immunofluorescence, Staining, Software, Expressing

5) Product Images from "The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis"

Article Title: The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis

Journal: Nature Communications

doi: 10.1038/s41467-018-07922-3

Knocking out TOP1MT restrains cell proliferation and sensitizes cells to glucose starvation. a Representative Ki67 immunofluorescence staining of WT and TOP1MT -KO xenograft tumors. Scale bar, 50 μm. b , c Quantification of the fraction of Ki67-positive cells ( b ) and nuclei count per field ( c ) measured by ZEN software (6 images per animal, 5 animals per genotype). d Heat map showing significant changes in gene expression profiles analyzed with the nCounter PanCancer Progression panel in four TOP1MT -deficient vs. four WT tumors (89 genes, p
Figure Legend Snippet: Knocking out TOP1MT restrains cell proliferation and sensitizes cells to glucose starvation. a Representative Ki67 immunofluorescence staining of WT and TOP1MT -KO xenograft tumors. Scale bar, 50 μm. b , c Quantification of the fraction of Ki67-positive cells ( b ) and nuclei count per field ( c ) measured by ZEN software (6 images per animal, 5 animals per genotype). d Heat map showing significant changes in gene expression profiles analyzed with the nCounter PanCancer Progression panel in four TOP1MT -deficient vs. four WT tumors (89 genes, p

Techniques Used: Immunofluorescence, Staining, Software, Expressing

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    NanoString Technologies Inc pancancer progression panel nanostring ncounter reporter codeset
    Volcano plots comparing differential gene expression between subregions. (A) Volcano plot of 770 genes from the <t>NanoString</t> <t>PanCancer</t> progression panel comparing differential gene expression between PT deep and PT sup . The x-axis is the log 2 fold change of gene expression between PT sup and PT deep. The y-axis is the −log 10 adjusted p value results (false discovery rate correction). Genes of interest have been annotated within the plot. Grey dots are genes which are similarly expressed in PT deep and PT sup . Green dots are genes which are statistically significant and belong to the ‘tumour growth’ pathway. Orange dots are genes which are statistically significant and belong to the ‘ECM remodelling’ pathway. Black dots are genes which are statistically significant and belong to other pathways. In general, genes which are at the extreme ends of the volcano are highly differentially expressed in that particular subregion compared with the other and are of greatest clinical interest. (B) Volcano plot of genes comparing LN met and PT sup . Red dots are genes which are statistically significant and belong to the ‘angiogenesis’ pathway. Blue dots are genes which are statistically significant and belong to the ‘tumour invasion’ pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT sup . (C) Volcano plot of genes compared between LN met and PT deep . Red dots are genes which are statistically significant and belong to the angiogenesis pathway. Blue dots are genes which are statistically significant and belong to the tumour invasion pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT deep . ECM, extracellular matrix; LN met , lymph node metastasis; PT deep , primary tumour deep; PT sup , primary tumour superficial.
    Pancancer Progression Panel Nanostring Ncounter Reporter Codeset, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pancancer progression panel nanostring ncounter reporter codeset/product/NanoString Technologies Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pancancer progression panel nanostring ncounter reporter codeset - by Bioz Stars, 2022-09
    90/100 stars
      Buy from Supplier

    90
    NanoString Technologies Inc ncounter pancancer progression panel
    Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the <t>nCounter</t> Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter <t>PanCancer</t> Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).
    Ncounter Pancancer Progression Panel, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ncounter pancancer progression panel/product/NanoString Technologies Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ncounter pancancer progression panel - by Bioz Stars, 2022-09
    90/100 stars
      Buy from Supplier

    90
    NanoString Technologies Inc nanospring ncounter pancancer progression panel
    Heatmap of heteronemin regulated pathway scores. Two types of cholangiocarcinoma cells, SSP25 cells and HuccT1 cells, were treated with 5 µM heteronemin for 24 h. Total RNA was collected, and mRNAs were detected by NanoString® analysis using an <t>nCounter</t> <t>PanCancer</t> Progression Panel (NanoString Technologies, Inc., Seattle, WA, USA). The pathway scores were analyzed by nSolverTM software (NanoString Technologies, Seattle, WA, USA).
    Nanospring Ncounter Pancancer Progression Panel, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nanospring ncounter pancancer progression panel/product/NanoString Technologies Inc
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nanospring ncounter pancancer progression panel - by Bioz Stars, 2022-09
    90/100 stars
      Buy from Supplier

    Image Search Results


    Volcano plots comparing differential gene expression between subregions. (A) Volcano plot of 770 genes from the NanoString PanCancer progression panel comparing differential gene expression between PT deep and PT sup . The x-axis is the log 2 fold change of gene expression between PT sup and PT deep. The y-axis is the −log 10 adjusted p value results (false discovery rate correction). Genes of interest have been annotated within the plot. Grey dots are genes which are similarly expressed in PT deep and PT sup . Green dots are genes which are statistically significant and belong to the ‘tumour growth’ pathway. Orange dots are genes which are statistically significant and belong to the ‘ECM remodelling’ pathway. Black dots are genes which are statistically significant and belong to other pathways. In general, genes which are at the extreme ends of the volcano are highly differentially expressed in that particular subregion compared with the other and are of greatest clinical interest. (B) Volcano plot of genes comparing LN met and PT sup . Red dots are genes which are statistically significant and belong to the ‘angiogenesis’ pathway. Blue dots are genes which are statistically significant and belong to the ‘tumour invasion’ pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT sup . (C) Volcano plot of genes compared between LN met and PT deep . Red dots are genes which are statistically significant and belong to the angiogenesis pathway. Blue dots are genes which are statistically significant and belong to the tumour invasion pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT deep . ECM, extracellular matrix; LN met , lymph node metastasis; PT deep , primary tumour deep; PT sup , primary tumour superficial.

    Journal: Gut

    Article Title: Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination

    doi: 10.1136/gutjnl-2020-320805

    Figure Lengend Snippet: Volcano plots comparing differential gene expression between subregions. (A) Volcano plot of 770 genes from the NanoString PanCancer progression panel comparing differential gene expression between PT deep and PT sup . The x-axis is the log 2 fold change of gene expression between PT sup and PT deep. The y-axis is the −log 10 adjusted p value results (false discovery rate correction). Genes of interest have been annotated within the plot. Grey dots are genes which are similarly expressed in PT deep and PT sup . Green dots are genes which are statistically significant and belong to the ‘tumour growth’ pathway. Orange dots are genes which are statistically significant and belong to the ‘ECM remodelling’ pathway. Black dots are genes which are statistically significant and belong to other pathways. In general, genes which are at the extreme ends of the volcano are highly differentially expressed in that particular subregion compared with the other and are of greatest clinical interest. (B) Volcano plot of genes comparing LN met and PT sup . Red dots are genes which are statistically significant and belong to the ‘angiogenesis’ pathway. Blue dots are genes which are statistically significant and belong to the ‘tumour invasion’ pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT sup . (C) Volcano plot of genes compared between LN met and PT deep . Red dots are genes which are statistically significant and belong to the angiogenesis pathway. Blue dots are genes which are statistically significant and belong to the tumour invasion pathway. Black dots are genes which are statistically significant and belong to other pathways. Grey dots are genes which are similarly expressed in LN met and PT deep . ECM, extracellular matrix; LN met , lymph node metastasis; PT deep , primary tumour deep; PT sup , primary tumour superficial.

    Article Snippet: The ‘PanCancer Progression Panel’ NanoString nCounter Reporter CodeSet (Nanostring Technologies, USA) was used for this study.

    Techniques: Expressing

    Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the nCounter Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter PanCancer Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).

    Journal: The New England journal of medicine

    Article Title: Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19

    doi: 10.1056/NEJMoa2015432

    Figure Lengend Snippet: Relative Expression Analysis of Angiogenesis-Associated Genes in Lungs from Patients Who Died from Covid-19 or Influenza A(H1N1). RNA was isolated from sections sampled directly adjacent to those used for complementary histologic and immunohistochemical analyses. RNA was isolated with the Maxwell RNA extraction system (Promega) and, after quality control through Qubit analysis (ThermoFisher), was used for further analysis. During the NanoString procedure, individual copies of all RNA molecules were labeled with gene-specific bar codes and counted individually with the nCounter Analysis System (NanoString Technologies). The expression of angiogenesis-associated genes was measured with the NanoString nCounter PanCancer Progression panel (323 target genes annotated as relevant for angiogenesis). The resulting gene-expression data were normalized to negative control lanes (arithmetic mean background subtraction), positive control lanes (geometric mean normalization factor), and all reference genes present on the panel (geometric mean normalization factor) with the use of nSolver Analysis Software, version 4.0. Shown in the Venn diagram are only genes that are statistically differentially expressed as compared with expression in controls in both disease groups (Student’s t-test, controlled for the familywise error rate with a Benjamini–Hochberg false discovery rate threshold of 0.05). Up-regulation and down-regulation of genes is indicated by colored arrowheads suffixed to the gene symbols (purple denotes up-regulation, red denotes down-regulation).

    Article Snippet: A multiplexed analysis of angiogenesis-related gene expression examining 323 genes from the nCounter PanCancer Progression Panel (NanoString Technologies) revealed differences between the specimens from patients with Covid-19 and those from patients with influenza.

    Techniques: Expressing, Isolation, Immunohistochemistry, RNA Extraction, Labeling, Negative Control, Positive Control, Software

    Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC (waterfall plot). The genesets visualised are custom genesets for “angiogenesis response”, “blood coagulation”, “hypoxia” responses based on nanoString's nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see table 2 ), MSigDB Hallmark gene set for IFN-α and IFN-γ and MSigDB Gene Ontology (GO) gene sets for “Regulation of response to cytokine stimulus’ and “Positive regulation of cytokine production involved in immune response’. Genesets ordered by gene counts. Refer to comprehensive list in table 1 . GSEA conducted using limma-fry with FDR

    Journal: The European Respiratory Journal

    Article Title: Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

    doi: 10.1183/13993003.01881-2021

    Figure Lengend Snippet: Gene set enrichment analyses (GSEA) reveals upregulated cytokine responses with accompanying coagulopathies in COVID-19 infection. GSEA for differentially expressed genes comparing COVID-19 and uninfected samples were conducted using the estimated log2 fold change and p-values with the distribution of significantly differentiated genesets visualised as a function of the log2 fold change (logFC) and genes sorted by the logFC (waterfall plot). The genesets visualised are custom genesets for “angiogenesis response”, “blood coagulation”, “hypoxia” responses based on nanoString's nCounter® PanCancer Progression Panel were identified by GSEA to be differentially upregulated in COVID-19 samples. (see table 2 ), MSigDB Hallmark gene set for IFN-α and IFN-γ and MSigDB Gene Ontology (GO) gene sets for “Regulation of response to cytokine stimulus’ and “Positive regulation of cytokine production involved in immune response’. Genesets ordered by gene counts. Refer to comprehensive list in table 1 . GSEA conducted using limma-fry with FDR

    Article Snippet: Gene set enrichment using blood coagulation, hypoxia responses and angiogenesis related genes from nanoString's nCounter® PanCancer Progression Panel further confirmed the upregulation of pathways associated with blood coagulation and angiogenesis responses ( ).

    Techniques: Infection, Coagulation

    Heatmap of heteronemin regulated pathway scores. Two types of cholangiocarcinoma cells, SSP25 cells and HuccT1 cells, were treated with 5 µM heteronemin for 24 h. Total RNA was collected, and mRNAs were detected by NanoString® analysis using an nCounter PanCancer Progression Panel (NanoString Technologies, Inc., Seattle, WA, USA). The pathway scores were analyzed by nSolverTM software (NanoString Technologies, Seattle, WA, USA).

    Journal: Marine Drugs

    Article Title: Heteronemin Induces Anti-Proliferation in Cholangiocarcinoma Cells via Inhibiting TGF-β Pathway

    doi: 10.3390/md16120489

    Figure Lengend Snippet: Heatmap of heteronemin regulated pathway scores. Two types of cholangiocarcinoma cells, SSP25 cells and HuccT1 cells, were treated with 5 µM heteronemin for 24 h. Total RNA was collected, and mRNAs were detected by NanoString® analysis using an nCounter PanCancer Progression Panel (NanoString Technologies, Inc., Seattle, WA, USA). The pathway scores were analyzed by nSolverTM software (NanoString Technologies, Seattle, WA, USA).

    Article Snippet: A total of 770 mRNA expressions were detected by a Nanospring® nCounter PanCancer Progression Panel (NanoString Technologies, Inc., Seattle, WA, USA).

    Techniques: Software

    Heteronemin regulated significant pathway change in SSP25 and HuccT1 cells. SSP25 cells and HuccT1 cells were treated with 5 µM heteronemin for 24 h. Total RNA was extracted and mRNAs were detected by NanoString® analysis using an nCounter PanCancer Progression Panel. The pathway scores were analyzed by nSolverTM software.

    Journal: Marine Drugs

    Article Title: Heteronemin Induces Anti-Proliferation in Cholangiocarcinoma Cells via Inhibiting TGF-β Pathway

    doi: 10.3390/md16120489

    Figure Lengend Snippet: Heteronemin regulated significant pathway change in SSP25 and HuccT1 cells. SSP25 cells and HuccT1 cells were treated with 5 µM heteronemin for 24 h. Total RNA was extracted and mRNAs were detected by NanoString® analysis using an nCounter PanCancer Progression Panel. The pathway scores were analyzed by nSolverTM software.

    Article Snippet: A total of 770 mRNA expressions were detected by a Nanospring® nCounter PanCancer Progression Panel (NanoString Technologies, Inc., Seattle, WA, USA).

    Techniques: Software