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macos java application v4.1.0  (Broad Institute Inc)

 
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    Broad Institute Inc macos java application v4.1.0
    Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis <t>(GSEA)</t> for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also <xref ref-type=Figure S3 . " width="250" height="auto" />
    Macos Java Application V4.1.0, supplied by Broad Institute 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/product/macos+java+application+v4%2E1%2E0/pmc11326933-334-9-22?v=Broad+Institute+Inc
    Average 90 stars, based on 1 article reviews
    macos java application v4.1.0 - by Bioz Stars, 2026-08
    90/100 stars

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    1) Product Images from "Pandemic-associated pernio harbors footprints of an abortive SARS-CoV-2 infection"

    Article Title: Pandemic-associated pernio harbors footprints of an abortive SARS-CoV-2 infection

    Journal: iScience

    doi: 10.1016/j.isci.2024.110525

    Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also <xref ref-type=Figure S3 . " title="... in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also Figure S3 .

    Techniques Used: Infection, Quantitative RT-PCR, Control, Virus, Plaque Assay, Positive Control, RNA Sequencing, Quantitative Proteomics



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    macos java application v4.1.0  (Broad Institute Inc)
    90
    Broad Institute Inc macos java application v4.1.0
    Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis <t>(GSEA)</t> for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also <xref ref-type=Figure S3 . " width="250" height="auto" />
    Macos Java Application V4.1.0, supplied by Broad Institute 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/product/macos+java+application+v4%2E1%2E0/pmc11326933-334-9-22?v=Broad+Institute+Inc
    Average 90 stars, based on 1 article reviews
    macos java application v4.1.0 - by Bioz Stars, 2026-08
    90/100 stars
    		  Buy from Supplier

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    Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also <xref ref-type=Figure S3 . " width="100%" height="100%">

    Journal: iScience

    Article Title: Pandemic-associated pernio harbors footprints of an abortive SARS-CoV-2 infection

    doi: 10.1016/j.isci.2024.110525

    Figure Lengend Snippet: Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also Figure S3 .

    Article Snippet: Output from differential expression analysis was used to run Gene Set Enrichment Analysis (GSEA) (MacOS Java Application v4.1.0) (made available by the Broad Institute and the University of California) looking for enrichment of Molecular Signatures Database curated gene set C5 with a gene ranking factor of -log10( p -value)∗sign(log2FoldChange).

    Techniques: Infection, Quantitative RT-PCR, Control, Virus, Plaque Assay, Positive Control, RNA Sequencing, Quantitative Proteomics