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linear models microarray data (limma) r package  (Agilent technologies)


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    Agilent technologies linear models microarray data (limma) r package
    Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The <t>microarray</t> data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( <xref ref-type= Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) . " width="250" height="auto" />
    Linear Models Microarray Data (Limma) R Package, supplied by Agilent technologies, 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/linear+models+for+microarray+data+package/pmc08899024-59-15-5
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    linear models microarray data (limma) r package - by Bioz Stars, 2026-09
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    1) Product Images from "Unspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand"

    Article Title: Unspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2022.831680

    Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The microarray data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( <xref ref-type= Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) . " title="... (E) Heatmap of log2-transformed gene expression data. The microarray data was normalized using quantile normalization. Duplicate probes ..." property="contentUrl" width="100%" height="100%"/>
    Figure Legend Snippet: Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The microarray data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) .

    Techniques Used: Transformation Assay, Expressing, Microarray, Inhibition, Activation Assay, Two Tailed Test

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    Article Snippet: Affymetrix datasets were preprocessed and normalized with the Robust Multi-Array Average (RMA) approach [ ] using Expression Console (Affymetrix, Santa Clara, CA, USA). .. The expression values of Agilent microarray data were normalized using the Loess algorithm. ..

    Microarray:

    Article Title: A comprehensive meta-analysis of transcriptome data to identify signature genes associated with pancreatic ductal adenocarcinoma
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    Article Title: Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
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    In Silico:

    Article Title: A transcriptomics approach to expand therapeutic options and optimize clinical trials in oncology
    Article Snippet: .. The dataset used in our in silico analysis consists of Agilent microarray data generated from tumor and analogous organ-matched normal lung tissues from each patient. ..

    Generated:

    Article Title: A transcriptomics approach to expand therapeutic options and optimize clinical trials in oncology
    Article Snippet: .. The dataset used in our in silico analysis consists of Agilent microarray data generated from tumor and analogous organ-matched normal lung tissues from each patient. ..

    Indirect Immunoperoxidase Assay:

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    Gene Expression:

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    Article Snippet: .. The microarray data of the Agilent ovarian cancer cohort were extracted from Gene Expression Omnibus (GSE53963, GSE73614, GSE17260, GSE32062, GSE32063). ..

    Transformation Assay:

    Article Title: Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
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    RNA Sequencing:

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    Magnetic Resonance Imaging:

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    Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The <t>microarray</t> data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( <xref ref-type= Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) . " width="250" height="auto" />
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    Image Search Results


    Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The microarray data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( <xref ref-type= Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) . " width="100%" height="100%">

    Journal: Frontiers in Immunology

    Article Title: Unspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand

    doi: 10.3389/fimmu.2022.831680

    Figure Lengend Snippet: Metabolic processes in CTLs are reprogrammed by high glucose. Primary human CD8 + T cells were stimulated with CD3/CD28 beads for 3 days in NG (5.6 mM) or HG (25 mM) medium. (A–D) Oxidative phosphorylation (n = 5 donors) and glycolysis (n = 3 donors) of CTLs from two independent experiments were determined with seahorse assay. One representative donor for oxidative phosphorylation and glycolysis is shown in (A, C) , respectively. (E) Heatmap of log2-transformed gene expression data. The microarray data was normalized using quantile normalization. Duplicate probes for genes were aggregated by taking the median intensity. Genes were filtered for those with an absolute fold change > 1.5, and a Benjamini-Hochberg adjusted p -value < 0.05. (F) Expression of glucose transporters at mRNA level from the transcriptomics data ( Table S1 ) of 6 donors collected from five independent stimulations and two independent microarray analyses. A.U. stands for arbitrary units. (G, H) ROS production in CD8 + T cells was determined at 6 hours after CD3/CD28 bead stimulation by DCFDA (n = 5 donors from three independent experiments). One representative donor is shown in (G) Connected lines in (H) are the data from the same donor. (I, J) H 2 O 2 enhances TRAIL expression in CTLs in NG. CD8 + T cells were stimulated with CD3/CD28 beads in presence or absence of H 2 O 2 for 3 days (n = 5 from three independent experiments). One representative donor is shown in (I, K–N) Inhibition of ROS production abolishes HG-enhanced TRAIL expression in CTLs. NAC ( K , L , 10 mM, n = 6 donors) or MitoQ ( M, N , 0.4 μM, n = 5 donors) from three independent experiments was added during the activation for 3 days. One representative donor for NAC and MitoQ is shown in (K, M) , respectively. Results are represented as Mean ± SD. Data were analyzed by two-tailed unpaired Student’s t test (B, D) , two-tailed paired Student’s t test (H) or one-way ANOVA with Bonferroni’s multiple comparison test (J, L, N) .

    Article Snippet: Differential expression analysis of the Agilent microarray data was performed with the Linear Models for Microarray Data (limma) R package ( ).

    Techniques: Transformation Assay, Expressing, Microarray, Inhibition, Activation Assay, Two Tailed Test