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raw intensity files from microarray experiment  (Partek)

 
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    Partek raw intensity files from microarray experiment
    Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by <t>microarray</t> analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).
    Raw Intensity Files From Microarray Experiment, supplied by Partek, 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/raw+microarray+files/raw+intensity+files+from+microarray+experiment/pmc05862258-142-6-0
    Average 90 stars, based on 1 article reviews
    raw intensity files from microarray experiment - by Bioz Stars, 2026-11
    90/100 stars

    Images

    1) Product Images from "Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model"

    Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

    Journal: Carcinogenesis

    doi: 10.1093/carcin/bgx097

    Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).
    Figure Legend Snippet: Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

    Techniques Used: Expressing, Microarray, Gene Expression, Quantitative RT-PCR

    SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.
    Figure Legend Snippet: SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

    Techniques Used: Microarray, Staining, Expressing

    Related Articles

    Microarray:

    Article Title: Duchenne muscular dystrophy hiPSC–derived myoblast drug screen identifies compounds that ameliorate disease in mdx mice
    Article Snippet: .. Raw microarray CEL files were extracted with Partek Genomics Suite 7.0 and the log 2 values quantile normalized with the RMA protocol, then mean-subtracted for each transcript before hierarchical clustering. ..

    Article Title: Blood transcriptomic signatures associated with depression, or the risk for depression, in pregnant women from the Psychiatry Research And Motherhood - Depression (PRAM-D) study.
    Article Snippet: .. Raw microarray data (.CEL files) were imported and analysed within the software Partek Genomic Suite 7.0 (Partek, St. Louis, MO, USA). ..

    Article Title: Duchenne muscular dystrophy hiPSC-derived myoblast drug screen identifies compounds that ameliorate disease in mdx mice.
    Article Snippet: .. Raw microarray CEL files were extracted with Partek Genomics Suite 7.0 and the log2 values quantile normalized with the RMA protocol, then mean-subtracted for each transcript before hierarchical clustering. ..

    Article Title: The Polyamine Putrescine Promotes Human Epidermal Melanogenesis.
    Article Snippet: .. The raw microarray .cel files were extracted, processed and imported into Partek Genomic SuiteTM (v6.6) (Partek Incorporated, St. Louis, MO,USA) with the core meta-probe set. ..

    Article Title: N‐α‐Acetyltransferase 10 inhibits invasion and metastasis of oral squamous cell carcinoma via regulating Pirh2‐p53 signalling pathway
    Article Snippet: .. The raw data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek) for analysis, and two‐way analysis of variance (2‐way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.

    Article Title: Tocotrienol-Rich Fraction (TRF) Treatment Promotes Proliferation Capacity of Stress-Induced Premature Senescence Myoblasts and Modulates the Renewal of Satellite Cells: Microarray Analysis
    Article Snippet: The arrays from three samples each of untreated young control, SIPS control, and TRF-treated cells were scanned and processed by using the AGCC Scan Control (Affymetrix). .. The raw CEL data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek, St. Louis, MO) for analysis, and two-way analysis of variance (2-way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.

    Software:

    Article Title: Blood transcriptomic signatures associated with depression, or the risk for depression, in pregnant women from the Psychiatry Research And Motherhood - Depression (PRAM-D) study.
    Article Snippet: .. Raw microarray data (.CEL files) were imported and analysed within the software Partek Genomic Suite 7.0 (Partek, St. Louis, MO, USA). ..

    other:

    Article Title: Identification of reproducible gene expression signatures in lung adenocarcinoma
    Article Snippet: The raw cel files of Affymetrix microarray retrieved from the website were imported into the Partek Genomics Suite version 6.4 to perform the pre-processing steps, including robust multiarray average and the quantile normalization method.

    Selection:

    Article Title: N‐α‐Acetyltransferase 10 inhibits invasion and metastasis of oral squamous cell carcinoma via regulating Pirh2‐p53 signalling pathway
    Article Snippet: .. The raw data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek) for analysis, and two‐way analysis of variance (2‐way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.

    Article Title: Tocotrienol-Rich Fraction (TRF) Treatment Promotes Proliferation Capacity of Stress-Induced Premature Senescence Myoblasts and Modulates the Renewal of Satellite Cells: Microarray Analysis
    Article Snippet: The arrays from three samples each of untreated young control, SIPS control, and TRF-treated cells were scanned and processed by using the AGCC Scan Control (Affymetrix). .. The raw CEL data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek, St. Louis, MO) for analysis, and two-way analysis of variance (2-way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.

    Profiling:

    Article Title: Tocotrienol-Rich Fraction (TRF) Treatment Promotes Proliferation Capacity of Stress-Induced Premature Senescence Myoblasts and Modulates the Renewal of Satellite Cells: Microarray Analysis
    Article Snippet: The arrays from three samples each of untreated young control, SIPS control, and TRF-treated cells were scanned and processed by using the AGCC Scan Control (Affymetrix). .. The raw CEL data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek, St. Louis, MO) for analysis, and two-way analysis of variance (2-way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.

    Analysis:

    Article Title: Tocotrienol-Rich Fraction (TRF) Treatment Promotes Proliferation Capacity of Stress-Induced Premature Senescence Myoblasts and Modulates the Renewal of Satellite Cells: Microarray Analysis
    Article Snippet: The arrays from three samples each of untreated young control, SIPS control, and TRF-treated cells were scanned and processed by using the AGCC Scan Control (Affymetrix). .. The raw CEL data files from microarray profiling were imported into the Partek Genomics Suite (v. 6.6; Partek, St. Louis, MO) for analysis, and two-way analysis of variance (2-way ANOVA) was applied with a fold change of 1.5 for the selection of differentially expressed genes at a significance level of p < 0.05. .. The differentially expressed gene lists were further correlated for their relevant biological function and reaction pathway by analysing the GSEA (Gene Set Enrichment Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) using the Partek Genomic Suite.



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    Image Search Results


    Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

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    Article Title: Genomic expression during human myelopoiesis

    doi: 10.1186/1471-2164-8-264

    Figure Lengend Snippet: Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

    Article Snippet: In particular, raw microarray data (Affymetrix .CEL files) were obtained for a total of 24 samples from 8 different cell types of all myelopoietic lineages, representing a reference dataset for a comprehensive analysis of genomic expression during cell differentiation.

    Techniques: Expressing, Microarray

    Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

    Journal: Carcinogenesis

    Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

    doi: 10.1093/carcin/bgx097

    Figure Lengend Snippet: Genetic deletion of SphK1 reduced CLDN2 in HER2/neu-induced mice breast tumors. (A) Whole genome expression profile evaluated by microarray analysis assessed the expression of 39000 gene transcripts. Gene expression microarray heatmap (n = 2 per group) of dysregulated genes. (B) Twenty molecules with the most significant expression changes (10 up-regulation and 20 down-regulation) between SphK1+/+ and SphK1−/− tumors are shown. (C) CLDN2 mRNA expression in tumors from SphK1+/+ and SphK1−/− mice was confirmed by qRT-PCR analysis and analyzed by unpaired t-test. ****P ≤ 0.0001 vs. SphK1+/+. (D) Representative paraffin-tumor sections immunostained for CLDN2 in tumors from SphK1+/+ and SphK1−/− mice (P = 0.1339).

    Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

    Techniques: Expressing, Microarray, Gene Expression, Quantitative RT-PCR

    SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

    Journal: Carcinogenesis

    Article Title: Genetic deletion of sphingosine kinase 1 suppresses mouse breast tumor development in an HER2 transgenic model

    doi: 10.1093/carcin/bgx097

    Figure Lengend Snippet: SphK1 and CLDN2 levels are increased in HER2-positive breast cancers in humans. Tissue microarray containing breast cancer samples from 92 HER2-positive breast cancer patients and matched adjacent normal breast tissues (n = 34) are stained for SphK1 and CLDN2. Staining were scored based on the intensity (0–3) and proportion (0–3), and the total scores were used for the analysis. [(A) and (B)] SphK1 and CLDN2 expressions were compared with pathological features including grade, stage and hormone receptor status. [(C) and (D)] Representative image of high, moderate and low SphK1 and CLDN2 expressing tumors.

    Article Snippet: Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

    Techniques: Microarray, Staining, Expressing