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idat files containing raw data from assessment of microarrays  (Illumina Inc)


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    Illumina Inc idat files containing raw data from assessment of microarrays
    Idat Files Containing Raw Data From Assessment Of Microarrays, supplied by Illumina 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/microarray+raw+files/idat+files+containing+raw+data+from+assessment+of+microarrays/pmc11592101-81-9-26
    Average 90 stars, based on 1 article reviews
    idat files containing raw data from assessment of microarrays - by Bioz Stars, 2026-11
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    Related Articles

    Methylation:

    Article Title: Stratifying Cumulus Cell Samples Based on Molecular Profiling to Help Resolve Biomarker Discrepancies and to Predict Oocyte Developmental Competence
    Article Snippet: The analysis was performed according to standard Illumina procedure except that the RNA was pre-amplified before use to ensure an optimum starting amount, using the TargetAmpTM-Nano labeling kit for Illumina Expression BeadChip (Epicenter, cat. no. TAN07924, Madison, WI, USA). .. The raw Illumina 450K methylation microarray data (two-color IDAT files) were used to read into the R environment using the function “read.450K.exp”. .. The following normalization methods were used to analyze the methylation array data: subset-quantile within array normalization (SWAN) (Maksimovic et al., 2012 [ ]), which performs normalization within the array and allows an Infinium I- and II-type probe on a single array to be normalized together.

    Article Title: Glucocorticoid-induced leucine zipper “quantifies” stressors and increases male susceptibility to PTSD
    Article Snippet: .. Briefly, raw microarray scan files from Illumina HT-12 v3.0 arrays (Illumina, San Diego, CA, USA) and Human Methylation 450k BeadChip (Illumina, San Diego, CA, USA) were exported using the Illumina Beadstudio program and loaded into R for downstream analysis ( www.R-project.org ). .. Evaluation of the different microarray steps was done using the Illumina internal controls.

    Microarray:

    Article Title: Stratifying Cumulus Cell Samples Based on Molecular Profiling to Help Resolve Biomarker Discrepancies and to Predict Oocyte Developmental Competence
    Article Snippet: The analysis was performed according to standard Illumina procedure except that the RNA was pre-amplified before use to ensure an optimum starting amount, using the TargetAmpTM-Nano labeling kit for Illumina Expression BeadChip (Epicenter, cat. no. TAN07924, Madison, WI, USA). .. The raw Illumina 450K methylation microarray data (two-color IDAT files) were used to read into the R environment using the function “read.450K.exp”. .. The following normalization methods were used to analyze the methylation array data: subset-quantile within array normalization (SWAN) (Maksimovic et al., 2012 [ ]), which performs normalization within the array and allows an Infinium I- and II-type probe on a single array to be normalized together.

    Article Title: Exploring the Wnt signaling pathway in schizophrenia and bipolar disorder
    Article Snippet: For this purpose, 842 samples (263 HCs, 338 SCZ, and 241 BD) passed labeling and scanning. .. Raw microarray scan files were exported using the Illumina GenomeStudio software and loaded into R for downstream analysis using specific packages provided by BioConductor . ..

    Article Title: Bithalamic Gliomas May Be Molecularly Distinct From Their Unilateral High-Grade Counterparts
    Article Snippet: .. Files with raw data generated by the iScan microarray scanner (Illumina, San Diego, CA) were read and processed using the minfi Bioconductor package as described in the Illumina GenomeStudio software (Illumina, San Diego, CA) ( 2 ). ..

    Article Title: Glucocorticoid-induced leucine zipper “quantifies” stressors and increases male susceptibility to PTSD
    Article Snippet: .. Briefly, raw microarray scan files from Illumina HT-12 v3.0 arrays (Illumina, San Diego, CA, USA) and Human Methylation 450k BeadChip (Illumina, San Diego, CA, USA) were exported using the Illumina Beadstudio program and loaded into R for downstream analysis ( www.R-project.org ). .. Evaluation of the different microarray steps was done using the Illumina internal controls.

    Article Title: Cognitive Performance Among Carriers of Pathogenic Copy Number Variants: Analysis of 152,000 UK Biobank Subjects.
    Article Snippet: .. We compared these with a large control dataset comprising 26,628 people, where we had access to raw CNV data or had ourselves called the CNVs from raw microarray files (Illumina or other versions of Affymetrix arrays). ..

    Software:

    Article Title: Exploring the Wnt signaling pathway in schizophrenia and bipolar disorder
    Article Snippet: For this purpose, 842 samples (263 HCs, 338 SCZ, and 241 BD) passed labeling and scanning. .. Raw microarray scan files were exported using the Illumina GenomeStudio software and loaded into R for downstream analysis using specific packages provided by BioConductor . ..

    Article Title: Bithalamic Gliomas May Be Molecularly Distinct From Their Unilateral High-Grade Counterparts
    Article Snippet: .. Files with raw data generated by the iScan microarray scanner (Illumina, San Diego, CA) were read and processed using the minfi Bioconductor package as described in the Illumina GenomeStudio software (Illumina, San Diego, CA) ( 2 ). ..

    Generated:

    Article Title: Bithalamic Gliomas May Be Molecularly Distinct From Their Unilateral High-Grade Counterparts
    Article Snippet: .. Files with raw data generated by the iScan microarray scanner (Illumina, San Diego, CA) were read and processed using the minfi Bioconductor package as described in the Illumina GenomeStudio software (Illumina, San Diego, CA) ( 2 ). ..

    other:

    Article Title: Problematic alcohol use associates with sodium channel and clathrin linker 1 ( SCLT1 ) in trauma-exposed populations
    Article Snippet: Total RNA (250 ng) were reverse transcribed to cDNA, converted to biotin-labeled cRNA using the Ambion kit (AMIL1791, Applied Biosystems, Foster City, CA).

    Article Title: Chemistry-first approach for nomination of personalized treatment in lung cancer
    Article Snippet: Illumina BeadChip Microarray Raw Illumina HumanWG-6 v3.0 BeadChip files were obtained from the Gene Expression Omnibus using accession number GSE32026 and normalized as described previously ( Kim et al., 2016 ).

    Article Title: TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
    Article Snippet: Illumina BeadChip Microarray Raw Illumina HumanWG-6 v3.0 BeadChip files were obtained from the Gene Expression Omnibus using accession number GEO: {"type":"entrez-geo","attrs":{"text":"GSE32036","term_id":"32036"}} GSE32036 and normalized as described previously ( 19 ).

    Control:

    Article Title: Cognitive Performance Among Carriers of Pathogenic Copy Number Variants: Analysis of 152,000 UK Biobank Subjects.
    Article Snippet: .. We compared these with a large control dataset comprising 26,628 people, where we had access to raw CNV data or had ourselves called the CNVs from raw microarray files (Illumina or other versions of Affymetrix arrays). ..



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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.

    Journal: BMC Genomics

    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