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244 k cpg island microarray chip  (Agilent technologies)


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    Agilent technologies 244 k cpg island microarray chip
    244 K Cpg Island Microarray Chip, 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/244+k+microarray/pm37018893-65-22-26
    Average 90 stars, based on 1 article reviews
    244 k cpg island microarray chip - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Labeling:

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (Macherey–Nagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 °C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods ). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function.
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (MachereyeNagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Methylation:

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (Macherey–Nagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 °C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods ). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function.
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (MachereyeNagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Microarray:

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (Macherey–Nagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 °C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods ). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function.
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (MachereyeNagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: .. Sequence annotation for 199,399 probes in Agilent 244 K CpG island microarray chip (Agilent Technologies, USA), mapped 87% (165,826) of probes to CpG islands and the rest 13% (33,573) to CpG shores. ..

    Hybridization:

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (Macherey–Nagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 °C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods ). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function.
    Article Snippet: The PCR product was purified using the NucleoSpin® Gel and PCR Clean-up kit (MachereyeNagel, Germany), subsequently labeled with cyanine3 and cyanine5 (Amersham Biosciences, USA) by using BioPrime array CGH genomic labeling system (Thermo Fisher Scientific, USA). .. Equal concentrations of labeled cyanine3 and cyanine5 enriched for unmethylated and methylated DNA fragments respectively were co-hybridized onto the Agilent 244 K CpG island microarray chip (Agilent Technologies, USA) at 65 C, and speed of the hybridization rotator was set to rotate at 18 rpm for 40 h. Slides were washed with wash buffer after hybridization, dried and scanned using G2505B DNA microarray scanner (Agilent Technology, USA) with Sure Scan High resolution technology (Methodology detailed in Supplementary Methods). .. Agilent Feature Extraction software (v 10.5.1.1) was used to extract background corrected loess normalized green and red processed signal intensities within the array.

    Sequencing:

    Article Title: Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function
    Article Snippet: .. Sequence annotation for 199,399 probes in Agilent 244 K CpG island microarray chip (Agilent Technologies, USA), mapped 87% (165,826) of probes to CpG islands and the rest 13% (33,573) to CpG shores. ..



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    a TCGA matched samples (520 from BRCA, 150 from GBM) run on both <t>microarray</t> and RNA-seq were split into a training set (2/3) and test set (1/3). b RNA-seq samples were titrated into each training set, 10% at a time (0–100%), resulting in eleven training sets for each normalization method. Each RNA-seq sample replaces its matched microarray sample. Cross-platform normalization methods were applied to each training set independently. c We used three supervised algorithms to train classifiers (molecular subtype and mutation status of TP53 and PIK3CA in both BRCA and GBM) on each training set and tested on the microarray and RNA-seq test sets. The test sets were projected onto and back out of the training set space using unsupervised Principal Components Analysis to obtain reconstructed test sets. The subtype classifiers trained in step 3A were used to predict on the reconstructed test sets. Pathways regulating gene expression were identified using the unsupervised method PLIER.
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    a TCGA matched samples (520 from BRCA, 150 from GBM) run on both microarray and RNA-seq were split into a training set (2/3) and test set (1/3). b RNA-seq samples were titrated into each training set, 10% at a time (0–100%), resulting in eleven training sets for each normalization method. Each RNA-seq sample replaces its matched microarray sample. Cross-platform normalization methods were applied to each training set independently. c We used three supervised algorithms to train classifiers (molecular subtype and mutation status of TP53 and PIK3CA in both BRCA and GBM) on each training set and tested on the microarray and RNA-seq test sets. The test sets were projected onto and back out of the training set space using unsupervised Principal Components Analysis to obtain reconstructed test sets. The subtype classifiers trained in step 3A were used to predict on the reconstructed test sets. Pathways regulating gene expression were identified using the unsupervised method PLIER.

    Journal: Communications Biology

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

    doi: 10.1038/s42003-023-04588-6

    Figure Lengend Snippet: a TCGA matched samples (520 from BRCA, 150 from GBM) run on both microarray and RNA-seq were split into a training set (2/3) and test set (1/3). b RNA-seq samples were titrated into each training set, 10% at a time (0–100%), resulting in eleven training sets for each normalization method. Each RNA-seq sample replaces its matched microarray sample. Cross-platform normalization methods were applied to each training set independently. c We used three supervised algorithms to train classifiers (molecular subtype and mutation status of TP53 and PIK3CA in both BRCA and GBM) on each training set and tested on the microarray and RNA-seq test sets. The test sets were projected onto and back out of the training set space using unsupervised Principal Components Analysis to obtain reconstructed test sets. The subtype classifiers trained in step 3A were used to predict on the reconstructed test sets. Pathways regulating gene expression were identified using the unsupervised method PLIER.

    Article Snippet: For BRCA (520 pairs of matched samples), we used log 2 -transformed, lowess normalized Agilent 244 K microarray data and RSEM (RNA-seq by Expectation Maximization) gene-level count RNA-seq data .

    Techniques: Microarray, RNA Sequencing Assay, Mutagenesis, Expressing