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dna oligo microarray  (SwitchGear Genomics)

 
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    SwitchGear Genomics dna oligo microarray
    Schematic of the HaloCHIP-chip <t>microarray</t> experiment design . HaloCHIP <t>DNA</t> (10-50 ng) obtained for both the experimental HaloTag-CREB and untransfected control sample was purified and amplified to a concentration of 1-10 μg using the whole genome amplification (WGA) method (Sigma) . The HaloTag-CREB amplified sample was labelled with Cy5 (green) and the untransfected control sample with Cy3 (red), then hybridized to a custom DNA <t>oligo</t> microarray manufactured by Roche NimbleGen. The oligo array was designed to cover on average a 1.8 kb region of 27,661 human promoter regions that contain 33,255 TSS predicted by SwitchGear Genomics. To obtain coverage of each promoter, an average of fourteen 50mer single stranded DNA probes, shown in purple, per promoter were used, with an average spacing of 131 bp per probe.
    Dna Oligo Microarray, supplied by SwitchGear Genomics, 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-based+transcriptome-wide+mrna+expression+levels/dna+oligo+microarray/pmc02774331-84-1-13
    Average 90 stars, based on 1 article reviews
    dna oligo microarray - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays"

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-497

    Schematic of the HaloCHIP-chip microarray experiment design . HaloCHIP DNA (10-50 ng) obtained for both the experimental HaloTag-CREB and untransfected control sample was purified and amplified to a concentration of 1-10 μg using the whole genome amplification (WGA) method (Sigma) . The HaloTag-CREB amplified sample was labelled with Cy5 (green) and the untransfected control sample with Cy3 (red), then hybridized to a custom DNA oligo microarray manufactured by Roche NimbleGen. The oligo array was designed to cover on average a 1.8 kb region of 27,661 human promoter regions that contain 33,255 TSS predicted by SwitchGear Genomics. To obtain coverage of each promoter, an average of fourteen 50mer single stranded DNA probes, shown in purple, per promoter were used, with an average spacing of 131 bp per probe.
    Figure Legend Snippet: Schematic of the HaloCHIP-chip microarray experiment design . HaloCHIP DNA (10-50 ng) obtained for both the experimental HaloTag-CREB and untransfected control sample was purified and amplified to a concentration of 1-10 μg using the whole genome amplification (WGA) method (Sigma) . The HaloTag-CREB amplified sample was labelled with Cy5 (green) and the untransfected control sample with Cy3 (red), then hybridized to a custom DNA oligo microarray manufactured by Roche NimbleGen. The oligo array was designed to cover on average a 1.8 kb region of 27,661 human promoter regions that contain 33,255 TSS predicted by SwitchGear Genomics. To obtain coverage of each promoter, an average of fourteen 50mer single stranded DNA probes, shown in purple, per promoter were used, with an average spacing of 131 bp per probe.

    Techniques Used: Microarray, Control, Purification, Amplification, Concentration Assay, Whole Genome Amplification

    Related Articles

    Genome Wide:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. A custom oligo array was designed to cover a genome-wide set of human promoter regions predicted by SwitchGear Genomics (more detail can be found at ). .. The oligo array composed of approximately ~385,000 50mer probes was manufactured by Roche-NimbleGen Systems.

    Article Title: Control of creatine metabolism by HIF is an endogenous mechanism of barrier regulation in colitis
    Article Snippet: .. Input and HIF ChIP-DNA were hybridized to a custom microarray designed to cover a genome-wide set of human promoter regions of ≤2 kb (Switchgear Genomics). ..

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. A custom DNA oligo microarray was designed based upon promoter regions defined by SwitchGear Genomics genome-wide set of predicted transcription start sites (Figure ) [ - ]. ..

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
    Article Snippet: .. A custom DNA oligo microarray was designed based upon promoter regions defined by SwitchGear Genomics genome-wide set of predicted transcription start sites (Figure 3) [47-50]. ..

    Chromatin Immunoprecipitation:

    Article Title: Control of creatine metabolism by HIF is an endogenous mechanism of barrier regulation in colitis
    Article Snippet: .. Input and HIF ChIP-DNA were hybridized to a custom microarray designed to cover a genome-wide set of human promoter regions of ≤2 kb (Switchgear Genomics). ..

    Microarray:

    Article Title: Control of creatine metabolism by HIF is an endogenous mechanism of barrier regulation in colitis
    Article Snippet: .. Input and HIF ChIP-DNA were hybridized to a custom microarray designed to cover a genome-wide set of human promoter regions of ≤2 kb (Switchgear Genomics). ..

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays
    Article Snippet: .. A custom DNA oligo microarray was designed based upon promoter regions defined by SwitchGear Genomics genome-wide set of predicted transcription start sites (Figure ) [ - ]. ..

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
    Article Snippet: .. A custom DNA oligo microarray was designed based upon promoter regions defined by SwitchGear Genomics genome-wide set of predicted transcription start sites (Figure 3) [47-50]. ..

    Real-time Polymerase Chain Reaction:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
    Article Snippet: .. Primers sequences used for PPV and NPV qPCR validation along with their corresponding amplified promoter can be found in supplemental materials: http://www.switch geargenomics.com/creb_supp_data/ Oligo array design and analysis A custom oligo array was designed to cover a genomewide set of human promoter regions predicted by SwitchGear Genomics (more detail can be found at http:// www.switchgeargenomics.com). .. The oligo array composed of approximately ~385,000 50mer probes was manufactured by Roche-NimbleGen Systems.

    Biomarker Discovery:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
    Article Snippet: .. Primers sequences used for PPV and NPV qPCR validation along with their corresponding amplified promoter can be found in supplemental materials: http://www.switch geargenomics.com/creb_supp_data/ Oligo array design and analysis A custom oligo array was designed to cover a genomewide set of human promoter regions predicted by SwitchGear Genomics (more detail can be found at http:// www.switchgeargenomics.com). .. The oligo array composed of approximately ~385,000 50mer probes was manufactured by Roche-NimbleGen Systems.

    Amplification:

    Article Title: A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.
    Article Snippet: .. Primers sequences used for PPV and NPV qPCR validation along with their corresponding amplified promoter can be found in supplemental materials: http://www.switch geargenomics.com/creb_supp_data/ Oligo array design and analysis A custom oligo array was designed to cover a genomewide set of human promoter regions predicted by SwitchGear Genomics (more detail can be found at http:// www.switchgeargenomics.com). .. The oligo array composed of approximately ~385,000 50mer probes was manufactured by Roche-NimbleGen Systems.



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    Meta-data of genes shown in the cluster analysis of whose <t> mRNA </t> expression correlated with log 10 IC 50 -values of vitamin C in the NCI tumor cell line panel .
    Microarray Based Transcriptome Wide Mrna Expression Levels, supplied by Scherf GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Meta-data of genes shown in the cluster analysis of whose mRNA expression correlated with log 10 IC 50 -values of vitamin C in the NCI tumor cell line panel .

    Journal: Frontiers in Pharmacology

    Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

    doi: 10.3389/fphar.2017.00038

    Figure Lengend Snippet: Meta-data of genes shown in the cluster analysis of whose mRNA expression correlated with log 10 IC 50 -values of vitamin C in the NCI tumor cell line panel .

    Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

    Techniques: Expressing, Virus, Transduction, Activity Assay, Binding Assay, Coagulation, Phospho-proteomics, Residue, Sequencing, Membrane, Activation Assay, Control, Ubiquitin Proteomics

    Dendrograms and cluster image map of curcumin obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

    Journal: Frontiers in Pharmacology

    Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

    doi: 10.3389/fphar.2017.00038

    Figure Lengend Snippet: Dendrograms and cluster image map of curcumin obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

    Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

    Techniques: Expressing, Microarray

    Dendrograms and cluster image map of vitamin C obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

    Journal: Frontiers in Pharmacology

    Article Title: Pharmacogenomic Characterization and Isobologram Analysis of the Combination of Ascorbic Acid and Curcumin—Two Main Metabolites of Curcuma longa —in Cancer Cells

    doi: 10.3389/fphar.2017.00038

    Figure Lengend Snippet: Dendrograms and cluster image map of vitamin C obtained by hierarchical cluster analysis of mRNA expression of 40 genes in the NCI cell line panel as analyzed by the Novartis microarray platform . The dendrogram on the left shows the clustering of cell lines and the dendrogram on the top shows the clustering of genes. The cluster image map shows each single mRNA expression value obtained by microarray analysis. The expression values have been normalized and color-coded.

    Article Snippet: We correlated the IC 50 -values expressed on induction by curcumin and AA of 60 tumor cell lines by COMPARE analysis of microarray-based transcriptome-wide mRNA expression levels of these cell lines (Scherf et al., ).

    Techniques: Expressing, Microarray