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cdna array  (GoldenGate Software Inc)

 
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    Structured Review

    GoldenGate Software Inc cdna array
    Various plots of the raw signal from GoldenGate arrays measuring ASE . Panels A and B show boxplots of the summarized log 2 ( Cy 5) and log 2 ( Cy 3) intensities respectively from a representative SAM. The data from each array were plotted in a separate boxplot, and color coded by sample (blue - gDNA, red - <t>cDNA).</t> Arrays 4 and 7 have low signal in both channels (IQR ≤ 1) and were excluded from downstream analysis. Density plots for each channel from two typical gDNA and cDNA arrays are presented in panels C and D respectively. These plots also show the systematic difference in overall signal between gDNA and cDNA hybridizations. Smoothed MA -plots for the gDNA (E) and cDNA (F) also highlight the differences. In these plots, a higher density of points is represented by a darker shade of blue.
    Cdna Array, supplied by GoldenGate Software 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/goldengate+array/cdna+array/pmc02887809-44-5-41
    Average 90 stars, based on 1 article reviews
    cdna array - by Bioz Stars, 2026-09
    90/100 stars

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    1) Product Images from "Data analysis issues for allele-specific expression using Illumina's GoldenGate assay"

    Article Title: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

    Journal: BMC Bioinformatics

    doi: 10.1186/1471-2105-11-280

    Various plots of the raw signal from GoldenGate arrays measuring ASE . Panels A and B show boxplots of the summarized log 2 ( Cy 5) and log 2 ( Cy 3) intensities respectively from a representative SAM. The data from each array were plotted in a separate boxplot, and color coded by sample (blue - gDNA, red - cDNA). Arrays 4 and 7 have low signal in both channels (IQR ≤ 1) and were excluded from downstream analysis. Density plots for each channel from two typical gDNA and cDNA arrays are presented in panels C and D respectively. These plots also show the systematic difference in overall signal between gDNA and cDNA hybridizations. Smoothed MA -plots for the gDNA (E) and cDNA (F) also highlight the differences. In these plots, a higher density of points is represented by a darker shade of blue.
    Figure Legend Snippet: Various plots of the raw signal from GoldenGate arrays measuring ASE . Panels A and B show boxplots of the summarized log 2 ( Cy 5) and log 2 ( Cy 3) intensities respectively from a representative SAM. The data from each array were plotted in a separate boxplot, and color coded by sample (blue - gDNA, red - cDNA). Arrays 4 and 7 have low signal in both channels (IQR ≤ 1) and were excluded from downstream analysis. Density plots for each channel from two typical gDNA and cDNA arrays are presented in panels C and D respectively. These plots also show the systematic difference in overall signal between gDNA and cDNA hybridizations. Smoothed MA -plots for the gDNA (E) and cDNA (F) also highlight the differences. In these plots, a higher density of points is represented by a darker shade of blue.

    Techniques Used:

    Related Articles

    other:

    Article Title: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay
    Article Snippet: The data from a typical cDNA array (Figure ) is more diffuse, with a cluster of points occurring at low intensity, which presumably represents signal from SNPs in transcripts which are either non-expressed, or below the limits of detection using the GoldenGate technology.

    Article Title: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay.
    Article Snippet: The data from a typical cDNA array (Figure 1F) is more diffuse, with a cluster of points occurring at low intensity, which presumably represents signal from SNPs in transcripts which are either non-expressed, or below the limits of detection using the GoldenGate technology.



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