Infinium Mouse Methylation BeadChip GenomeStudio controls interpretation
To assess the performance of the Infinium Mouse Methylation BeadChip:
Create an Infinium Methylation project in the GenomeStudio 2011.1 Methylation Module using the Project Wizard as described in the GenomeStudio Methylation Module User Guide.
Infinium HD Methylation Controls are described in more detail in the Control Diagrams section (currently pages 96-103) of the Infinium HD Methylation Assay Reference Guide.
Infinium Methylation controls are viewed in GenomeStudio 2011.1 by navigating to Analysis > View Controls Dashboard.
The Mouse Methylation BeadChip includes control probes for both mouse and human targets.
Controls normalization for the Mouse Methylation BeadChip is not currently supported in GenomeStudio 2011.1 because the set of control probes used for normalization is specific to human sequences. BeadArray Controls Reporter (BACR) is not compatible with the Mouse Methylation Beadchip.
The following tables are a guide to evaluating the controls performance for the Mouse Methylation BeadChip. The expected intensity applies to only the targeted species, ie, probes labeled MUS apply only to mouse samples, and probes labeled HSA apply only to human samples.
Table 1: Sample-Independent Controls
Purpose | Name | Evaluate Green (GRN) | Evaluate Red (RED) | Expected Intensity |
STAINING | STN-DNP-High | - | + | High |
STAINING | STN-DNP-Bkg | - | + | Background |
STAINING | STN-Biotin-High | + | - | High |
STAINING | STN-Biotin-Bkg | + | - | Background |
EXTENSION | EXT-G | + | - | High |
EXTENSION | EXT-T | - | + | High |
EXTENSION | EXT-A | - | + | High |
EXTENSION | EXT-C | + | - | High |
HYBRIDIZATION | HYB-Low | + | - | Low |
HYBRIDIZATION | HYB-Medium | + | - | Medium |
HYBRIDIZATION | HYB-High | + | - | High |
TARGET REMOVAL | TRM-1 | - | + | Low |
TARGET REMOVAL | TRM-2 | - | + | Low |
Table 2: Sample-Dependent Controls
Purpose | Name | Species Targeted | Evaluate Green (GRN) | Evaluate Red (RED) | Expected Intensity |
BISULFITE CONVERSION I | BS1-396C_MUS | Mus musculus | + | - | High |
BISULFITE CONVERSION I | BS1-396U_MUS | Mus musculus | + | - | Background |
BISULFITE CONVERSION I | BS1-140C_MUS | Mus musculus | + | - | Low |
BISULFITE CONVERSION I | BS1-140U_MUS | Mus musculus | + | - | Background |
BISULFITE CONVERSION I | BS1-409C_MUS | Mus musculus | - | + | High |
BISULFITE CONVERSION I | BS1-409U_MUS | Mus musculus | - | + | Background |
BISULFITE CONVERSION I | BS1-318C_MUS | Mus musculus | - | + | Medium |
BISULFITE CONVERSION I | BS1-318U_MUS | Mus musculus | - | + | Background |
BISULFITE CONVERSION I | BS1-317C_MUS | Mus musculus | - | + | Low |
BISULFITE CONVERSION I | BS1-317U_MUS | Mus musculus | - | + | Background |
BISULFITE CONVERSION I | BS1-C1_HSA | Homo sapiens | + | - | High |
BISULFITE CONVERSION I | BS1-C2_HSA | Homo sapiens | + | - | Medium |
BISULFITE CONVERSION I | BS1-C3_HSA | Homo sapiens | - | + | High |
BISULFITE CONVERSION I | BS1-C4_HSA | Homo sapiens | - | + | High |
BISULFITE CONVERSION I | BS1-C5_HSA | Homo sapiens | - | + | High |
BISULFITE CONVERSION I | BS1-U1_HSA | Homo sapiens | + | - | Background |
BISULFITE CONVERSION I | BS1-U2_HSA | Homo sapiens | + | - | Background |
BISULFITE CONVERSION I | BS1-U3_HSA | Homo sapiens | - | + | Background |
BISULFITE CONVERSION I | BS1-U4_HSA | Homo sapiens | - | + | Background |
BISULFITE CONVERSION I | BS1-U5_HSA | Homo sapiens | - | + | Background |
BISULFITE CONVERSION II | BS2-330_MUS | Mus musculus | - | + | High |
BISULFITE CONVERSION II | BS2-505_MUS | Mus musculus | - | + | High |
BISULFITE CONVERSION II | BS2-649_MUS | Mus musculus | - | + | High |
BISULFITE CONVERSION II | BS2-1_HSA | Homo sapiens | - | + | High |
BISULFITE CONVERSION II | BS2-3_HSA | Homo sapiens | - | + | High |
BISULFITE CONVERSION II | BS2-4_HSA | Homo sapiens | - | + | High |
SPECIFICITY I | SP1-PM1_HSA | Homo sapiens | + | - | High |
SPECIFICITY I | SP1-PM2_HSA | Homo sapiens | + | - | High |
SPECIFICITY I | SP1-PM3_HSA | Homo sapiens | + | - | High |
SPECIFICITY I | SP1-MM1_HSA | Homo sapiens | + | - | Background |
SPECIFICITY I | SP1-MM2_HSA | Homo sapiens | + | - | Background |
SPECIFICITY I | SP1-MM3_HSA | Homo sapiens | + | - | Background |
SPECIFICITY I | SP1-PM4_HSA | Homo sapiens | - | + | High |
SPECIFICITY I | SP1-PM5_HSA | Homo sapiens | - | + | High |
SPECIFICITY I | SP1-PM6_HSA | Homo sapiens | - | + | High |
SPECIFICITY I | SP1-MM4_HSA | Homo sapiens | - | + | Background |
SPECIFICITY I | SP1-MM5_HSA | Homo sapiens | - | + | Background |
SPECIFICITY I | SP1-MM6_HSA | Homo sapiens | - | + | Background |
SPECIFICITY II | SP2-1_HSA | Homo sapiens | - | + | High |
SPECIFICITY II | SP2-2_HSA | Homo sapiens | - | + | High |
SPECIFICITY II | SP2-3_HSA | Homo sapiens | - | + | High |
NON-POLYMORPHIC | NPM-A_MUS | Mus musculus | - | + | High |
NON-POLYMORPHIC | NPM-T_MUS | Mus musculus | - | + | High |
NON-POLYMORPHIC | NPM-C_MUS | Mus musculus | + | - | High |
NON-POLYMORPHIC | NPM-G_MUS | Mus musculus | + | - | High |
NON-POLYMORPHIC | NPM-A_HSA | Homo sapiens | - | + | High |
NON-POLYMORPHIC | NPM-T_HSA | Homo sapiens | - | + | High |
NON-POLYMORPHIC | NPM-C_HSA | Homo sapiens | + | - | High |
NON-POLYMORPHIC | NPM-G_HSA | Homo sapiens | + | - | High |
NEGATIVE* | NEG-# | Homo sapiens, Mus musculus | + | + | Background |
* Average intensity and standard deviation of 404 negative control probes.
Infinium Mouse Methylation BeadChip product files are available on the Infinium Mouse Methylation BeadChip Support Resources page.
For additional questions on Infinium controls evaluation, contact Illumina Technical Support at techsupport@illumina.com.
For any feedback or questions regarding this article (Illumina Knowledge Article #5666), contact Illumina Technical Support techsupport@illumina.com. |
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