Infinium Mouse Methylation BeadChip - GenomeStudio Controls Dashboard Interpretation

The Illumina Infinium Mouse Methylation BeadChip enables cost-effective DNA methylation analysis for nearly all murine strains commonly used in research, supporting methylation profiling in models that simulate human disease states. After processing this BeadChip, Illumina recommends using the GenomeStudio 2011 Methylation Module for quality control (QC), including assessment of the built-in BeadChip controls through interpretation of the Controls Dashboard.

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 Infinium HD Methylation Assay Reference Guide under 'System Controls'.

• 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.

Note: 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 Infinium Mouse Methylation BeadChips have two sets of built-in controls. Sample-independent Controls evaluate BeadChip and reagent performance of the assay. Sample-dependent Controls evaluate the overall performance of the samples. In general, 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.

Infinium Mouse Demo Data can be downloaded from the Infinium Mouse Methylation Beadchip Product Files page. Opening the demo project in GenomeStudio allows users to view the appearance of the Controls Dashboard directly. The demo project includes regular mouse samples as well as human-mouse xenograft samples, which will return signals from both human- and mouse-targeted control probes.

For more information on the Infinium Mouse Methylation BeadChip, please consult the product Data Sheet.

For additional questions on Infinium controls evaluation, contact Illumina Technical Support at [e-mail].

For any feedback or questions regarding this article (Illumina Knowledge Article #5666), contact Illumina Technical Support [e-mail].