Infinium Mouse Methylation BeadChip GenomeStudio controls interpretation
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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 .
Infinium HD Methylation Controls are described in more detail in the Control Diagrams section (currently pages 96-103) of the .
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.
For additional questions on Infinium controls evaluation, contact Illumina Technical Support at techsupport@illumina.com.
Infinium Mouse Methylation BeadChip product files are available on the page.
For any feedback or questions regarding this article (Illumina Knowledge Article #5666), contact Illumina Technical Support .