07/28/21
To assess the performance of the Infinium Mouse Methylation BeadChip:
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 |
Evaluate 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.