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To analyze differences in methylation between our experimental groups, we need to create a list of deferentially methylated loci.

Select Create Marker List from the Analysis section of the Illumina BeadArray Methylation workflow
Select 1/anova-1way_autosomal_only (ANOVA-1way_autosomal_only) as the source spreadsheet from the left-hand panel
Select Naive shPOU5F1 and Naive shNANOG and Primed shCTRL vs. Naive shCTRL from the Contrast: find genes that change between two categories section of the ANOVA Streamlined tab of the List Manager dialog
Set Fold change > to 3
Set OR Fold change < to -3
Set file name as CpG of interest
Leave the rest of the option set to defaults (Figure 1)

Genomics Suite Documentation > Create a marker list > figure26alt.png

The new spreadsheet Naive_shPOU5F1_and Naive_shNANOG_and_Primed_shCTRL_vs_Naive_shCTRL (CpG of interest) will open in the Analysis tab (Figure 2).

Genomics Suite Documentation > Create a marker list > figure28alt.png

You may want to save the project before proceeding to the next section of the tutorial.