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• 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 LCLs vs. Naive shCTRLB cells 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 20
• Set OR Fold change < to -320
• Set p-value with FDR to 0.005
• Set file name as CpG of interestLCLs vs. B cells
• Leave the rest of the option set to defaults (Figure 1)
  
  

• Select Create
• Select Close to exit the List Manager dialog

The new spreadsheet Naive_shPOU5F1_and Naive_shNANOG_and_Primed_shCTRL_vs_Naive_shCTRL (CpG of interestspreadsheet LCLs vs. B cells (LCLs vs. B cells) will open in the Analysis tab (Figure 2). 

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