Additional file 1: of A robust internal control for high-precision DNA methylation analyses by droplet digital PCR

Table S1. Sequence information for the ddPCR assays used in the present study. Table S2. The PCR thermal cycling conditions (T100 Thermal Cycler, Bio-Rad). Table S3. Gene copy number states of ACTB, C-LESS, and the 4Plex in the 34 colorectal cancer cell lines. Figure S1. Droplet dPCR amplification of a non-CpG containing sequence shared by members of a gene family (approach A) provides poor results. Figure S2. Individual control assay candidates from approach B. Figure S3. The 4Plex shows a consistent amplification pattern across the cell line panel with V9P as an exception. Figure S4. Non-normalized VIM concentrations are lower with a control assay included in the reaction. Figure S5. A tendency of lower variation in 4Plex-normalized target gene concentrations is seen in replicates of the same sample. Figure S6. PoDCall, the algorithm for automated threshold determination, corrects for shifts in baseline fluorescence between samples and performs better than the QuantaSoft software. (DOCX 791 kb)