Fig. 4.

MLH1 PCR to test efficiency of bisulfite conversion on FFPE derived DNA. a) MLH1 PCR of FFPE-derived bisulfite-treated DNA. Lane 1: 1Kb + ladder, Lane 2: 200 ng input DNA, Lane 3: 500 ng input DNA, Lane 4: Zymo methylated control DNA, Lane 5: unconverted genomic DNA, Lane 6: PCR negative (water). 2% agarose, run for 25 mins at 100 V. b) MLH1 PCR of RRBS libraries prepared from different amounts of FFPE-derived DNA. FFPE DNA was digested with MspI enzyme, A-tailed, end repaired and ligated to Illumina adaptors, and bisulfite converted. Then PCR was performed with MLH1 primers. Lane 1: 1Kb + ladder, Lane 2: 50 ng input DNA, Lane 3: 100 ng input DNA, Lane 4: 500 ng input DNA, Lane 5: Zymo methylated control DNA, Lane 6: PCR negative (water). 2% agarose, run for 25 mins at 100 V