Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Table 1 BS conversion protocols and parameters

Method	Denaturation temperature	Conversion temperature	Incubation time
Heat 1	High heat (99 °C)	65 °C	90 minutes^a
Heat 2	High heat (99 °C)	55 °C	10 h^b
Alkaline 1	Low heat (37 °C)	65 °C	90 minutes^a
Alkaline 2	Low heat (37 °C)	50 °C	12–16 h^c
Am-BS	Low heat (37 °C)	70 °C	30 minutes^d

^aImprint DNA Modification Kit (Sigma-Aldrich), one-step protocol for ‘Heat 1’ and 2-step protocol for ‘Alkaline 1’
^bEpiTect Bisulfite kit (Qiagen), FFPE protocol and doubled incubation time (see “Methods”)
^cEZ DNA Methylation Kit (Zymo Research)
^dProtocol conditions as described in Hayatsu et al. [25]

ISSN: 1474-760X