GSM9670343: E14 embryonic stem cell 48hr00a; Mus musculus; Bisulfite-Seq
2i_release: Cells were lysed by RLT plus lysis buffer (Qiagen) containing 0.5mM 2-mercaptoethanol. Total nucleic acid was purified from the lysate with RNAdvance magnetic beads (Beckman Coulter, A32649) using a Bravo Workstation pipetting robot (Agilent Technologies). BS-seq libraries were prepared from total nucleic acid using the bulk-cell method previously described (Smallwood et al., Nature Methods 11, 817-820) but with the following modifications: bisulfite conversion was carried out using the EZ Methylation Direct MagPrep kit (Zymo, D5044), with desulphonation and purification using magnetic beads, following the manufacturers' instructions but with half volumes. Primers for first and second strand synthesis contained a 3' random hexamer instead of a nonamer and biotin capture of first strand synthesis products was omitted, substituting an extra AMPure XP (Beckman Coulter, A63881) purification between second strand synthesis and PCR amplification. In order to avoid potential batch effects which could mask subtle differences between samples all libraries were prepared in parallel with the pre-PCR purification steps carried out using a Bravo Workstation pipetting robot (Agilent Technologies). PBAT Bilsulfite-seq