GSM2771849: Ba_BS; Mus musculus; Bisulfite-Seq
Cells were collected, seperated from feeders by pre-plating and genomic DNA was extracted using the Blood & Cell Culture DNA Mini kit (Qiagen). High molecular weight DNA (400ng) was spiked with unmethylated bacteriophage λ DNA (5 ng of λ DNA per microgram of genomic DNA; Promega), with methylated T7 phage DNA (5 ng of T7 DNA per microgram of genomic DNA) and also with the manufacture's digestion and sequencing control (each 20 ng per microgram of genomic DNA). Genomic DNA with the spike-in controls was sheared using Covaris LE220 focused-ultrasonicator to a mean fragment size of 800bp, purified, denatured and the sample was evenly split for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water. Both aliquots were then processed in parallel for all stages of the protocol. Illumina compatible adapters and library specific indexes were incorporated through ten PCR cycles. The quality control of the library was monitored using the Agilent 2100 Bioanalyzer DNA 7500 assay, and the concentration was estimated using the KAPA Library Quantification Kit for Illumina® Platforms, v1.14 (Kapa Biosystems). WGBS and oxWGBS following the workflow of  CEGX TrueMethyl® Whole Genome kit, v3.1 (Cambridge Epigenetix) in HydroxyMethyl mode