title: Targeted bisulfite sequencing Clone 8 Bin 5
design: Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacture's instructions. Assays targeting CpG sites along the chromosomal integration region comprising the continuous sequence covering all DNA binding sites, promoter and EBFP2 were developed using the Rosefinch tool from Zymo Research. Primers were used to amplify bisulfite-converted DNA from the samples, using the EZ DNA Methylation-Lightning Kit for conversion. Amplified products were pooled, barcoded, and prepared for sequencing on an Illumina MiSeq system with a V2 300bp kit, following paired-end sequencing. Trim Galore was used to trim low quality nucleotides and adapter sequences.