title: WGBS of chicken: cecum trt
design: two-day old SE negative Jining Bairi chickens were randomly divided into two groups and raised in two separated isolators with the same condition.Three individual cecum samples from each of inoculated and control groups at 3 day post inoculation were randomly selected for genomic DNA extraction.Three genomic DNA samples in each of inoculated and control groups were mixed in equal amount to generate one pooled sample for sequencing.The DNA samples were sheared with Covaris ultrasonicator (Life Technology, US). The fragmented DNA was purified using AMPure XP beads and end repaired. After end repair and adenylation, cytosine-methylated barcodes were then ligated to sonicated DNA.Subsequently, 100-300bp insert size targets were purified by 2% agarose gel electrophoresis. Bisulfite conversion was conducted using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA). The final libraries were generated by PCR amplification and then analyzed by an Agilent 2100 Bioanalyzer (Agilent Technology, US) and quantified by QRT-PCR using QPCR NGS Library Quantification Kit (Agilent, Santa Clara, CA, USA). The constructed libraries were sequenced using Illumina HiSeq 4000 (Illumina, San Diego, CA, USA) by Biomarker Technology Co., Ltd (Beijing, China).