Generic sample from Danio rerio
Danio rerio
DNA was extracted from nuclei using phenol-chloroform and digested separately with 10U of AluI, MseI, or MnlI restriction enzymes overnight at 37C, or 2ul DNA Fragmentase  (NEB M0348S) for 60 min. For all samples unmethylated lambda DNA was added to 1% final concentration (Promega Madison, WI 53711). Methylated paired-end adapters were ligated to sheared DNA according to the Illumina library preparation protocol. Sodium bisulfite conversion was performed using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with an additional incubation step at 60C for 120 min to increase conversion rate. Bisulfite treated DNA was then PCR amplified with 16 cycles and sequenced. note: AluI digested DNA library was generated first to test success of library preparation. DNA from MseI, MnlI and Fragmetnase digestion was combined to generate another library. Both libraries show good converion rate and were combined in final analysis. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
strain
Tubingen
label
PE: paired end, SE: single end
development stage
2 to 16 cell stage