GSM3590961: Cdx2 ES ssDNA-seq; Mus musculus; OTHER
Briefly, live cells were treated with 100 mM KMnO4 then lysed. Each subsequent treatment was followed by phenol:chloroform extraction. Lysates were first treated with proteinase and Rnase, then free 3' ends blocked by cordycepin-5'-triphosphate addition wtih TdT. ssDNA was digested with S1 nuclease then free 3' ends biotinylated. Samples were sonicated with Covaris S220 to generate DNA fragments between 200 and 700 bp and biotinylated fragments pulled down using streptavidin-coated beads. Fragments were released by incubating with S1 nuclease and purified with MinElute PCR Purification Kit (Qiagen) Libraries were prepared using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer's instructions without size selection.