GSM5196893: F0Saline-F1HDM (MeDIP-Seq); Mus musculus; MeDIP-Seq
DNA was isolated from lung tissues using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD), according to manufacturer's instructions. Sample DNA concentrations were quantified with the Quanti-iTM Picogreen dsDNA assay kit (Invitrogen, CA). DNA from each treatment group (pooled from mice of 3 individual dams) was fragmented on Covaris S2 and had an average length of 200 bp. Hydroxymethylated and methylated DNA was captured using the hMethylCap and MethylCap kit (Diagenode, NJ) respectively.  DNA was eluted from the protein complex. Two hundred fifty ng fragmented DNAs were amplified, ligated with linkers, and subjected to flow cells using the HiSeq2000 platform according to the manufacturer's NGS ChIP protocol (Illumina, CA). We used the DNA Sample Prep Master Mix Set 1 (NEB E6040) in combination with the Multiplexing Sample Preparation Oligo Kit (96 samples, Illumina PE-400-1001). We used 250ng of fragmented DNA and performed Library preparation on Apollo 324 with PrepXDNA Library Kit 24 samples per kit (400007) or PrepX-32-DNA Library Kit 96 samples per kit (400021) according to the kit's protocol.