title: GSM1938088: MCF7_LTED.RE.slide2; Homo sapiens; MRE-Seq
library_construction_protocol: Genomic DNA was isolated from 3 x 10^6 cells using the Quick-gDNA MiniPrep kit from Zymo Research (Irvine, CA) according to the manufacturers instructions. The quality of the isolated high molecular weight DNA was confirmed by agarose gel electrophoresis. Methyl-MAPS libraries were prepared according to the protocol in Edwards et al Genome Research 2010. In brief, genomic DNA was split and unmethylated and methylated compartments were independently obtained by limit digestions of 10–15 ug of DNA with McrBC or five tetranucleotide methylation-sensitive restriction endonucleases (RE; HpaII, HhaI, AciI, BstUI, HpyCH4IV). Digested fragments were size selected by gel-electrophoresis for fragments >800 bp. Mate-pair SOLiD sequencing libraries were then prepared using custom 6 bp barcodes. As part of the Methyl-MAPS protocol, EcoP15I CAP linkers are ligated onto the ends of the fragments. The fragments are then circularized with biotinylated internal adapters, and digested with EcoP15I, which cleaves the DNA 25-27 bp away from its recognition site. Consequently, although we sequence 35 bp for both the F3 and R3 tags, only 25 bp comprise the genomic sequence tag. Each library was loaded on two sequencing slides.
identifiers.namespace: GEO
identifiers.id: GSM1938088