title: GSM2813725: untreated control 1; Homo sapiens; Bisulfite-Seq
library_construction_protocol: Puregene Gentra Triplicate samples of YB5 cells treated with 10 µM HH1 and DMSO controls were analyzed for DNA methylation changes by reduced representation bisulfite sequencing (RRBS) (Gu et al. Nature Protocols 2011, doi:10.1038/nprot.2010.190). We followed the NEB protocol for methylated adaptors. Briefly, 1 microgram of genomic DNA was spiked 100 picograms of lambda phage DNA as the unmethylated standard and digested with MspI. Ends of restriction fragments were filled in, 3'-dA tailed and methylated adaptors (NEB E7535) were ligated to the ends of restriction fragments. Bisulfite treatment using the Epitect kit (Qiagen) followed. Bisulfite-converted libraries were amplified using EpiMark Taq DNA polymerase (NEB) and primers with barcode indices. The libraries were pooled and sequenced at Fox Chase Cancer Center Genomics Facility on Illumina HiSeq2500 instrument using single end reads of 50 bases. We used Bismark v0.18.1 to align the sequences to hg19 human genome assembly. We used methylKit v1.3.3 to analyze differential methylation.
attributes.tag: GEO Accession
attributes.value: GSM2813725