GSM4237420: Cyst 6 from an ADPKD kidney; Homo sapiens; Bisulfite-Seq
Genomic DNA was extracted from formalin-fixed sections of ADPKD cyst walls using the QIAmp DNA FFPE Mini Kit (Qiagen), following manufacturer's instruction, excluding paraffin melting steps Libraries were prepared from 500 ng of genomic DNA. DNA was digested with MspI (New England Biolabs, Ipswich, MA), followed by end repair and the addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated to the generated fragments. Fragments were bisulfite modified using the MethylCode DNA Methylation kit (Invitrogen, Carlsbad, CA) and amplified by PCR before selecting fragments between 40 and 220 bp on a 3% (w/v) NuSieve GTG Agarose gel (Lonza, Basel, Switzerland) and AMPure XP Bead Purification (New England Biolabs, Ipswich, MA). The resulting library was sequenced on an Illumina platform with a single-ended 100 bp run.