title: Bisulfite-Seq of Homo Sapien: polyp (villous histology; low grade dysplasia) tissue: Sample A29_10008351
design: "RRBS was performed at the Mayo Clinic Genotyping Shared Resource facility. Briefly, DNA (250ng) was digested with Msp1 (New England Biolabs, Catalog Number: R0106M) and purified using Qiaquick Nucleotide Removal Kit (Qiagen, Catalog Number: 28004). End-repair A tailing was performed (New England Biolabs, Catalog Numbers: M0212L) and TruSeq methylated indexed adaptors (Illumina, Catalog Number: 15025064) were ligated with T4 DNA ligase (New England Biolabs, Catalog Number: M0202L). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter, Catalog Number: A63882). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research, Catalog Number: D5001) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 oC for 30 sec and 50 oC for 15 min. Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies, Catalog Number: 600414). Library quantification was performed using Qubits dsDNA HS Assay Kit (Life Technologies, Catalog Number: Q32854) and the Bioanalyzer DNA 1000 Kit (Agilent Technologies, Catalog Number: 5067-1504). The final libraries from RRBS were prepared for sequencing per the manufacturer's instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3."
attributes.tag: alignment_software
attributes.value: bsmap v2.73