Computational protocol: DNA methylation results depend on DNA integrity—role of post mortem interval

Similar protocols

Protocol publication

[…] Bisulfite sequence primers were designed using the software packages MethylPrimer Express (ABI Life Technologies, Grand Island, USA), Geneious (Biomatters, Auckland, New Zealand) and the Netprimer tool (PREMIER Biosoft International, Palo Alto, USA) for validation of different melting temperatures. Primers were ordered from Metabion (Steinkirchen, Germany). Touchdown PCRs (Korbie and Mattick, ) with starting temperatures of 70°C (ALDH2) and 62°C (SLC6A4), respectively, were performed using a semi-nested strategy and sequenced on a 3500XL genetic analyzer from ABI Life Technologies (Grand Island, USA) (see Table for primer details).Analysis of CpG-specific methylation percentage was processed by the Epigenetic Sequencing Methylation (ESME) analysis software (Lewin et al., ) and the methylation rate (%) of each CpG site within the amplified region was estimated by the ratio between normalized peak values of Cytosine (C) and Thymine (T). […]

Pipeline specifications

Software tools Geneious, NetPrimer
Application qPCR
Organisms Homo sapiens, Sus scrofa
Chemicals Acetaldehyde, Serotonin