Computational protocol: Neuron-specific methylome analysis reveals epigenetic regulation and tau-related dysfunction of BRCA1 in Alzheimer’s disease

Similar protocols

Protocol publication

[…] Genomic DNA (500 ng) was bisulfite-converted using an EZ DNA methylation kit (Zymo Research) and analyzed using an Illumina Infinium HumanMethylation450 BeadChip (Illumina) and iScan scanner (Illumina). We processed the methylation array data using the statistical computing package R 3.0.2 (www.r-project.org/) and the Bioconductor package ChAMP (). Idat files were imported to calculate methylation levels (β values) for each probe. The β-mixture quantile (BMIQ) normalization method () was used to reduce probe-type bias, and batch correction was performed using the ComBat method (). For each probe, we compared β values between AD and NC samples using two one-sided Student’s t tests: P (AD < NC) and P (AD > NC). We defined probes with P values < 0.05 and mean β differences between AD and NC > 0.05 as DMPs. Regions with no less than three consecutive DMPs were defined as DMRs. […]

Pipeline specifications

Software tools ChAMP, BMIQ, ComBat
Application DNA methylation array analysis
Organisms Homo sapiens, Mus musculus
Diseases Alzheimer Disease, Liver Diseases, Neurodegenerative Diseases