genomic DNA was extracted from pulverized trabecular bone using a phenol-cholorform protocol
Label
Cy5 and Cy3
Label protocol
400ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)
Hybridization protocol
Infinium MethylationEPIC array
Scan protocol
standard illumina scanner
Description
medial condyle distal femur trabecular bone from chimpanzee
Data processing
Raw fluorescent data were normalized using the Noob background correction method with dye-bias normalization followed with a between-array normalization method (functional normalization) as implemented in the R package minfi. After normalization, methylation values (beta values) for each site were calculated as the ratio of methylated probe signal intensity to the sum of both methylated and unmethylated probe signal intensities. Those probes with failed detection levels (p-value > 0.05) in greater than 10% of samples were removed. Cross-reactive probes, probes containing SNPs at the CpG site, probes detecting SNP information, probes detecting methylation at non-CpG sites, and probes targeting sites within the sex chromosomes were also removed using the minfi package in R. Lastly, probes that were determined to be non-specific to each nonhuman primate genome were also removed. Filtering for these files was based on Hernando-Herraez et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate nonhuman primate genome, and only those probes that successfully mapped to the genome, had only 1 unique hit, and targeted CpG sites were retained. Additionally, probes were kept for subsequent analyses only if they had 0 mismatches in 5bp closest to and including the CpG site, and had 0-2 mismatches in 45bp not including the CpG site. - Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and great ape evolution. PLOS Genet 2013;9:e1003763. Nonhuman Primate Genome: Pan troglodytes
