Active and senescent human hematopoietic stem and progenitor cell whole genome bisulfite sequencing

Libraries for whole-genome bisulfite sequencing were generated from 5 ng of purified DNA from paired senescent and active CD34+ cells from 3 healthy humans (33, 45, and 53 years of age) using the NuGen Ovation Ultralow MethylSeq Kit following the manufacturer’s protocol. Reads were aligned using Biscuit (https://github.com/zwdzwd/biscuit) and Metilene was used forcalling of differentially methylated regions (Juhling et al., 2016b). DMRs were scanned for overlap with linked regions and the target genes used for prediction of RNA expression differences. Motif analysis of DMRs was conducted using the PWMEnrich package (http://www.bioconductor.org/packages/2.12/bioc/html/PWMEnrich.html) with Hocomoco and Factorbook motif databases provided in the motifbreakR package (Coetzee et al., 2015)