age group: nonagenarian Sex: female cell type: peripheral blood mononuclear cells ratio of cd4+/cd8+ cells: 7.99 percentage of cd14+ cells: 15.2 percentage of cd4+cd28- cells: 3.1 percentage of cd8+cd28- cells: 35.2 maternal age at death: 72 paternal age at death: 52
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted from PBMCs with QIAamp DNA Mini kit (Qiagen, CA, USA), following the manufacturer's instructions for spin protocol.
Label
Cy5 and Cy3
Label protocol
Standard Illumina Protocol.
Hybridization protocol
Four µl of bisulfite-converted DNA was whole genome amplified, enzymatically fragmented and hybridized to the Infinium HumanMethylation450 BeadChip according to the manufacturer's protocol.
Scan protocol
The BeadChips were scanned with the iScan reader.
Description
28798
Data processing
GenomeStudio software V2011.1, R version 3.0.2. Processed average beta values (background correction, normalisation with the dasen method (individually for Infinium I and II chemistries), batch effects corrected with BMIQ method and R package Combat). Prior to any processing, all unspecific or polymorphic sites (N=76775) were removed based on database information [Chen et al., Epigenetics 2013, 8:203-209]. Samples and target sites of a technically poor quality were filtered out by excluding sites with a beadcount of <3 in 5% of the samples (N=526) and sites for which 1% of the samples showed a detection p-value >0.05 (N=740).
