gender: Female cell type: Lymphoblastoid Cell Line
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted from lymphoblastoid Cell Line
Label
cy3 and cy5
Label protocol
Standard illumina protocols
Hybridization protocol
The samples were bisulphite-converted and hybridized to the Infinium HumanMethylation450 BeadChip at the University of Chicago Functional Genomics facility.
Scan protocol
not provided
Description
Sample 2
Data processing
To ensure high data quality, probes were mapped to a bisulfite converted genome and only uniquely mapped probes were retained. Next we excluded probes that were not on the autosomes. Finally, we discarded any probes overlapping SNPs segregating in our panel, leaving 329,469 probes for analysis. We quantile-normalized these data to a standard normal first, across all probes within an individual and then across all individuals at a probe. Finally, we regressed out four principal components from the data to account for unobserved confounders. Normalized data: Normalized average beta (PCs removed). Un-normalized data: Unmethylated and methylated signal intensities and detection p-value.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]
