Sex: M cell type: CD4 full_diagnosis: CD simplified_diagnosis: CD age at sample: 18.3 patient_number: 9013
Extracted molecule
genomic DNA
Extraction protocol
DNA was extracted using the QIAGEN Allprep kit according to instructions
Label
Cy5 and Cy3
Label protocol
DNA was bisulphite converted using the EZ-96 DNA Methylation kit (Zymo Research, Irving CA). Standard Illumina Protocol
Hybridization protocol
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol
HiScan H166
Description
sample
Data processing
Data were processed using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. In methylumi, probes were background adjusted, corrected from dye colour bias, and quantile normalised. Intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ). Inter-array batch effects were corrected for using ComBat. Whole blood DNA methylation samples were processed separately using the lumi, methylumi and minfi packages in R (R Foundation for Statistical Computing, Vienna). Probes were filtered out if the detection p value of 0.01 or if >5% of probes failed. Probes containing single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.01 in the European population in the 1000 Genomes Project were also removed. Samples with >5% of probes failing and those failing a sex check (based on X chromosome methylation level) were also removed. Probes were background adjusted, corrected from dye colour bias, and quantile normalised. Whole blood samples from two datasets were combined at this stage. Subsequently, intra-array and probe design variation was corrected for using beta-mixture quantile dilatation (BMIQ) and inter-array batch effects were corrected for using ComBat. The data matrix can be found on the SuperSeries GSE87650 record.
