|
| Status |
Public on Nov 13, 2016 |
| Title |
P009001-30102013-TB-01 [Whole blood] |
| Sample type |
genomic |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Whole blood
Sex: M
smoking status: Never
simplified_diagnosis: CD
age: 21
patient_number: 9001
scan_date: 11/20/2014
|
| 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.The processed data matrix (ProcessedMethWb.txt) represents beta values following background adjustment and correction for dye colour bias. For the final analysis in the published paper additional whole blood DNA samples were added from GSE87640.
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.
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
Nov 13, 2016 |
| Contact name |
Nichols Ventham |
| E-mail(s) |
[email protected]
|
| Organization name |
Univerisity of Edinburgh
|
| Department |
CGEM
|
| Lab |
Gastrointestinal Unit
|
| Street address |
Western General Hospital
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 6XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE87648 |
Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Whole blood, Methylation profiling] |
| GSE87650 |
Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease |
|
