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Sample GSM2337314 Query DataSets for GSM2337314
Status Public on Nov 13, 2016
Title P008617-28022012-TB-S001 [Whole blood]
Sample type genomic
 
Source name Whole blood
Organism Homo sapiens
Characteristics cell type: Whole blood
Sex: M
smoking status: Ex
simplified_diagnosis: HS
age: 60
patient_number: 8617
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

Supplementary file Size Download File type/resource
GSM2337314_9989536087_R02C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM2337314_9989536087_R02C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data are available on Series record

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