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Sample GSM2336975 Query DataSets for GSM2336975
Status Public on Nov 13, 2016
Title P008918-22072013-TDM-01
Sample type genomic
 
Source name monocytes
Organism Homo sapiens
Characteristics Sex: M
cell type: monocytes
full_diagnosis: UC
simplified_diagnosis: UC
age at sample: 42.7
patient_number: 8918
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.
 
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)
GSE87640 Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Cells, Methylation profiling]
GSE87650 Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease

Data table header descriptions
ID_REF
VALUE Beta value (following quantile normalisation)

Data table
ID_REF VALUE
cg00000029 0.470784223424471
cg00000108 0.912381368089706
cg00000109 0.819263268414509
cg00000165 0.21290207366648
cg00000236 0.698305017706561
cg00000289 0.609376693927346
cg00000292 0.765849715375773
cg00000321 0.366964969220258
cg00000363 0.400281070884001
cg00000622 0.0463444190418995
cg00000658 0.805181785086548
cg00000714 0.23508390216801
cg00000721 0.897194748842538
cg00000734 0.108139409787472
cg00000769 0.0953722862227121
cg00000807 0.854711004043057
cg00000884 0.853367075798506
cg00000905 0.185615488262238
cg00000924 0.556368513823512
cg00000948 0.839847047156114

Total number of rows: 485577

Table truncated, full table size 13795 Kbytes.




Supplementary file Size Download File type/resource
GSM2336975_9647455004_R02C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM2336975_9647455004_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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