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Sample GSM3113052 Query DataSets for GSM3113052
Status Public on Jun 01, 2018
Title 3999431077_R03C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 42
groupid: 3
gender: F
Treatment protocol Individuals with a self-reported history of doctor's diagnosed depression & a self-reported history of an inflammatory disorder (code = 1); Individuals with a self-reported history of doctor's diagnosed depression (code = 2); Individuals with a self-reported history of an inflammatory disorder (code = 3); Healthy controls (code = 4 )
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from whole blood using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.
Label Cy3, Cy5
Label protocol 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.
 
Hybridization protocol Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.
Scan protocol Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).
Data processing Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on Illumina’s database and probes identified by Chen et al.* were removed. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
 
Submission date Apr 26, 2018
Last update date Jun 01, 2018
Contact name Therese M Murphy
E-mail(s) t.murphy@exeter.ac.uk
Organization name University of Exeter
Department University of Exeter Medical School
Street address RILD building
City Exeter
ZIP/Postal code EX2 5DW
Country United Kingdom
 
Platform ID GPL13534
Series (1)
GSE113725 DNA methylation and inflammation marker profiles associated with a history of depression.

Data table header descriptions
ID_REF
VALUE Normalized Average Beta values for each sample

Data table
ID_REF VALUE
cg00000029 0.555900650327851
cg00000108 0.842333481976511
cg00000109 0.537967407859923
cg00000165 0.141762977850032
cg00000236 0.56514218594525
cg00000289 0.414538217574695
cg00000292 0.820887474826358
cg00000321 0.326671772564263
cg00000363 0.21939115731422
cg00000622 0.0248392153376978
cg00000658 0.668250072691622
cg00000714 0.236452773781427
cg00000721 0.831512265883647
cg00000734 0.0813364351000252
cg00000769 0.0827975010685248
cg00000807 0.681981918773471
cg00000884 0.799301208284106
cg00000905 0.126502751991787
cg00000924 0.603749987242338
cg00000948 0.548735155196351

Total number of rows: 430574

Table truncated, full table size 12244 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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