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Sample GSM3113072 Query DataSets for GSM3113072
Status Public on Jun 01, 2018
Title 3999431010_R06C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 47
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 0.383250013430322
cg00000108 0.857964639843699
cg00000109 0.76514510472931
cg00000165 0.180685897937064
cg00000236 0.622403853376399
cg00000289 0.533685899703051
cg00000292 0.776236719676404
cg00000321 0.294908251028999
cg00000363 0.408973483913337
cg00000622 0.0316530505814187
cg00000658 0.699760361876389
cg00000714 0.109065281905119
cg00000721 0.881883584332662
cg00000734 0.066601494269176
cg00000769 0.0995919206209124
cg00000807 0.750256418595746
cg00000884 0.771965359473644
cg00000905 0.0998697358523295
cg00000924 0.56437206199425
cg00000948 0.807002566087917

Total number of rows: 430574

Table truncated, full table size 12270 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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