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Sample GSM3113043 Query DataSets for GSM3113043
Status Public on Jun 01, 2018
Title 3999431002_R05C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 41
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 0.445295604483583
cg00000108 0.903814998680408
cg00000109 0.800115322874387
cg00000165 0.1743213790791
cg00000236 0.678002156738037
cg00000289 0.533433282896298
cg00000292 0.850604124733818
cg00000321 0.244569800517685
cg00000363 0.358586937898164
cg00000622 0.0288779909433013
cg00000658 0.711069622833026
cg00000714 0.171715954011349
cg00000721 0.867067578054103
cg00000734 0.0862118326209254
cg00000769 0.0652084076842676
cg00000807 0.753955310295946
cg00000884 0.731474765292076
cg00000905 0.167273132349192
cg00000924 0.570401607716023
cg00000948 0.807754737386827

Total number of rows: 430574

Table truncated, full table size 12268 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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