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Sample GSM3113018 Query DataSets for GSM3113018
Status Public on Jun 01, 2018
Title 3999078111_R04C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 32
groupid: 1
gender: M
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 0.468774971417332
cg00000108 0.909398479435149
cg00000109 0.798383488659896
cg00000165 0.189279574557842
cg00000236 0.687638292767455
cg00000289 0.545822950662233
cg00000292 0.800267122768827
cg00000321 0.22075999825409
cg00000363 0.34824899004307
cg00000622 0.0273135984224401
cg00000658 0.730326621606163
cg00000714 0.200078483169189
cg00000721 0.861872901712658
cg00000734 0.0710967115920697
cg00000769 0.0958438396601331
cg00000807 0.787236376532252
cg00000884 0.736356135909594
cg00000905 0.0959914248770491
cg00000924 0.602732751145134
cg00000948 0.80359291452157

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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