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Sample GSM3113015 Query DataSets for GSM3113015
Status Public on Jun 01, 2018
Title 3999078111_R01C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 37
groupid: 4
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 0.39823730729425
cg00000108 0.89550524532936
cg00000109 0.829465230657382
cg00000165 0.171128729795214
cg00000236 0.633774068050578
cg00000289 0.598774114267948
cg00000292 0.797921412570745
cg00000321 0.261182449695727
cg00000363 0.317692203483134
cg00000622 0.0312511827713588
cg00000658 0.739397116794197
cg00000714 0.155005520889091
cg00000721 0.85799081596609
cg00000734 0.0780781985775221
cg00000769 0.0941315890589893
cg00000807 0.768290243118151
cg00000884 0.75330871733479
cg00000905 0.0814673550482931
cg00000924 0.597040464391173
cg00000948 0.806934528939809

Total number of rows: 430574

Table truncated, full table size 12271 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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