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Sample GSM3113092 Query DataSets for GSM3113092
Status Public on Jun 01, 2018
Title 3999431078_R04C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 53
groupid: 2
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 0.347522518474421
cg00000108 0.905067981246288
cg00000109 0.768223342932987
cg00000165 0.136934035226925
cg00000236 0.649984638920163
cg00000289 0.598860801405981
cg00000292 0.804697866252442
cg00000321 0.249693022408453
cg00000363 0.280574986631577
cg00000622 0.0508595707510525
cg00000658 0.735702949927816
cg00000714 0.159690800638604
cg00000721 0.861896904764424
cg00000734 0.0751026108946599
cg00000769 0.0819056755169032
cg00000807 0.79564122702907
cg00000884 0.794428768580294
cg00000905 0.0983749288010072
cg00000924 0.594218571076785
cg00000948 0.806967937328949

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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