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Sample GSM3113006 Query DataSets for GSM3113006
Status Public on Jun 01, 2018
Title 3999941048_R03C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 53
groupid: 2
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 0.469210691466188
cg00000108 0.904271716449267
cg00000109 0.783800365904126
cg00000165 0.164874253266309
cg00000236 0.647338774702339
cg00000289 0.583445510596131
cg00000292 0.757006147244271
cg00000321 0.260309821977097
cg00000363 0.25941986196289
cg00000622 0.0307756005421814
cg00000658 0.750568604985256
cg00000714 0.141186824878629
cg00000721 0.857231896971666
cg00000734 0.0911611876684165
cg00000769 0.101306310778357
cg00000807 0.745932572200949
cg00000884 0.777747734695177
cg00000905 0.0875355166833502
cg00000924 0.572988253974363
cg00000948 0.816507707977914

Total number of rows: 430574

Table truncated, full table size 12269 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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