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Sample GSM3113009 Query DataSets for GSM3113009
Status Public on Jun 01, 2018
Title 3999941048_R01C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 32
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 0.375488339122314
cg00000108 0.901536627975084
cg00000109 0.785578798978276
cg00000165 0.19881875156892
cg00000236 0.720364836469481
cg00000289 0.570718941295957
cg00000292 0.796745052197257
cg00000321 0.231610757509925
cg00000363 0.376445819703887
cg00000622 0.0402992038203962
cg00000658 0.728492714572096
cg00000714 0.155355224925154
cg00000721 0.865576529686499
cg00000734 0.071350983290415
cg00000769 0.108030833730474
cg00000807 0.784938186342755
cg00000884 0.804293957916605
cg00000905 0.0884361856380408
cg00000924 0.577973558943729
cg00000948 0.796985155272376

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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