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Sample GSM3113027 Query DataSets for GSM3113027
Status Public on Jun 01, 2018
Title 3999078062_R01C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 40
groupid: 4
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 0.37070687147119
cg00000108 0.905312871185143
cg00000109 0.780311014033704
cg00000165 0.174122269706943
cg00000236 0.639130089888485
cg00000289 0.608931877881211
cg00000292 0.802759210431168
cg00000321 0.229714090181689
cg00000363 0.264846776196886
cg00000622 0.0230620385577262
cg00000658 0.755270639902513
cg00000714 0.15327077586615
cg00000721 0.863260672727105
cg00000734 0.0847609253501587
cg00000769 0.0958979110035717
cg00000807 0.788957396353714
cg00000884 0.754677783006099
cg00000905 0.0981861337866662
cg00000924 0.608580269531031
cg00000948 0.7911916666906

Total number of rows: 430574

Table truncated, full table size 12272 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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