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Sample GSM3113082 Query DataSets for GSM3113082
Status Public on Jun 01, 2018
Title 3999442083_R05C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 50
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 0.414798813871763
cg00000108 0.922175984457804
cg00000109 0.787590590518922
cg00000165 0.16364323761572
cg00000236 0.679182683689086
cg00000289 0.620317836183272
cg00000292 0.819106665830693
cg00000321 0.21100508192162
cg00000363 0.267146880924604
cg00000622 0.0344591463284197
cg00000658 0.762366126181808
cg00000714 0.138622841511896
cg00000721 0.864145457182757
cg00000734 0.0723587118381554
cg00000769 0.0920553097982336
cg00000807 0.777951933975611
cg00000884 0.794265762283406
cg00000905 0.0836749938477152
cg00000924 0.546267198593879
cg00000948 0.803144187493723

Total number of rows: 430574

Table truncated, full table size 12268 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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