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Sample GSM3113074 Query DataSets for GSM3113074
Status Public on Jun 01, 2018
Title 3999442083_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 31
groupid: 4
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 0.441242764925473
cg00000108 0.897546106929946
cg00000109 0.80226543816392
cg00000165 0.140004870273621
cg00000236 0.657442798108037
cg00000289 0.582203005205652
cg00000292 0.801450850099886
cg00000321 0.203021074980513
cg00000363 0.328235749074457
cg00000622 0.0438439916851692
cg00000658 0.727615491077135
cg00000714 0.151942854307091
cg00000721 0.876257943460747
cg00000734 0.0734933301223599
cg00000769 0.103796544540176
cg00000807 0.7755576962989
cg00000884 0.805047965443964
cg00000905 0.0999588493409397
cg00000924 0.610550910810571
cg00000948 0.801873812246844

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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