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Sample GSM3113054 Query DataSets for GSM3113054
Status Public on Jun 01, 2018
Title 3999431077_R05C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 56
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 0.362624244704032
cg00000108 0.916702739006361
cg00000109 0.746993980610542
cg00000165 0.168169895524713
cg00000236 0.691965073283735
cg00000289 0.542316161377406
cg00000292 0.774047549156567
cg00000321 0.193750068036591
cg00000363 0.349942303540453
cg00000622 0.0392017751006518
cg00000658 0.735576386875153
cg00000714 0.186658050623331
cg00000721 0.875237450152522
cg00000734 0.0658934020181271
cg00000769 0.0894510105869146
cg00000807 0.774619132239276
cg00000884 0.764357981111405
cg00000905 0.109325444889593
cg00000924 0.575903197239101
cg00000948 0.805146396148701

Total number of rows: 430574

Table truncated, full table size 12267 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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