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Sample GSM3112957 Query DataSets for GSM3112957
Status Public on Jun 01, 2018
Title 3998998207_R05C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 54
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 0.411728165797306
cg00000108 0.902425735120461
cg00000109 0.757846095324698
cg00000165 0.129513727819029
cg00000236 0.639681469236079
cg00000289 0.51593441493586
cg00000292 0.756579160033099
cg00000321 0.238760172953395
cg00000363 0.298744049223078
cg00000622 0.0431063740634887
cg00000658 0.703564638250782
cg00000714 0.145951268613825
cg00000721 0.892024994321445
cg00000734 0.0852777599982189
cg00000769 0.105191864965666
cg00000807 0.789832251195814
cg00000884 0.787662814375833
cg00000905 0.0771195391089848
cg00000924 0.601012114760478
cg00000948 0.814860368075939

Total number of rows: 430574

Table truncated, full table size 12271 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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