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Sample GSM3112923 Query DataSets for GSM3112923
Status Public on Jun 01, 2018
Title 3998998174_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 48
groupid: 3
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 0.397643042610198
cg00000108 0.886630434539405
cg00000109 0.796711361933962
cg00000165 0.130877535497223
cg00000236 0.618622645121044
cg00000289 0.569639845038833
cg00000292 0.729144476376133
cg00000321 0.218818053969383
cg00000363 0.333003912613171
cg00000622 0.0386751761375305
cg00000658 0.719045403862134
cg00000714 0.145740612033522
cg00000721 0.889210106082858
cg00000734 0.0717081894326926
cg00000769 0.0937484591949504
cg00000807 0.750693379581595
cg00000884 0.757195407463358
cg00000905 0.0845182316020315
cg00000924 0.597882560908162
cg00000948 0.827844071558836

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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