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Sample GSM3113084 Query DataSets for GSM3113084
Status Public on Jun 01, 2018
Title 3999431078_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 49
groupid: 3
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 0.38159918454184
cg00000108 0.878049487633649
cg00000109 0.833250702191834
cg00000165 0.164849717105748
cg00000236 0.604382248931488
cg00000289 0.516889472068569
cg00000292 0.762791185945267
cg00000321 0.218950743170832
cg00000363 0.329046955963933
cg00000622 0.037078558527332
cg00000658 0.68505915591399
cg00000714 0.140418920532751
cg00000721 0.884005083086438
cg00000734 0.0656726040811492
cg00000769 0.0646757288162331
cg00000807 0.808460849176714
cg00000884 0.773581326038889
cg00000905 0.09581331121071
cg00000924 0.58270621891804
cg00000948 0.828037430586293

Total number of rows: 430574

Table truncated, full table size 12270 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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