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Sample GSM3113053 Query DataSets for GSM3113053
Status Public on Jun 01, 2018
Title 3999431077_R04C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 53
groupid: 1
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 0.393228435870494
cg00000108 0.910942351422582
cg00000109 0.780091348277291
cg00000165 0.184137523768551
cg00000236 0.657607572999514
cg00000289 0.500530071369044
cg00000292 0.772584332166888
cg00000321 0.277663222350278
cg00000363 0.35014990674406
cg00000622 0.03856061657663
cg00000658 0.726480196649387
cg00000714 0.171161963189156
cg00000721 0.843672650278226
cg00000734 0.0778689047250163
cg00000769 0.09024254027921
cg00000807 0.742807193370002
cg00000884 0.811904980980926
cg00000905 0.0983916712143266
cg00000924 0.560563298563832
cg00000948 0.78721243770785

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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