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Sample GSM3112986 Query DataSets for GSM3112986
Status Public on Jun 01, 2018
Title 3998998246_R05C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 44
groupid: 1
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 0.42516345071271
cg00000108 0.877188912349533
cg00000109 0.78399466550592
cg00000165 0.181823795832521
cg00000236 0.651334244022507
cg00000289 0.561809787070582
cg00000292 0.800441226841422
cg00000321 0.198923567376015
cg00000363 0.292875931265767
cg00000622 0.0253021240199049
cg00000658 0.74264950132467
cg00000714 0.138801909173859
cg00000721 0.874340223056715
cg00000734 0.0759645726094748
cg00000769 0.101710861808465
cg00000807 0.765554536551057
cg00000884 0.775020416234843
cg00000905 0.0825722642521659
cg00000924 0.586794587270344
cg00000948 0.784529910307518

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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