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Sample GSM3112947 Query DataSets for GSM3112947
Status Public on Jun 01, 2018
Title 3998998192_R06C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 34
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 0.422738746637677
cg00000108 0.904202955662909
cg00000109 0.800176355200121
cg00000165 0.134241956159537
cg00000236 0.674080905663858
cg00000289 0.597035004339902
cg00000292 0.763444162277213
cg00000321 0.340351529259389
cg00000363 0.347989745830562
cg00000622 0.0343279990835461
cg00000658 0.71211128154189
cg00000714 0.156586158698131
cg00000721 0.866901723151357
cg00000734 0.069682673088396
cg00000769 0.106150522939381
cg00000807 0.808665117516188
cg00000884 0.76617023368997
cg00000905 0.0818823841486524
cg00000924 0.588217334743018
cg00000948 0.836838593521736

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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