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Sample GSM3113067 Query DataSets for GSM3113067
Status Public on Jun 01, 2018
Title 3999431010_R01C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 49
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 0.393400809152129
cg00000108 0.903287356526013
cg00000109 0.822194795493587
cg00000165 0.182168522600718
cg00000236 0.687296757489829
cg00000289 0.579522229735761
cg00000292 0.770794623409312
cg00000321 0.279637140253362
cg00000363 0.264469527274316
cg00000622 0.0265586557982517
cg00000658 0.746502957605389
cg00000714 0.132906141252623
cg00000721 0.849527578951692
cg00000734 0.0728442207368994
cg00000769 0.106021539796235
cg00000807 0.790185173210768
cg00000884 0.753865430814618
cg00000905 0.0801491076473877
cg00000924 0.58735017019545
cg00000948 0.80765268357756

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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