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Sample GSM3113075 Query DataSets for GSM3113075
Status Public on Jun 01, 2018
Title 3999442083_R03C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 30
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 0.407821409406181
cg00000108 0.887696188437125
cg00000109 0.784768159679415
cg00000165 0.126182741632624
cg00000236 0.64413841167171
cg00000289 0.544820489544295
cg00000292 0.840742238963401
cg00000321 0.216370952819095
cg00000363 0.315022441869282
cg00000622 0.0390898359919412
cg00000658 0.655575004070536
cg00000714 0.188405039835345
cg00000721 0.903514548307119
cg00000734 0.0586477741929427
cg00000769 0.0842363508466628
cg00000807 0.805724864607119
cg00000884 0.754896304273448
cg00000905 0.102501430660647
cg00000924 0.589846076134154
cg00000948 0.807684704767907

Total number of rows: 430574

Table truncated, full table size 12269 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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