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Sample GSM3112916 Query DataSets for GSM3112916
Status Public on Jun 01, 2018
Title 3998998123_R05C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 61
groupid: 2
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 0.426349531996314
cg00000108 0.89968117342585
cg00000109 0.765606847604698
cg00000165 0.15644500120931
cg00000236 0.663041714890096
cg00000289 0.462257159842632
cg00000292 0.808019428266364
cg00000321 0.244183169568988
cg00000363 0.318937976878879
cg00000622 0.0330562081072472
cg00000658 0.748635043087577
cg00000714 0.172521308793796
cg00000721 0.842341277579434
cg00000734 0.0714881973893555
cg00000769 0.0940188077197467
cg00000807 0.794196364250997
cg00000884 0.738715008466777
cg00000905 0.0927378815686486
cg00000924 0.591822021118431
cg00000948 0.822512313847613

Total number of rows: 430574

Table truncated, full table size 12267 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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