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Sample GSM3112973 Query DataSets for GSM3112973
Status Public on Jun 01, 2018
Title 3998998240_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 51
groupid: 4
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 0.390016179138271
cg00000108 0.89410008282227
cg00000109 0.79795912649269
cg00000165 0.173852045373817
cg00000236 0.607202975240879
cg00000289 0.470311396742026
cg00000292 0.74668539753621
cg00000321 0.265267060042661
cg00000363 0.320835328668936
cg00000622 0.034144762123136
cg00000658 0.7141094009854
cg00000714 0.12708802591014
cg00000721 0.887902343506158
cg00000734 0.0730042196175868
cg00000769 0.106783582831771
cg00000807 0.778224732600095
cg00000884 0.79309311750909
cg00000905 0.0714187754604468
cg00000924 0.582715799095528
cg00000948 0.815395552191806

Total number of rows: 430574

Table truncated, full table size 12268 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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