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Sample GSM3113094 Query DataSets for GSM3113094
Status Public on Jun 01, 2018
Title 3999215194_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 39
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 0.374230508841892
cg00000108 0.904654767188876
cg00000109 0.794310704154247
cg00000165 0.213038183931163
cg00000236 0.66918336004979
cg00000289 0.62433997201052
cg00000292 0.796789636182144
cg00000321 0.212822876202417
cg00000363 0.284224873846254
cg00000622 0.0371712506103642
cg00000658 0.754444995700474
cg00000714 0.105311963786237
cg00000721 0.872499735042808
cg00000734 0.0711888335128721
cg00000769 0.0992345855060845
cg00000807 0.821531718160159
cg00000884 0.731291283559466
cg00000905 0.0762511143470463
cg00000924 0.588528326273762
cg00000948 0.82107867350981

Total number of rows: 430574

Table truncated, full table size 12275 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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