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Sample GSM3113028 Query DataSets for GSM3113028
Status Public on Jun 01, 2018
Title 3999078062_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 59
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 0.369212914867211
cg00000108 0.899244262167739
cg00000109 0.785987202588065
cg00000165 0.129123545489877
cg00000236 0.65518011666858
cg00000289 0.558452136266235
cg00000292 0.773779966120491
cg00000321 0.227522558269406
cg00000363 0.208079121498927
cg00000622 0.0297664871565761
cg00000658 0.767469849856195
cg00000714 0.116648519634503
cg00000721 0.876816572386263
cg00000734 0.0862822084357217
cg00000769 0.0900450070829183
cg00000807 0.794399517188066
cg00000884 0.712863053490208
cg00000905 0.147139941487339
cg00000924 0.59220553294375
cg00000948 0.810125734471957

Total number of rows: 430574

Table truncated, full table size 12270 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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