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Sample GSM3112979 Query DataSets for GSM3112979
Status Public on Jun 01, 2018
Title 3998998240_R02C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 48
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 0.347253530193056
cg00000108 0.896380895053264
cg00000109 0.778546567656748
cg00000165 0.136770699463203
cg00000236 0.60787513033218
cg00000289 0.523762493827315
cg00000292 0.778959880005435
cg00000321 0.199374508365856
cg00000363 0.337096209615272
cg00000622 0.0315011664214258
cg00000658 0.768902488517656
cg00000714 0.141777817756022
cg00000721 0.885880636123787
cg00000734 0.0624474858288251
cg00000769 0.0978077532589433
cg00000807 0.782028682600907
cg00000884 0.780617285479059
cg00000905 0.0745039833265159
cg00000924 0.565642922847728
cg00000948 0.809062694935184

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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