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Sample GSM3112941 Query DataSets for GSM3112941
Status Public on Jun 01, 2018
Title 3998998192_R06C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 57
groupid: 3
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 0.333386610352135
cg00000108 0.896879904544201
cg00000109 0.834623088449721
cg00000165 0.150067205401168
cg00000236 0.616410344136657
cg00000289 0.603421578772205
cg00000292 0.749510987551503
cg00000321 0.208819274529856
cg00000363 0.233692114128387
cg00000622 0.0258236753287683
cg00000658 0.747753762103961
cg00000714 0.129513923404749
cg00000721 0.854114338619218
cg00000734 0.0845232630447501
cg00000769 0.086542971737682
cg00000807 0.80476075881051
cg00000884 0.776939332703449
cg00000905 0.0947533864970889
cg00000924 0.599783881373707
cg00000948 0.820779952174457

Total number of rows: 430574

Table truncated, full table size 12271 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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