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Sample GSM3112977 Query DataSets for GSM3112977
Status Public on Jun 01, 2018
Title 3998998240_R06C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 19
groupid: 1
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 0.479703350240256
cg00000108 0.865856582366698
cg00000109 0.736312408182954
cg00000165 0.16926660160343
cg00000236 0.629238525604573
cg00000289 0.473508968177435
cg00000292 0.808157453351723
cg00000321 0.269911715785449
cg00000363 0.284290217162251
cg00000622 0.0279462357929946
cg00000658 0.683851791444917
cg00000714 0.174946324714124
cg00000721 0.879245760825391
cg00000734 0.0758289728898977
cg00000769 0.109607850728161
cg00000807 0.73973926578554
cg00000884 0.721598642204801
cg00000905 0.0893229869285049
cg00000924 0.565653644607708
cg00000948 0.809852076291603

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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