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Sample GSM3112949 Query DataSets for GSM3112949
Status Public on Jun 01, 2018
Title 3998998207_R02C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 58
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 0.437548366978687
cg00000108 0.956119763885926
cg00000109 0.776175199693191
cg00000165 0.158612317549846
cg00000236 0.658988866988934
cg00000289 0.493051974652543
cg00000292 0.763729717745338
cg00000321 0.20372964709441
cg00000363 0.302865197462029
cg00000622 0.0220918718720103
cg00000658 0.696777766170459
cg00000714 0.162359131266424
cg00000721 0.876336162348389
cg00000734 0.0798134591095025
cg00000769 0.0959724040424664
cg00000807 0.773694099110323
cg00000884 0.719284918859568
cg00000905 0.103585913924592
cg00000924 0.580197936341736
cg00000948 0.794099226910248

Total number of rows: 430574

Table truncated, full table size 12266 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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