NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3112971 Query DataSets for GSM3112971
Status Public on Jun 01, 2018
Title 3998998195_R06C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 59
groupid: 4
gender: M
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 0.346614542254793
cg00000108 0.899775186043119
cg00000109 0.778845410780505
cg00000165 0.167776551017245
cg00000236 0.672424377815077
cg00000289 0.593295418135213
cg00000292 0.768040184675818
cg00000321 0.22132557576289
cg00000363 0.422021117673292
cg00000622 0.0351915907221344
cg00000658 0.744435547416007
cg00000714 0.137719368425934
cg00000721 0.84879143796333
cg00000734 0.0722776158975603
cg00000769 0.102134121662802
cg00000807 0.73851285082591
cg00000884 0.805369841198274
cg00000905 0.075998484842178
cg00000924 0.576744782978191
cg00000948 0.826096355129108

Total number of rows: 430574

Table truncated, full table size 12272 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap