NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3112985 Query DataSets for GSM3112985
Status Public on Jun 01, 2018
Title 3998998246_R03C01
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 55
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 0.335871147362738
cg00000108 0.881466299626817
cg00000109 0.800141590147384
cg00000165 0.136398918077552
cg00000236 0.675426719526254
cg00000289 0.467625176032981
cg00000292 0.771641766216177
cg00000321 0.205660417230187
cg00000363 0.281081988017868
cg00000622 0.0352168918726958
cg00000658 0.739802687479337
cg00000714 0.153482447524467
cg00000721 0.846464247847173
cg00000734 0.0811535563165565
cg00000769 0.0928684132606296
cg00000807 0.771027435907798
cg00000884 0.811091173291826
cg00000905 0.105987538836735
cg00000924 0.567558297815419
cg00000948 0.818004595034699

Total number of rows: 430574

Table truncated, full table size 12269 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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