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Sample GSM3112953 Query DataSets for GSM3112953
Status Public on Jun 01, 2018
Title 3998998207_R01C02
Sample type genomic
 
Source name whole blood
Organism Homo sapiens
Characteristics age: 46
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 0.438816343723673
cg00000108 0.878136692580244
cg00000109 0.843408318081624
cg00000165 0.169167458872436
cg00000236 0.621307625071838
cg00000289 0.50072079876139
cg00000292 0.824745728800097
cg00000321 0.231161869059009
cg00000363 0.359367879983377
cg00000622 0.0265206908057685
cg00000658 0.742367379291671
cg00000714 0.146015311421195
cg00000721 0.858156797004167
cg00000734 0.076005870582677
cg00000769 0.0859399127649448
cg00000807 0.768030226305461
cg00000884 0.815526322900132
cg00000905 0.0814630652644011
cg00000924 0.546945428291727
cg00000948 0.808449465939724

Total number of rows: 430574

Table truncated, full table size 12267 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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