|
| Status |
Public on Jun 01, 2018 |
| Title |
3999431078_R06C01 |
| Sample type |
genomic |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
age: 54
groupid: 1
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. |
|
