|
| Status |
Public on Jun 03, 2021 |
| Title |
PRISM_PDB_393Case |
| Sample type |
genomic |
| |
|
| Source name |
white blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
mmed: 11.65731845
umed: 11.16741815
phenotype: Case
array: R05C01
slide: 8655685080
scan_date: 21/06/2013
tissue: white blood cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood using standard protocols. Bisulfite conversion was performed on 500µg of DNA using Zymo EZ-96 DNA methylation Kit (Zymo Research, USA). DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturer’s protocol
|
| Label |
Cy3, Cy5
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Description |
DNA CpG sites
|
| Data processing |
The R package RnBeads version 1.10.8 was used for quality control. Samples with low methylated or unmethylated median intensity (<11.0) were excluded (n=35) along with samples with sex mismatch between reported and predicted sex (n=0). Probes with the following criteria were excluded: detection P value >0.05, cross reactive probes, containing a SNP within 3 bp of nucleotide extension site, or those located on sex chromosomes. Additionally, 723 sites were further excluded from the dataset for previously established association with smoking. A total of 56,356 probes were excluded from the initial 485,512 leaving 429,156 CpGs for analysis.
The Enmix method from RnBeads was used for background correction whilst
SWAN from RnBeads was used for between and within array normalization
The M-values, derived using the formulae log2((methylated signal+1)/(unmethylated signal+1)), were used
|
| |
|
| Submission date |
Dec 29, 2020 |
| Last update date |
Apr 22, 2022 |
| Contact name |
Omar M E Albagha |
| E-mail(s) |
oalbagha@hbku.edu.qa
|
| Organization name |
Hamad Bin Khalifa University
|
| Department |
Health and Life Sciences
|
| Street address |
Luqta Street, Education City
|
| City |
Doha |
| ZIP/Postal code |
P.O. Box: 34110 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE163970 |
Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status |
|
| Relations |
| Reanalyzed by |
GSM6058435 |
