|
| Status |
Public on Dec 17, 2019 |
| Title |
EA0996: Newcastle Early Arthritis Clinic number 996 |
| Sample type |
genomic |
| |
|
| Source name |
Rheumatoid Arthritis T cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 53
tissue: peripheral blood
cell type: CD4+ T cells
first_diagnosis: Undifferentiated Inflammatory Arthritis
working_diagnosis: Rheumatoid Arthritis
|
| Growth protocol |
Whole peripheral blood was stored at room temperature for ≤4 hours before processing. After monocyte depletion by immuno-rosetting, an automated magnetic bead-based positive selection protocol was used to isolate CD4+ cells (Stemcell Technologies, Vancouver, Canada) yielding a median cell purity of 98.9%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA/RNA Mini Kit (Qiagen, UK).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol.
|
| |
|
| Hybridization protocol |
400ng of DNA was bisulphite-converted and hybridised to the Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.
|
| Scan protocol |
Illumina iScan.
|
| Description |
Freshly isolated and purified peripheral blood T cells
|
| Data processing |
Failed probes whose detection p-values were >0.01 in >10% samples were excluded prior to functional normalisation as implemented in the minfi R package, following which additional probes were removed due to; (i) cross-hybridization, (ii) mapping to sex chromosomes, or (iii) presence of a SNP (MAF>0.05) at the interrogated CpG, probe sequence or single base extension site.
matrix processed value definition: Normalized average Beta values (Functional normalisation)
|
| |
|
| Submission date |
Sep 17, 2019 |
| Last update date |
Dec 21, 2019 |
| Contact name |
Arthur Pratt |
| E-mail(s) |
arthur.pratt@newcastle.ac.uk
|
| Organization name |
Newcastle University
|
| Department |
Faculty of Medical Sciences
|
| Lab |
Musculoskeletal Research Group
|
| Street address |
Framlington Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE137593 |
Early arthritis CD4+ T cell DNA methylation profiling |
| GSE137634 |
Lymphocyte DNA methylation mediates genetic risk at shared immune mediated disease loci |
|
