|
| Status |
Public on Dec 17, 2019 |
| Title |
T cells Newcastle Early Arthritis Clinic number 1008 |
| Sample type |
RNA |
| |
|
| Source name |
Disease control T cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 1008
gender: M
age: 70
tissue: peripheral blood
cell type: CD4+ T cells
first_diagnosis: Psoriatic Arthritis
working_diagnosis: Psoriatic Arthritis
|
| Growth protocol |
Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.
|
| Label |
biotin
|
| Label protocol |
50ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).
|
| |
|
| Hybridization protocol |
Illumina HT12 BeadChip.
|
| Scan protocol |
Illumina iScan.
|
| Description |
Freshly isolated and purified peripheral blood T cells- GEO: GSM2129029
|
| Data processing |
Samples with mean detection pvalue > 0.05 and probes whose detection p-value was >0.05 in over 25% of samples were excluded prior to background correction and quantile normalization, following which additional probes were removed where they mapped to (i) sex chromosomes, (ii) repeat or intronic/intergenic regions or (iii) unmapped regions.
|
| |
|
| Submission date |
Dec 12, 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 |
GPL10558 |
| Series (2) |
| GSE137634 |
Lymphocyte DNA methylation mediates genetic risk at shared immune mediated disease loci |
| GSE141934 |
Transcriptional data of inflamatory arthritis T cells. |
|
| Relations |
| Reanalysis of |
GSM2129029 |
