|
| Status |
Public on Nov 26, 2019 |
| Title |
SLE_CD8_2 |
| Sample type |
genomic |
| |
|
| Source name |
CD8+ T cell DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD8+ T cell
disease status: lupus
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMCs) were extracted from whole blood via Ficoll-Paque PLUS density centrifugation (GE Healthcare Bio-Sciences). Total T cells were isolated using negative selection by magnetic bead separation with the Human Pan T cell Isolation II kit (Miltenyi Biotec). Flow cytometry sorting was used to isolate CD3+CD56-TCRab+CD8+ T cells using the following fluorophore-conjugated antibodies: APC anti-human CD56 (clone: HCD56), FITC anti-human CD8a (clone: RPA-T8), Pacific Blue anti-human CD3 (clone: HIT3a), and PE anti-human alpha/beta-TCR (clone: IP26) (BioLegend). DNA was extracted from CD8+ T cells using the DNeasy Blood and Tissue kit (Qiagen) and bisulfite converted with the EZ DNA Methylation kit (Zymo Research) for DNA methylation analysis.
|
| Label |
biotin
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Description |
lupus CD8+ T cell
|
| Data processing |
Methylation beta values were calculated from raw intensity values using GenomeStudio Methylation module software (Illumina; ver 1.9.0) after subtracting background, normalization to control probes, error correction using the Illumina custom model, and correction for false discovery rate.
|
| |
|
| Submission date |
Nov 27, 2018 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Amr Sawalha |
| E-mail(s) |
asawalha@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
4401 Penn Avenue
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL23976 |
| Series (1) |
| GSE123003 |
Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells |
|
