|
| Status |
Public on Jul 27, 2016 |
| Title |
IGC_YidX |
| Sample type |
RNA |
| |
|
| Source name |
Human peripheral blood CD4+ T cells from CD patient
|
| Organism |
Homo sapiens |
| Characteristics |
patient: IGC
diagnosis: Crohn's Disease (CD)
antigen: YidX
gender: female
age (years): 49
cd evolution time (years): 9
disease activity: inactive
|
| Growth protocol |
Antigen-specific CD4+T cells were expanded from CFSE-labelled peripheral blood mononuclear cells (PBMCs), by culturing them in the presence of protein antigen and recombinant IL-2 (for the last 7 days) for 2 weeks. Proliferating cells (CFSE-, CD4+, viable) cells were isolated by FACS sorting, and set in culture for a second round of antigen-specific stimulation in the presence of autologous PBMCs for 10 days. After that time, cells were harvested, washed and resuspended in Trizol for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Standard Affymetrix protocol using a Gene chip scanner 3000
|
| Description |
Gene expression data from human peripheral blood antigen-specific CD4+T cells from CD patient
|
| Data processing |
The data were analyzed with Bioconductor tools in R (version 2.15.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).
|
| |
|
| Submission date |
Jul 02, 2015 |
| Last update date |
Jul 28, 2016 |
| Contact name |
Azucena Salas |
| E-mail(s) |
[email protected]
|
| Organization name |
IDIBAPS
|
| Department |
Gastroenterology
|
| Street address |
Rosselló, 149-153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL20650 |
| Series (1) |
| GSE70469 |
Expression data from antigen-specific CD4+T cells from peripheral blood of patietns with CD and healthy controls. |
|
