|
| Status |
Public on Aug 26, 2013 |
| Title |
Th1Th17, patient 661 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells (PBMC)
|
| Organism |
Homo sapiens |
| Characteristics |
donor: 661
cell type: CD4+ Th cells
cell subset: Th1Th17 cells
|
| Treatment protocol |
Sorted Th1Th17 and Th1 subsets were stimulated with immobilized CD3 and soluble CD28 Abs (1 µg/ml) for 3 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol and quantified by Pearl nanophotometer (Implen, Munich, Germany) (typically, 106 cells yielded 3-5 µg RNA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Briefly, the quality of total RNA was first tested using an Agilent 2100 Bioanalyzer chip. Then, high quality RNA was reverse transcribed and hybridized on the GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix).
|
| Scan protocol |
GeneChip scan was carried out at McGill University & Genome Quebec Innovation Centre according to the Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).
|
| Description |
Gene expression data from circulating Th1Th17 cells
|
| Data processing |
Gene expression data was analyzed using Bioconductor limma package. The R software package was used to preprocess and normalize the probes intensities using RMA.
|
| |
|
| Submission date |
Aug 25, 2013 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Jean-Philippe Goulet |
| E-mail(s) |
jp.goulet@umontreal.ca
|
| Organization name |
Université de Montréal
|
| Street address |
C.P. 6128, succursale Centre-ville
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3X 3J7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE50175 |
Expression data from human Th1 and Th1Th17 cells |
|
| Relations |
| Reanalyzed by |
GSE86362 |
