|
| Status |
Public on Sep 26, 2008 |
| Title |
patient#1 plus |
| Sample type |
RNA |
| |
|
| Source name |
CD4+ T cells, aCD28+aCD3, 24hr
|
| Organism |
Homo sapiens |
| Characteristics |
patient#1
|
| Treatment protocol |
CD4 T-cells were negatively selected with a StemSep device (StemCell Technologies) from the PBMCs.
|
| Growth protocol |
RPMI 1640, 10% FBS, anti-CD28 mAb (at 1mg/mL) with plate-bound anti-CD3 mAb, 24hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy mini kit with DNase (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Labeling using GeneChip IVT Labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Human Genome U133 plus 2.0 probe arrays (Affymetrix).
|
| Scan protocol |
The Affymetrix GeneChip scanner using default settings.
|
| Description |
Gene expression data from aCD28/aCD3 stimulated CD4+ T cells of a patient#1.
|
| Data processing |
Data analysis was performed with GeneSpring software version 7.2 (Agilent Technologies). To normalize the variations in staining intensity among chips, the 'Average Difference' values for all genes on a given chip were divided by the median value for expression of all genes on the chip. To eliminate genes containing only a background signal, genes were selected only if the raw values of the 'Average Difference' were more than 50, and expression of the gene was judged to be 'Present' by the GeneChip Operating Software version 1.4 (Affymetrix).
|
| |
|
| Submission date |
Sep 22, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
naomi takahashi |
| E-mail(s) |
takanao.ped@tmd.ac.jp
|
| Phone |
+81-3-5803-5245
|
| Fax |
+81-3-5803-5245
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Department of Pediatrics and Developmental Biology
|
| Street address |
1-5-45 Yushima
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE12875 |
Impaired T-cell function in patients with novel ICOS |
|
| Relations |
| Reanalyzed by |
GSE86362 |
| Reanalyzed by |
GSE119087 |
