|
| Status |
Public on Feb 09, 2017 |
| Title |
PBL from Tolerant 5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from 20 pooled cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pool of 20 cell lines from Pat Brown's lab
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Patient peripheral blood (10 ml) was harvested in EDTA tubes from a peripheral vein or arterio-venous fistula. Peripheral blood leukocytes (PBL) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and 10 million cells were frozen in Trizol reagent (Invitrogen,Life Technologies, San Diego, CA) for RNA extraction.
|
| Label |
Cy3
|
| Label protocol |
Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method described by Wang et al. (Nat Biotechnol, 2000).
|
| |
|
| Channel 2 |
| Source name |
Total RNA from Peripheral Blood Leukocytes (PBL), TOL5
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: PBL from TOL5
cell type: Peripheral blood leukocytes
treatment: renal transplant
response: Tolerant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Patient peripheral blood (10 ml) was harvested in EDTA tubes from a peripheral vein or arterio-venous fistula. Peripheral blood leukocytes (PBL) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and 10 million cells were frozen in Trizol reagent (Invitrogen,Life Technologies, San Diego, CA) for RNA extraction.
|
| Label |
Cy5
|
| Label protocol |
Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method described by Wang et al. (Nat Biotechnol, 2000).
|
| |
|
| |
| Hybridization protocol |
cDNA microarrays, containing ~32,000 cDNA clones (12,400 known unique genes), were processed using established protocols, using 2 μg RNA in each channel against a “common reference” RNA pool.
|
| Scan protocol |
Hybridized microarrays were scanned using GenePix 4000 (Axon Instruments, Union City, CA) and fluorescent images were analyzed with the GenePix Pro software package.
|
| Description |
Tolerant, Biological replicate 5 of 12
|
| Data processing |
Defective spots were flagged and removed. Defective spots were flagged and removed, generating a data file with 11,820 clones under low stringency retrieval settings (80% representative data, signal/noise ratio of expression measurements > 1.5, signal >200 in both channels and expression cut-off of 2-fold in one or more array). Data were centered prior to statistical analysis.
|
| |
|
| Submission date |
Jun 05, 2013 |
| Last update date |
Feb 09, 2017 |
| Contact name |
Daniel BARON |
| E-mail(s) |
daniel.baron@univ-nantes.fr
|
| Organization name |
Institut national de la santé et de la recherche médicale-INSERM
|
| Department |
UMR1064 - Centre de Recherche en Transplantation & Immunologie
|
| Lab |
Tolerance et regulation lymphocytaire
|
| Street address |
30 Bd Jean Monnet
|
| City |
Nantes |
| State/province |
Loire-Atlantique (44) |
| ZIP/Postal code |
44093 |
| Country |
France |
| |
|
| Platform ID |
GPL6271 |
| Series (1) |
| GSE47683 |
Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance |
|
| Relations |
| Reanalyzed by |
GSE49198 |
