|
| Status |
Public on Feb 24, 2009 |
| Title |
Patient TX26, renal graft bx 1.32, diagnosis CAN III |
| Sample type |
RNA |
| |
|
| Source name |
Chronic allograft nephropathy biopsy grade III from human transplanted kidney
|
| Organism |
Homo sapiens |
| Characteristics |
Patient identifier: TX26, Sex: male, Age of patient: 33, Serum creatinine: 572 microMol/L, Renal graft bx: 1.32, Banff'97: CAN III,
|
| Biomaterial provider |
Hôpital Tenon, Paris, France
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen, Hilden, Germany).
|
| Label |
biotin
|
| Label protocol |
Labeled probes were prepared either according to the Affymetrix 2-cycle cDNA amplification protocol (Affymetrix, Santa Clara, CA) from 50 ng total RNA of all biopsy samples, or from 5 microg of total RNA of all control kidney samples according to the standard Affymetrix protocol. The cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray high-yield T7 DNA transcription kit; ENZO Life Sciences, Inc.). The biotinylated cRNA was purified on an affinity resin (RNeasy; Qiagen), quantified, and fragmented into strands of 50–200 nucleotides in length.
|
| |
|
| Hybridization protocol |
Hybridization of arrays was carried out at 45°C for about18 h, then arrays were stained on a GeneChip Fluidics Workstation 450 according to the manufacturer’s technical manual (Affymetrix).
|
| Scan protocol |
GeneChips were scanned on a GeneArray Scanner 3000 according to the manufacturer’s technical manual (Affymetrix).
|
| Description |
Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of chronic allograft nephropathy grade III.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
|
| |
|
| Submission date |
Oct 31, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Friedrich Raulf |
| E-mail(s) |
friedrich.raulf@novartis.com
|
| Phone |
+41 61 324 6880
|
| Fax |
+41 61 324 3576
|
| Organization name |
Novartis Pharma AG
|
| Department |
Novartis Institutes for BioMedical Research / ATDA
|
| Lab |
Raulf
|
| Street address |
WSJ-386.6.09
|
| City |
Basel |
| ZIP/Postal code |
4002 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE9489 |
Analyses of heterogeneous renal allograft biopsies reveal conserved rejection signatures and molecular pathways I |
| GSE9493 |
Transcriptomic analyses of renal allograft biopsies reveal conserved rejection signatures and molecular pathways |
|
| Relations |
| Reanalyzed by |
GSE119087 |
