|
| Status |
Public on May 24, 2010 |
| Title |
renal allograft biopsy, (U of A/Chicago) 144A2AGX7 |
| Sample type |
RNA |
| |
|
| Source name |
renal allograft biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
failed=1/non failed=0: 0
time of biopsy post transplant (days): 2533
time from biopsy to failure/censoring (days): 1206
rejection/non rejection: nonrej
sample included in the main analysis- the first biopsy per patient from the 105 late (> 1 year) patients: 1
|
| Treatment protocol |
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.
|
| Growth protocol |
All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4ug/core, (RNA integrity number >7).
|
| Label |
biotin
|
| Label protocol |
RNA (1-2ug) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).
|
| Description |
Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant
|
| Data processing |
Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
|
| |
|
| Submission date |
Apr 17, 2010 |
| Last update date |
Jul 15, 2011 |
| Contact name |
Jeff Reeve |
| E-mail(s) |
jreeve@ualberta.ca
|
| Organization name |
University of Alberta
|
| Lab |
Halloran
|
| Street address |
250 HMRC University of Alberta
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2S2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE21374 |
Expression data from human renal allograft biopsies |
|
