|
| Status |
Public on Feb 13, 2013 |
| Title |
Nephrectomy2_GSM880246 reanalysis |
| Sample type |
RNA |
| |
|
| Source name |
nephrectomy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nephrectomy
diagnosis (good,bad): nephrectomy
dgf status: nephrectomy
geo sample: GSM880246
|
| 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 4µg/core, (RNA integrity number >7).
|
| Label |
biotin
|
| Label protocol |
RNA (1-2µg) 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).
|
| Data processing |
Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
|
| |
|
| Submission date |
May 08, 2012 |
| Last update date |
Feb 13, 2013 |
| Contact name |
Jessica Chang |
| E-mail(s) |
jjchang@ualberta.ca
|
| Organization name |
University of Alberta
|
| Department |
Medicine
|
| Lab |
ATAGC
|
| Street address |
250 Heritage Medical Research Centre
|
| City |
Edmonton |
| ZIP/Postal code |
T6G 2S2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE37838 |
Comparing molecular assessment of implantation biopsies with histologic and demographic risk assessment. |
|
| Relations |
| Reanalysis of |
GSM880246 |
