|
| Status |
Public on Feb 10, 2018 |
| Title |
WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=2) |
| Sample type |
RNA |
| |
|
| Source name |
Warm Ischemic (60 min)+6h cold storage (ischemia 4°C UW) porcine kidney, corticomedullary junction biopsy
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Large White pig
age: 3 months
treatment group: Warm Ischemic (60 min)+6h cold storage (ischemia 4°C UW)
tissue: kidney (corticomedullary junction)
|
| Treatment protocol |
CONTROL samples: 5 independent porcine kidneys (from Large White pig) were removed and then immediately sampled and frozen. WARM ISCHEMIA samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then immediately sampled and frozen. WARM ISCHEMIA + 6h and 24h COLD STORAGE samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then flushed with cold (4°C) University of Wisconsin preservation solution (UW) and stored at 4°C, at 6h of cold storage kidneys were sampled and frozen and at 24h of cold storage these same kidneys were sampled and frozen.
|
| Growth protocol |
We used 3 months old Large White pigs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from renal cortex or corticomedullary junction were extracted using a commercial kit including a Dnase to remove genomic DNA (Rneasy plus mini, Qiagen, France), following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
The labeling was done using the Low Input Quick Amp Labeling kit (Agilent)
|
| |
|
| Hybridization protocol |
The slides (Agilent Porcine V2 ref 026440) were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent)
|
| Scan protocol |
The slides were scanned on a Tecan MS200 scanner.
|
| Description |
WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=2)
|
| Data processing |
The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The data from all the microarrays were transformed in log2 intensity. Then they were normalized together using the “limma” package function “normalizeQuantiles” and the “quantile” method. Normalization of the data was performed using the Bioconductor packages (http://www.bioconductor.org) and R software v2.15.2.
|
| |
|
| Submission date |
Jan 26, 2018 |
| Last update date |
Feb 10, 2018 |
| Contact name |
Sebastien Giraud |
| Organization name |
Inserm U1313 IRMETIST, Université de Poitiers, CHU de Poitiers-Service Biochimie
|
| Street address |
CHU de Poitiers, 2 rue de la miletrie
|
| City |
Poitiers |
| ZIP/Postal code |
86000 |
| Country |
France |
| |
|
| Platform ID |
GPL16571 |
| Series (1) |
| GSE109719 |
Kinetic of gene expression signatures on ischemia porcine kidney |
|
