|
| Status |
Public on Mar 22, 2016 |
| Title |
Porcine_kidney_ischemia_(n=2) |
| Sample type |
RNA |
| |
|
| Source name |
Ischemic_porcine_kidney
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Large White pig
age: 3 months
tissue: kidney (cortex)
sample group: ISCHEMIA
|
| Treatment protocol |
ISCHEMIA samples: Three independent porcine kidney (from different 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 for 24h, then kidneys were immediatly sampled and frozen. CONTROL samples: Three independent porcine kidney (from different pig) were removed and then immediatly sampled and frozen.
|
| Growth protocol |
We used 3 months old Large White pigs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from renal cortex was 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 |
ISCHEMIA (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 |
Mar 21, 2016 |
| Last update date |
Mar 22, 2016 |
| 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) |
| GSE79418 |
Gene expression signatures of ischemia on porcine kidney |
|
