|
| Status |
Public on Nov 04, 2017 |
| Title |
UNx 34 |
| Sample type |
RNA |
| |
|
| Source name |
UNx group
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: Male
tissue: kidney
strain: Wistar
|
| Growth protocol |
The kidney was harvested, placed on ice and a piece consisting of both outer medulla and cortex was excised. The kidney tissue was homogenised in lysis buffer (Macherey Nagel, Düren, Germany) on a TissueLyser LT (Qiagen, Venlo, Netherlands) for 30 seconds at 1,250 rpm and centrifuged at 1000 × g for 10 minutes at 4°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
otal RNA was obtained using an RNA Isolation Kit (Macherey Nagel) in accordance with the manufacturer’s instructions
|
| Label |
Biotin
|
| Label protocol |
A target preparation of 150 ng RNA was used for cDNA synthesis, in vitro transcription and terminal labeling utilizing the WT PLUS reagent kit (Affymetrix).
|
| |
|
| Hybridization protocol |
The generated target RNA was loaded onto the Affymetrix Clariom D array cartridge and hybridized for 16 hours at 45°C. After washing and staining in the GeneChip Fluidics Station, the array was scanned in the GeneChip Scanner 7G.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
RMA expression value derived from Expression Console software
|
| Data processing |
Raw data were processed with the Affymetrix Console Software according to the RMA. Normalized gene expression data was analysed in the open source software Multiexperiment Viewer version 4.9.0, which is part of the TM4 microarray software suite.The statistical analysis was done by employing the Significance Analysis of Microarrays (SAM)-method. The number of permutations was set to 200, S0 was selected according to the method by Tusher et al, and the K-nearest neighbors method for imputation of missing data, with k = 10, was used. Unpaired two-class analysis was performed. A false discovery rate (FDR) of 10% was selected.
|
| |
|
| Submission date |
Jun 27, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Casper Kierulf Lassen |
| E-mail(s) |
cklassen@dadlnet.dk
|
| Organization name |
Aarhus University
|
| Department |
Department of Clinical Medicine
|
| Street address |
Palle Juul-Jensens Boulevard 99
|
| City |
Aarhus N |
| ZIP/Postal code |
8200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL23629 |
| Series (1) |
| GSE100540 |
The transcriptional response to unilateral nephrectomy with and without ischemia-reperfusion injury |
|
