|
| Status |
Public on Feb 08, 2017 |
| Title |
Medulla_18 - treated |
| Sample type |
RNA |
| |
|
| Source name |
treated (diet containing lithium (40 mmol/kg food for 7 days, followed by 60mmol/kg food for the rest of the experimental period. Total 6 months treatment)
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: renal medulla
strain: Wistar
gender: male
|
| Treatment protocol |
The two kidneys from each animal were cut in half longitudinally; one half was put in 10% neutral buffered formalin for histology, and the other 3 halves were snap frozen in liquid nitrogen and stored at -80°C until further use.
|
| Growth protocol |
Male Wistar rats were separated in two groups: The control group received a standard rodent diet (Specialty Foods, Perth, Australia) and tap water ad libitum for 6 months. The experimental group was fed 60 mM lithium/kg dry food for 6 months. Water was available ad libitum. All rats given lithium were supplied with a salt block to maintain sodium balance and prevent lithium intoxication. At 6 months, the animals were sacrificed by decapitation and their kidneys removed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the kidneys was isolated with TrizolR (Invitrogen, Life Technologies, USA), followed by cleaning in Norgen Total RNA columns (Norgen Biotek Corp., Canada). RNA was quantified using a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and its (purity and) quality determined on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
50 ng total RNA was processed by using a GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA) and hybridised to Affymetrix Rat Gene 1.0 ST gene chips.
|
| Scan protocol |
Chips were stained and washed with an Affymetrix GeneChip Fluidics Station 450, and scanned in an Affymetrix GeneChip 7G Plus scanner. All procedures were done according to the manufacturer's instructions.
|
| Data processing |
Cel files were imported with RMA background correction, quantile normalization, log base 2 transformation, and median polish, using PArtek Genomcis Suite v 6.5 (www.Partek.com). Batch effect removal was applied using ANOVA for the factor Scan date. Gene summary and quantification was performed on the basis of the mean of the expression values of the exons per gene.
probe group file: RaEx-1_0-st-v1.r2.pgf
meta-probeset file: RaEx-1_0-stv1.r2.dt1.rn4.full.mps
|
| |
|
| Submission date |
Jun 22, 2016 |
| Last update date |
Feb 08, 2017 |
| Contact name |
Philipp Strauss |
| E-mail(s) |
Philipp.Strauss@uib.no
|
| Organization name |
University of Bergen
|
| Street address |
Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst
|
| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE83610 |
Renal fibrosis mRNA classifier: validation in experimental lithium-induced interstitial fibrosis in the rat kidney |
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