|
| Status |
Public on Jun 03, 2015 |
| Title |
Rat_Liver_P3R2_2 |
| Sample type |
RNA |
| |
|
| Source name |
Male rat liver, re-fed after P3 (P3r2)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
gender: male
tissue: liver
nutritional state: re-feeding after phase 3
|
| Treatment protocol |
Liver samples were quickly collected from freshly sacrificed rats, and pieces were immediately frozen in liquid nitrogen and stored at -80°C until analysis. Frozen liver samples homogenization was obtained using a laboratory ball mill.
|
| Growth protocol |
Male rats were nutritionally manipulated to create three different metabolic statuses, i.e., the fed and two fasted states (phase 2 and phase 3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from homogenized liver samples with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cRNA were synthesized from total RNA depletd in rRNA. Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix). All assays were performed as per the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev. 2) (http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st).
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| |
|
| Hybridization protocol |
Samples were hybridized with GeneChip Rat Exon 1.0 ST Arrays (Affymetrix) and scanned within the IGBMC microarray and sequencing platform (Strasbourg, France).
|
| Scan protocol |
Array scanning using an Affymetrix GeneChip Scanner 3000 7G was performed according to the manufacturer's instructions (Affymetrix).
|
| Data processing |
Raw data were processed with the GeneChip Operating v1.4 (GCOS) and Expression Console v1.1 softwares (Affymetrix) for background correction, normalization and quantification. Data analysis and statistical evaluations were performed with customized R codes (version 2.8.1, http://www.r-project.org/). Analysis was performed on the extended set of probesets. Reference genes were eliminated. Levels of expression were considered differential on the basis of ANOVA and post-hoc Tukey tests results. Hierarchical clustering was performed using the Cluster v3.0 software. Dendrograms were generated and vizualized using the Treeview v1.1.3 program.
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| |
|
| Submission date |
Jun 13, 2012 |
| Last update date |
Jul 30, 2015 |
| Contact name |
Fabrice Bertile |
| E-mail(s) |
fbertile@unistra.fr
|
| Phone |
+33368852681
|
| Organization name |
CNRS, IPHC
|
| Department |
Analytical Sciences
|
| Lab |
LSMBO
|
| Street address |
25 rue Becquerel
|
| City |
Strasbourg |
| ZIP/Postal code |
F-67087 |
| Country |
France |
| |
|
| Platform ID |
GPL6543 |
| Series (1) |
| GSE38695 |
Exacerbated oxidative stress in the fasting liver according to fuel partitioning |
|
