|
| Status |
Public on Mar 28, 2014 |
| Title |
K-rasG12Dint +HFD, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
duodenum, K-rasG12Dint, HFD
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J mix
genotype/variation: K-rasG12Dint
age: 8 months
Sex: female
tissue: duodenum
treatment: high-fat diet
|
| Treatment protocol |
Mice were euthanized with carbon dioxide inhalation.
|
| Growth protocol |
Animals were housed at pathogen-free facility, under 12 hours dark/light cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were homogenized in Trizol buffer and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer's instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. 0.3 µg of total RNA was used as start Material. The labeling reaction was performed by using the GeneChip® WT PLUS Reagent Kit from Affymetrix (Cat N° 902281) following manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Biotinylated fragmented ssDNA was hybridized onto the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix) according to the manufacturer's recommendation. The hybridization was performed for 16 h at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendation.
|
| Scan protocol |
Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).
|
| Description |
group6_394D
|
| Data processing |
Data were quantile normalized and log2 transformed using R and Bioconductor package limma.
|
| |
|
| Submission date |
Mar 26, 2014 |
| Last update date |
Mar 28, 2014 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Human Genetics
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Justus-von-Liebig-Weg 11
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37077 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17777 |
| Series (1) |
| GSE56257 |
High-fat diet-mediated dysbiosis promotes intestinal carcinogenesis independent of obesity |
|
