|
| Status |
Public on Jan 27, 2016 |
| Title |
Liver_mouse_FXRKO_vehicle_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
liver, FXR knockout, vehicle for 7 days
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: FXR KO
gender: male
tissue: liver
treatment: vehicle (1% methyl cellulose)
time point: 7 days
mouse_id: 26
|
| Treatment protocol |
At the age of 9-12 weeks, mice received a daily oral gavage with the semi-synthetic FXR agonist obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid; 10 mg/kg/day), or vehicle (1% methyl cellulose) for 7 days. Livers were then isolated, snap frozen in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
Male C57BL/6 wild-type (WT) and FXR-/- mice [PMID: 11030617] were housed in a room with controlled temperature (20-24°C), relative humidity (55%±15%) and a 12h light dark cycle. Mice were fed chow and demineralized water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
|
| Label |
biotin
|
| Label protocol |
One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
|
| Description |
A410_E7_LIVER_26_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.0).
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
Jan 27, 2016 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11533 |
| Series (2) |
| GSE76162 |
Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid [mouse] |
| GSE76163 |
Gene expression profiling in human precision-cut liver slices upon treatment with the FXR agonist obeticholic acid |
|
