|
| Status |
Public on Nov 27, 2013 |
| Title |
JNK1KO BDL 48h rep3 |
| Sample type |
RNA |
| |
|
| Source name |
liver from JNK1 null [JNK1-/-] mice, 48 hrs after bile duct ligation
|
| Organism |
Mus musculus |
| Characteristics |
treatment: bile duct ligation
time: 48 h
genetic background: C57/BL6
genotype: JNK1 null (JNK1-/-)
gender: male
tissue: liver
age: 8 weeks
|
| Treatment protocol |
Induction of liver fibrosis was performed in 7-8 weeks old age-matched male mice (n = 9-10 per group) by ligating the common bile duct (BDL). Control treated animals were opened and immediately closed (sham). Mice were sacrificed 48h and 28days later.
|
| Growth protocol |
JNK1-deficient mice were purchased from Harlan Laboratories (Bar Harbor, ME). JNK1f/f (C57BL/6 background) mice were kindly donated by Dr. Roger J. Davis (Howard Hughes Medical Institute, Chevy Chase, MD) and crossed with transgenic animals expressing the Cre transgene under control of a postnatal activated albumin promoter by crossing giving yield to the JNK1Δhepa strain, mice with specific deletion of JNK1 only in hepatocytes. Mice were maintained on standard laboratory chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from the liver using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. 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 (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).
|
| |
|
| Hybridization protocol |
The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST peg arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument.
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
Nov 27, 2013 |
| 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 (1) |
| GSE40041 |
Jnk1 in murine hepatic stellate cells is a crucial mediator of liver fibrogenesis |
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