Mice had free access to chow and water. Depending on the mouse model and experiment, livers were removed from mice at the age of 8 or 52 weeks, or at the indicated time points after treatment with diethylnitrosamine (DEN) or after bile duct ligation (BDL). After removal, tissues were immediately snap-frozen in liquid nitrogen and stored at -80 until RNA isolation.
Growth protocol
Alb-Cre and Jnk2-deficient mice on a C57BL/6 background were purchased from The Jackson Laboratory (Bar Harbor, ME). Jnk1LoxP/LoxP /Jnk2−/− (JNKΔhepa) mice were created as previously reported (Cubero et al., 2016; Das et al., 2007; Das et al., 2009). NEMO∆hepa/JNKΔhepa mice, and their respective controls (NEMO∆hepa and NEMOf/f mice) were created as described in the current manuscript.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated by Directzol RNA Miniprep (Zymo Research, Irvine, CA). 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 analysis 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
Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
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 (Affymetrix, Santa Clara, CA, USA).
Scan protocol
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
Data processing
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).
