KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat anti-Hspd1 | Santa Cruz | Cat# sc-1052; RRID: AB_631683 |
| Goat anti-GP73 | Santa Cruz | sc-48011; RRID: AB_2113325 |
| Rabbit anti-c-Jun | Abcam | Cat# ab31367; RRID: AB_731606 |
| p-c-Jun | Cell Signaling | Cat# 9164L; RRID: AB_330893 |
| Rabbit anti-p-JNK | Abcam | Cat# ab131499; RRID: AB_11157976 |
| Rabbit anti-JNK | Cell Signaling | Cat# 9252; RRID: AB_2250373 |
| Rabbit anti-p-Erk1/2 | Cell Signaling | Cat# 4370; RRID: AB_2315112 |
| Erk1/2 | Cell Signaling | Cat# 9107; RRID: AB_2235073 |
| Rabbit anti-CHOP | Cell Signaling | Cat# 5554S; RRID: AB_10694399 |
| Rabbit anti-p-p38 MAPK | Cell Signaling | Cat# 4511; RRID: AB_2139682 |
| Rabbit anti-p38 MAPK | Cell Signaling | Cat# 9212; RRID: AB_330713 |
| Rabbit anti-p-Akt | Cell Signaling | Cat# 4060; RRID: AB_2315049 |
| Rabbit anti-Akt | Cell Signaling | Cat# 2938; RRID: AB_915788 |
| Gapdh | Cell Signaling | Cat# 2118; RRID: AB_561053 |
| Rabbit anti-Pcna | Santa Cruz | Cat# sc-7907; RRID: AB_2160375 |
| HRP-anti rabbit IgG | Jackson | Cat# 111-055-045; RRID: AB_2337950 |
| HRP-anti mouse IgG | Jackson | Cat# 115-035-003; RRID: AB_10015289 |
| HRP-anti Goat | Dako | Cat# P0449; RRID: AB_2617143 |
| Mouse anti-8-ohdg | Abcam | Cat# ab48508; RRID: AB_867461 |
| Goat anti-Afp | R&D | Cat# AF5369; RRID: AB_2258018 |
| Rabbit anti-Collagen Type IV | Cedarlane | Cat# CL50451AP; RRID: AB_10059811 |
| Rabbit anti-cleaved Caspase-3 | Cell Signaling | Cat# 9661; RRID: AB_2341188 |
| Rabbit anti-Cytokeratin | Dako | Cat# Z0622; RRID: AB_2650434 |
| Rat anti-F4/80 | BioLegend | Cat# 123105; RRID: AB_893499 |
| Rabbit anti-Glutamine Synthetase | Abcam | Cat# ab16802; RRID: AB_302521 |
| Rabbit anti-Ki67 | NeoMarkers | Cat# RM-9106-S0; RRID: AB_2341197 |
| Rat anti-Ly6G | BD | Cat# 551459; RRID: AB_394206 |
| Rabbit anti-Rela | NeoMarkers | Cat# RB-1638-P0; RRID: AB_59726 |
| Rabbit anti-Tnf | Abcam | Cat# ab6671; RRID: AB_305641 |
| Rabbit anti-Tnfr1 | Abcam | Cat# ab19139; RRID: AB_2204128 |
| Rabbit anti-c-Myc | Abcam | Cat# ab32072; RRID: AB_731658 |
| Rat anti-CK19 | Developmental Studies Hybridoma Bank | Cat# TROMA-III; RRID: AB_2133570 |
| Bacterial and Virus Strains | ||
| AAV8-Cre | VectorBiolabs | Cat#7060 |
| Biological Samples | ||
| Liver tissues from mice after bile duct ligation | Jors et al., 2015 | N/A |
| Liver tissues from mice fed with CDE | Jors et al., 2015 | N/A |
| Liver tissues from mice fed with DDC | Jors et al., 2015 | N/A |
| Liver tissues from CRISPR/Cas9 mulitplex mutagenesis model | Weber et al., 2015 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| SP600125 | Abcam | CAS: 129-56-6 |
| JNK-IN-8 | Merck | CAS: 1410880-22-6 |
| JNK6o | Bio-techne | CAS: 894804-07-0 |
| S3I-201 | Biovision | CAS: 501919-59-1 |
| LY-294002 | Sigma | CAS: 934389-88-5 |
| Isoliquiritigenin | Sigma | CAS: 961-29-5 |
| TPCA-1 | Sigma | CAS: 507475-17-4 |
| NBP2–29328 | Novus Biologicals | Cat#NBP2–29328 |
| Critical Commercial Assays | ||
| Mouse Genome CGH Oligo Microarrays | Agilent | Cat#4839A |
| REPLI-g Whole Genome Amplification Kit | Qiagen | Cat#150025 |
| TNF Quantikine-Elisa-Kit | R&D | Cat#SMAT00B |
| Mouse Il6 Elisa kit | RayBiotech | Cat#ELM-IL6 |
| RNAscope 2.0 in situ hybridization kit | Advanced Cell Diagnostics | Cat#310033 |
| Deposited Data | ||
| aCGH data | This paper | The accession number for the aCGH data reported in this paper is arrayexpress: E-MTAB-4624 |
| Intrahepatic cholangiocarcinomas data set in TCGA | TCGA | http://cancergenome.nih.gov/ |
| Experimental Models: Cell Lines | ||
| HuCCT-1 | Roland Rad | Cellbankaustralia, JCRB0425 |
| ETK-1 | Roland Rad | N/A |
| HepG2 | ATCC | HB-8065 |
| Huh7 | Ulrike Protzer | N/A |
| HepRG | Ulrike Protzer | N/A |
| mICC | Roland Rad | N/A |
| Experimental Models: Organisms/Strains | ||
| Hspd1flox/flox | Taconic-Artemis; Dirk Haller (Berger et al., 2016) | N/A |
| R26R-Confetti | Jackson | JAX: 013731 |
| Tnfr1−/− | Jackson | JAX: 003242 |
| Alb-Cre | Jackson | JAX: 003574 |
| JNK1/2flox/flox | Roger Davis | N/A |
| Oligonucleotides | ||
| qRT-PCR primers | This paper | Please see Table S1. |
| Recombinant DNA | ||
| pT3 EF1a-KrasG12D-IRES-GFP | Darjus F. Tschaharganeh | N/A |
| pT3 EF1a-NICD-IRES-cherry | Darjus F. Tschaharganeh | N/A |
| pT3 EF1a-myrAKT | Xin Chen (Fan et al., 2012) | N/A |
| pX330 sgp53 | Darjus T. | N/A |
| Software and Algorithms | ||
| Agilent Technologies’ Feature Extraction (version 10.7.3.1) | Agilent | http://www.agilent.com |
| RCircos | http://bioconductor.org | |
| CGHcall | http://bioconductor.org | |
| CGHregions | http://bioconductor.org | |