| Antibodies |
|
| Rabbit monoclonal anti-ARIDI A (clone D2A8U) |
Cell Signaling Technology |
Cat# 12354; RRID:AB_2637010 |
| Rabbit monoclonal anti-Smad2/3 (clone D7G7) |
Cell Signaling Technology |
Cat# 8685; RRID:AB_10889933 |
| Rabbit monoclonal anti-Phospho-Smad2(Ser465/ 467)/Smad3(Ser423/425) (clone D27F4) |
Cell Signaling Technology |
Cat# 8828; RRID:AB_2631089 |
| Rabbit monoclonal anti-GAPDH (clone 14C10) |
Cell Signaling Technology |
Cat# 2118; RRID:AB_561053 |
| Rabbit monoclonal anti-GFP (clone D5.1) |
Cell Signaling Technology |
Cat# 2956; RRID:AB_1196615 |
| Mouse monoclonal anti-THBS1 (clone A6.1) |
ThermoFisher |
Cat# MA5-13398; RRID:AB_10984611 |
| Rabbit polyclonal anti-Ki67 |
Abcam |
Cat# ab66155; RRID:AB_1140752 |
| Rabbit anti-p15(INK4b) |
ThermoFisher |
Cat# PA5-49749; RRID:AB_2635202 |
| Rabbit anti-CDK4 |
ThermoFisher |
Cat# MA5-41183; RRID:AB_2898937 |
| Rabbit anti-Cyclin A2 |
ThermoFisher |
Cat# MA5-32353; RRID:AB_2809634 |
| Rat anti-CK19 |
Developmental Studies Hybridoma Bank Univ Iowa |
Cat# TROMA-III; RRID:AB_2133570 |
|
| Bacterial and virus strains |
|
| AAV8.TBG.PI.Cre.rBG |
Penn Vector Core |
Cat# CS1380 |
| Ad5-CMV-Cre |
Baylor Gene Vector Core |
Cat# 013018 |
| Ad5-CMV-eGFP |
Baylor Gene Vector Core |
Cat# 050917 |
|
| Chemicals, peptides, and recombinant proteins |
|
| hTGF-β1 |
Cell Signaling Technology |
Cat# 8915 |
| mTGF-β 1 |
Cell Signaling Technology |
Cat# 5231 |
| LY2157299 |
MedChemExpress |
Cat# HY-13226 |
|
| Critical commercial assays |
|
| Senescence b-Galactosidase Staining Kit |
Cell Signaling Technology |
Cat# 9860 |
| RNeasy kit |
Qiagen |
Cat# 74104 |
| Click-IT EdU |
Invitrogen |
C10337 |
|
| Deposited data |
|
| Raw and analyzed data (SuperSeries) |
This paper |
[GEO]: GSE207895
|
| MEF RNA-seq (SubSeries) |
This paper |
[GEO]: GSE207891
|
| MEF ATAC-seq (SubSeries) |
This paper |
[GEO]: GSE207888
|
| MMNK1 RNA-seq (SubSeries) |
This paper |
[GEO]: GSE207892
|
|
| Experimental models: Cell lines |
|
| Mouse: primary liver tumor cell lines |
This paper |
N/A |
| Mouse: MEF cells |
This paper |
N/A |
| Human: MMNK-1 cells |
Maruyama et al., 2004
|
Cat# JCRB1554, RRID:CVCL_M266 |
|
| Experimental models: Organisms/strains |
|
| Mouse: Tg(Alb-cre)21Mgn |
Gift from Dr. Magnuson |
RRID:IMSR_JAX:003574 |
| Mouse: Krastm4Tyj
|
Gift from Dr. Jacks |
RRID:IMSR_JAX:008179 |
| Mouse: Trp53tm1Brn
|
Gift from Dr. Berns |
RRID:IMSR_JAX:008462 |
| Mouse: Arid1atm1.1Zhwa
|
Gift from Dr. Wang |
RRID:IMSR_JAX:027717 |
| Mouse: Krt19tm1(cre/ERT)Ggu
|
Gift from Dr. Gu |
MGI:J:136694JAX:026925 |
| Mouse: Gt(ROSA)26Sortm1(EYFP)Cos/J |
Jackson Laboratory |
RRID:IMSR_JAX:006148 |
|
| Oligonucleotides |
|
| See oligonucleotide list in Table S3
|
|
N/A |
|
| Recombinant DNA |
|
| Human ARID1A: pLKO shRNA Arid1a |
Sigma |
TRCN0000059088 |
| Human ARID1A: pLKO shRNA Arid1a |
Sigma |
TRCN0000059089 |
|
| Software and algorithms |
|
|
bcl2fastq version 2.19.1 |
illumina |
https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
|
|
FastP version 0.20.0 |
Chen et al., 2018
|
https://github.com/OpenGene/fastp
|
|
STAR 2.7.0f |
Dobin et al., 2013
|
https://github.com/alexdobin/STAR
|
|
Salmon 0.13.1 |
Patro et al., 2017
|
https://github.com/COMBINE-lab/salmon
|
|
DESeq2 1.22.1 |
Love et al., 2014
|
https://doi.org/10.18129/B9.bioc.DESeq2
|
|
Trimmomatic
|
Bolger et al., 2014
|
https://github.com/usadellab/Trimmomatic
|
|
Bowtie2
|
Langmead and Salzberg, 2012
|
https://github.com/BenLangmead/bowtie2
|
|
| Other |
|
| DDC diet |
Custom Animal Diets |
Cat# AD5001 |
