KEY RESOURCES TABLE
REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Rabbit monoclonal (Y69) anti-c-myc | Abcam | Cat#ab32072 |
Mouse monoclonal anti-hsp90 | BD Transduction Laboratories | Cat#610419 |
Rabbit monoclonal anti-hsp90 | Cell Signaling Technologies | Cat#4877S |
Rabbit polyclonal anti-p53 | Leica | Cat#P53-CM5P-L |
Rabbit Anti-Mouse IgG (H&L) | Abcam | Cat#ab46540 |
Rabbit polyclonal anti-pHH3 Serine 10 | Cell Signaling Technologies | Cat#9701S |
Goat Anti-Mouse IgG (H + L)-HRP Conjugate | Bio-Rad | Cat#1706516 |
Peroxidase AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | Cat#711-035-152 |
Bacterial and Virus Strains | ||
Stable Competent E.coli (High Efficiency) | New England Biolabs | Cat#C3040H |
5-alpha Competent E.coli (High Efficiency) | New England Biolabs | Cat#C2987U |
Chemicals, Peptides, and Recombinant Proteins | ||
4-hydroxy tamoxifen | Cayman Chemical Company | Cat#17308-10 |
Doxorubicin hydrochloride | Sigma-Aldrich | Cat#D1515-10MG |
Etoposide | Millipore Sigma | Cat#E1383-25MG |
Cycloheximide | Sigma-Aldrich | Cat#C4859-1ML |
Hexadimethrine bromide (polybrene) | Millipore Sigma | Cat#107689-10G |
Puromycin dihydrochloride | Sigma-Aldrich | Cat#58-58-2 |
Hygromycin B | Roche | Cat#10843555001 |
DMEM, high glucose, pyruvate | Gibco | Cat#11995065 |
Fetal Bovine Serum | Sigma-Aldrich | Cat#F0926-500ML |
L-Glutamine | Gibco | Cat#25030-081 |
Pen-strep | Gibco | Cat#15140-122 |
NEAA | Gibco | Cat#11140-050 |
2-mercaptoethanol | Gibco | Cat#21985023 |
SYBR Fast Master Mix | Kapa Biosystems | Cat#kk4602 |
Nitrocellulose membranes | Bio-Rad | Cat#1620112 |
ECL Prime Western Blotting detection reagent | GE Healthcare | Cat#RPN2232 |
Methanol-free formaldehyde | Thermo Scientific | Cat#28908 |
cOmplete, Mini Protease Inhibitor Cocktail | Roche | Cat#4693124001 |
PureProteome Protein G Magnetic Beads | Millipore Sigma | Cat#LSKMAGG02 |
Salmon Sperm DNA | Invitrogen | Cat#15632011 |
Mouse Cot-1 DNA | Invitrogen | Cat#18440016 |
Proteinase K | Roche | Cat#03115879001 |
Formamide | Millipore Sigma | Cat#F9037-100ML |
Stellaris® RNA FISH Hybridization Buffer | LGC Biosciences | Cat#SMF-HB1-10 |
Stellaris® RNA FISH Wash Buffer A | LGC Biosciences | Cat#SMF-WA1-60 |
Stellaris® RNA FISH Wash Buffer B | LGC Biosciences | Cat#SMF-WB1-20 |
VECTASHIELD® Antifade Mounting Medium with DAPI | Vector Laboratories | Cat#H-1200 |
Alexa Fluor® 488-5-UTP | Invitrogen | Cat#C11397 |
Alexa Fluor® 594-5-UTP | Invitrogen | Cat#C11400 |
TRIzol Reagent | Invitrogen | Cat#15-596-018 |
TRIzol-LS Reagent | Invitrogen | Cat#10296028 |
RNasin Plus RNase inhibitor | Promega | Cat#N2615 |
CutSmart® Buffer | New England Biolabs | Cat#B7204S |
BamHI-HF® | New England Biolabs | Cat#R3136L |
T4 DNA Ligase | New England Biolabs | Cat#M0202L |
Adenosine 5'-Triphosphate (ATP) | New England Biolabs | Cat#P0756L |
4-thiouridine (s4U) | Alfa Aesar | Cat#AAJ60679MC |
TURBO DNase | Invitrogen | Cat#AM2238 |
Agencourt RNAclean XP beads | Beckman Coulter | Cat#A63987 |
MTSEA biotin-XX | Biotium | Cat#900661 |
Critical Commercial Assays | ||
Mouse/Hepatocyte Nucleofector Kit | Lonza | Cat#VPL1004 |
RNeasy Mini Kit | Qiagen | Cat#Q74106 |
High Capacity cDNA Reverse Transcription Kit | Applied Biosystems | Cat#Q74106 |
Zero Blunt TOPO PCR Cloning Kit | Invitrogen | Cat#450245 |
Nucleobond Xtra BAC kit | Takara Bio USA | Cat#740436.10 |
Nick Translation System | Invitrogen | Cat#18160-010 |
TruSeq Stranded mRNA Library Prep | Illumina | Cat#20020594 |
Clontech SMARTer Stranded Total RNA-Seq kit Pico Input Mammalian | Takara Bio USA | Cat#634411 |
Vectastain Elite ABC-HRP Kit (Peroxidase, rabbit IgG) | Vector Laboratories | Cat#PK-6101 |
DAB Peroxidase (HRP) Substrate Kit | Vector Laboratories | Cat#SK-4100 |
Deposited Data | ||
Raw and analyzed data of mouse cell line | This study | GEO: GSE126940 |
Experimental Models: Cell Lines | ||
Mouse: Primary WT embryonic fibroblasts (MEFs) | This paper | N/A |
Mouse: K-rasG12D/+; p53LSL/LSL; Rosa-CreERT2 (KPR8) cell line | Feldser et al., 2010 | N/A |
Mouse: p53LSL/LSL; Rosa-CreERT2 (p53-restorable MEFs) | Ventura et al., 2007 | N/A |
Mouse: 3TZ (3T3 derivative) cell line | T. Jacks, MIT | N/A |
Human: fetal lung fibroblasts (TIG-1) | NIA Aging Cell Culture Repository | Cat#NG06173 |
Experimental Models: Organisms/Strains | ||
Mouse: Wild-type (WT) C57BL/6J | Jackson Laboratories | Cat#000664 |
Mouse: K-rasLSL-G12D/+ (K) | Jackson et al., 2001; Jackson Laboratories | Cat#008179 |
Mouse: p53FL/FL (P) | Jackson et al., 2005; Jackson Laboratories | Cat#008462 |
Mouse: Rosa26-Cas9LSL/LSL (C) | Platt et al., 2014; Jackson Laboratories | Cat#026556 |
Oligonucleotides | ||
qRT-PCR primers, see Table S1 | This paper | N/A |
PCR primers, see Table S1 | This paper | N/A |
smRNA FISH probes, see Table S1 | This paper | see Table S1 |
3C qPCR primers, see Table S1 | This paper | N/A |
ChIP qPCR primers, see Table S1 | This paper | N/A |
ASO sequences, see Table S1 | This paper | see Table S1 |
sgRNA sequences, see Table S1 | This paper; Xue et al., 2014 | N/A |
dRNA sequences, see Table S1 | This paper | N/A |
Recombinant DNA | ||
pCMV-dR8.2 dvpr | Stewart et al., 2003 | Addgene #8455 |
pCMV-VSV-G | Stewart et al., 2003 | Addgene #8454 |
pWZL Hygro | S. Lowe, unpublished | Addgene #18750 |
BRD001 | Broad Institute | N/A |
BRD004 | Broad Institute | N/A |
UGPC | This paper | N/A |
lenti-SAM-hygro | This paper | N/A |
Myc BAC | BACPAC Resources Center | Cat#RP23-55F11 |
Chr 6 BAC | BACPAC Resources Center | Cat#RP24-301E22 |
Software and Algorithms | ||
GraphPad Prism, version 8.2.1 for MacOS | N/A | www.graphpad.com |
Biorender | N/A | www.biorender.com |
Tophat (v2.0.14) | Trapnell et al., 2009 | http://ccb.jhu.edu/software/tophat/index.shtml |
stringtie (v1.2.4) | Pertea et al., 2015 | https://ccb.jhu.edu/software/stringtie/ |
HTSeq (v0.6.1) | Anders et al., 2015 | https://htseq.readthedocs.io/en/release_0.11.1/ |
EdgeR (v3.22.3) | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
FastUniq | Xu et al., 2012 | http://sourceforge.net/projects/fastuniq/ |
Cutadapt (v1.16) | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
HISAT2 (v2.1.0) | Kim et al., 2015 | https://ccb.jhu.edu/software/hisat2/index.shtml |
SAMtools (v1.5) | Li et al., 2009 | http://samtools.sourceforge.net |
STAR (v2.5.3a) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
DEseq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |