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. Author manuscript; available in PMC: 2021 Feb 20.
Published in final edited form as: Mol Cell. 2020 Jan 20;77(4):761–774.e8. doi: 10.1016/j.molcel.2019.12.014

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