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. Author manuscript; available in PMC: 2018 Feb 12.
Published in final edited form as: Cell. 2017 Nov 30;171(6):1284–1300.e21. doi: 10.1016/j.cell.2017.10.022
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-β-Actin Sigma-Aldrich Cat#A5441; RRID: AB_476744
Rat monoclonal anti-CD8a BioXCell Cat#BE0061; RRID: AB_1125541
Rat monoclonal anti-CD16/CD32 BD Biosciences Cat#553141; RRID: AB_394656
BV510 Rat monoclonal anti-CD45 BD Biosciences Cat#563891
Rat monoclonal anti-CD3 BD Biosciences Cat#560527; RRID: AB_1727463
FITC Rat monoclonal anti-CD8a Biolegend Cat#100706; RRID: AB_312745
Brilliant Violet Rat monoclonal anti-F4/80 Biolegend Cat#123137; RRID: AB_2563102
APC Rat monoclonal anti-CD11b Biolegend Cat#101212; RRID: AB_312795
APC Rat IgG2b, kappa Isotype Ctrl antibody Biolegend Cat#400611; RRID: AB_326555
Rat monoclonal anti-IFNγ BD Biosciences Cat#562018; RRID: AB_10896992
Rat anti-PD-1 IgG2a (RMP1-14) BioXCell Cat#BE0146; RRID: AB_10949053
Rat anti-IgG2a Isotype Control Clone 2A3 BioXCell Cat#BE0089; RRID: AB_1107769
Rat monoclonal anti-CD8a eBioscience Cat#14-0808; RRID: AB_2572860
Rat monoclonal anti-F4/80 Serotec Cat#MCAP497; RRID: AB_2335598
Rabbit monoclonal anti-Ki67 Cell signaling Cat#12202; RRID: AB_2620142
Rabbit monoclonal anti-c-MYC Cell signaling Cat#13987; RRID: AB_2631168
Rabbit monoclonal anti-Acetyl α Tubulin Cell signaling Cat# 5335; RRID: AB_10544694
Rabbit monoclonal anti-Acetylated Histone 3 Cell signaling Cat#4499; RRID: AB_10544537
Rabbit polyclonal anti-Histone H3 Cell signaling Cat#9715; RRID: AB_331563
Rabbit polyclonal anti-DNMT1 Sigma Aldrich Cat#D4692; RRID: AB_262096
Anti-rabbit secondary (western blot) GE Healthcare Cat#NA934V
Anti-mouse secondary (western blot) GE Healthcare Cat#NA931V
Mouse monoclona IgG1 Isotype Control Cell Signaling Cat#5415; RRID: AB_10829607
Rabbit anti-rat Biotinylated IgG Vector Cat#BA-4001; RRID: AB_10015300
Bacterial and Virus Strains
Ad-CMV-Cre Viral Vector Core, University of Iowa Cat#VVC-U-IOWA-5
Biological Samples
Patient-derived xenografts (PDX) The Jackson Laboratory Cat#TM00302
Chemicals, Peptides, and Recombinant Proteins
Azacidine Sigma-Aldrich Cat#A2385
ITF-2357 Apexbio Cat#A4093
MS-275 Syndax MTA
MCGD0103 Apexbio Cat#A4089
RGFP996 Apexbio Cat#A8803
Tubastatin Apexbio Cat#A4101
Vorinostat Cell signaling Cat#12520
Puromycin Sigma-Aldrich Cat#P7255
DMSO Sigma Cat#D2660
RPMI1640 Corning Cat#10-040
Fetal Bovine Serum Hyclone Cat#SH30910.03
0.25% Trypsin Corning Cat#25-053
DMEM Corning Cat#10-013
Pen/Strep GIBCO Cat#15140-122
m-CSF murine Peprotech Cat#315-02-100UG
ECM gel Sigma Aldrich Cat#E2170-10ML
Lipofectamine 2000 Invitrogen Cat#11668-022
Fixable Viability Dye eBioscience Cat# 65-0865-14
eBiosciences Stim cocktail eBioscience Cat# 00-4970-03
Propidium Iodide eBioscience Cat#00-6990-50
Critical Commercial Assays
RNeasy Mini kit QIAGEN Cat#74104
RNeasy Microkit QIAGEN Cat#74004
RNase free DNase Set QIAGEN Cat#79254
qScript cDNA SuperMix Quanta Cat#95048-025
iTaq universal sybr green supermix BioRad Cat#1725124
Homogenizer mini column Omega Cat#HCR003
Purelink midiprep Invitrogen Cat#K210014
Cell titer AQueous one Promega Cat#G3582
BrdU Cell Proliferation ELISA Calbiochem Cat#QIA58
Mouse Cytokine Array Q1 Raybiotech Cat#QAM-CYT-1-1
Sigma Whole Transcriptome Amplification kit Sigma Aldrich Cat#WTA2-10RXN
Deposited Data
Raw and analyzed data for gene expression This paper GEO: GSE104244
Experimental Models: Cell Lines
NCI-H1755 ( ATCC RRID: CVCL_1492
NCI-H520 ATCC RRID: CVCL_1566
NCI-H1650 ATCC RRID: CVCL_1483
NCI-H1975 ATCC RRID: CVCL_1511
NCI-H441 ATCC RRID: CVCL_1561
NCI-H661 ATCC RRID: CVCL_1577
NCI-H596 ATCC RRID: CVCL_1571
HCC4006 ATCC RRID: CVCL_1269
NCI-H1703 ATCC RRID: CVCL_1490
NCI-H838 ATCC RRID: CVCL_1594
NCI-H2170 ATCC RRID: CVCL_1535
NCI-H1792 ATCC RRID: CVCL_1495
NCI-H460 ATCC RRID: CVCL_0459
NCI-H23 ATCC RRID: CVCL_1547
A-549 ATCC RRID: CVCL_0023
NCI-H1299 ATCC RRID: CVCL_0060
HCC827 ATCC RRID: CVCL_DH92
LLC1 ATCC RRID: CVCL_4358
Experimental Models: Organisms/Strains
Mouse: B6.129S4-Krastm4Tyj/J The Jackson Laboratory RRID: IMSR_JAX:008179
Oligonucleotides
shMYC (TRCN0000010391) RNAi Consortium Cat# TRCN0000010391
Primers for qRT-PCR, see Table S1 This paper N/A
shDNMT1
MYC vector (Cheng et al., 2013) Addgene plasmid # 46970
pLV-AcGFP-N1 Clontech Cat#632154
Recombinant DNA
Syncytin-1 (5′ LTR-Syn-1-pGL3) (Chiappinelli et al., 2015) N/A
ERV-3 (p3Xflag-CMV-14) (Chiappinelli et al., 2015) N/A
pE-GFP-N1 Clontech Laboratories Cat#632469
pMD2.G Addgene # 12259
psPAX2 Addgene Addgene plasmid #12260
Software and Algorithms
GraphPad Prism GraphPad Software https://www.graphpad.com. RRID: SCR_002798
Gene set enrichment Analysis (Subramanian et al., 2005) http://www.broadinstitute.org/gsea. RRID: SCR_003199