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 |