| Antibodies |
|
| Rabbit monoclonal anti-Smad2 |
Cell Signaling Technology |
Cat#5339S; RRID: AB_10626777 |
| Rabbit monoclonal anti-Smad3 |
Cell Signaling Technology |
Cat#9523P; RRID: AB_2193182 |
| Rabbit monoclonal anti-Smad4 |
Cell Signaling Technology |
Cat#38454; RRID: AB_2728776 |
| Rabbit monoclonal anti-Smad4 (For IF) |
Cell Signaling Technology |
Cat#46535S; RRID: AB_2736998 |
| Rabbit monoclonal anti-phospho-Smad2 |
Cell Signaling Technology |
Cat#3108S; RRID: AB_490941 |
| Rabbit monoclonal anti-phospho-Smad3 |
Cell Signaling Technology |
Cat#9520P; RRID: AB_2193207 |
| Rabbit monoclonal anti-Smad1 |
Cell Signaling Technology |
Cat#9743S; RRID: AB_2107780 |
| Rabbit monoclonal anti-Smad5 |
Cell Signaling Technology |
Cat#12534S; RRID: AB_2797946 |
| Rabbit monoclonal anti-phospho-Smad1/5 |
Cell Signaling Technology |
Cat#9516S; RRID: AB_491015 |
| Rabbit monoclonal anti-p27 Kip1 |
Cell Signaling Technology |
Cat#3686S; RRID: AB_2077850 |
| Mouse monoclonal anti-p27 Kip1 (For IF) |
Cell Signaling Technology |
Cat#3698S; RRID: AB_2077832 |
| Mouse monoclonal anti-ERK1/2 |
BD Biosciences |
Cat#610031; RRID: AB_397447 |
| Mouse monoclonal anti-p38α |
BD Biosciences |
Cat#612168; RRID: AB_399540 |
| Mouse monoclonal anti-Phospho-p38 MAPK |
BD Biosciences |
Cat#612288; RRID: AB_399605 |
| Mouse monoclonal anti-phosphor-ERK1/2 |
Santa Cruz Biotechnology |
Cat#sc7383; RRID: AB_627545 |
| Rat monoclonal anti-vimentin |
R & D Systems |
Cat#MAB2105; RRID: AB_22141653 |
| Rabbit monoclonal anti-Nr2f1 |
Abcam |
Cat#ab181137; RRID: AB_2890250 |
| Rabbit polyclonal anti-Lamin B1 |
Abcam |
Cat#ab16048; RRID: AB_10107828 |
| Mouse monoclonal anti-H3K27ac |
EpiCypher |
Cat#13-0045; RRID: AB_2923489 |
| Mouse monoclonal anti-beta-tubulin |
Sigma-Aldrich |
Cat#T7816; RRID: AB_261770 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Dulbecco’s Modified Eagle Medium (DMEM) |
Fisher Scientific |
Cat#10-013-CV |
| Heat-inactivated fetal bovine serum (FBS) |
Peak Serum |
Cat#PS-FB1 |
| Penicillin and Streptomycin |
Fisher Scientific |
Cat#30-002-Cl |
| RPMI-1640 |
Fisher Scientific |
Cat#SH30027FS |
| Collagenase-1A |
Sigma Aldrich |
Cat#C9891 |
| 5-Azacytidine |
Sigma Aldrich |
Cat#A2385 |
| Charcoal-stripped FBS |
Thermo Fisher |
Cat#12676029 |
| all-trans retinoic acid |
Sigma Aldrich |
Cat#R2625 |
| AM80 |
Tocris |
Cat#3507 |
| Lipofectamine RNAiMax |
Invitrogen |
Cat#13778075 |
| 4X Laemmli sample buffer |
Bio-Rad |
Cat#1610747 |
| NE-PER Nuclear and Cytoplasmic extraction reagent |
Thermo Fisher |
Cat#78833 |
| M-MuLV reverse transcriptase enzyme |
New England Biolabs |
Cat#M0253S |
| PowerUP SYBR Green master mix |
Applied Biosystems |
Cat#A25741 |
| Antiigen retrieval buffer |
Invitrogen |
Cat#00-4955-58 |
| Normal goat serum |
Gibco |
Cat#PCN5000 |
| ProLong Gold Antifade Mounting medium with DAPI |
Invitrogen |
Cat#P36931
|
| Hematoxylin |
Fisher |
Cat#353032 |
| Eosin |
Fisher |
Cat#284532 |
| Organo/Limonene Mount |
Sigma |
Cat#O8015 |
| GIPZ lentiviral shRNA transduction starter kit |
Horizon |
Cat#RHS5086-EG4089 |
| KAPA HiFi DNA polymerase |
Roche |
Cat#07958838001 |
| AMPure XP beads |
NEB |
Cat#A63880 |
|
| Critical commercial assays |
|
| PCR Mycoplasma test kit |
PromoCell |
Cat#PK-CA91-1096 |
| RNeasy mini kit |
Qiagen |
Cat#74104 |
| Pierce BCA protein assay kit |
Thermo Scientific |
Cat#23227 |
| Amersham ECL Western Blot Detection |
GE Healthcare |
Cat#RPN2106 |
| KAPAHiFi HotStart HyperPrep kit |
Kapa Biosystems |
Cat#KK2601 |
| QIAquick PCR purification kit |
Qiagen |
Cat#28106 |
|
| Deposited data |
|
| Raw and analyzed data |
This paper |
GEO: GSE181837; GSE181838; GSE181839
|
| Raw and analyzed data |
This paper; Khalil et al.24
|
GEO: GSE172115
|
| HNSCC patient data |
Nagy et al.50
|
https://kmplot.com/analysis/
|
|
| Experimental models: Cell lines |
|
| HNSCC cell line: T-HEp3 |
Ossowski et al.20
|
RRID: CVCL_JB77 |
| HNSCC cell line: D-HEp3 |
Ossowski et al.20
|
RRID: CVCL_JB77 |
| Breast cancer cell line: 4T1 |
ATCC |
RRID: CVCL_0125 |
|
| Experimental models: Organisms/strains |
|
| Mouse: NU/J, strain#002019 |
The Jackson Laboratory |
RRID: IMSR_JAX:002019 |
| Egg: Specific Pathogen Free, premium plus, incubated |
Charles River |
Cat#10100331 |
|
| Oligonucleotides |
|
| NR2F1 siRNA#1: |
Thermo Fisher |
Cat#4390824 |
| NR2F1 siRNA#2: |
Thermo Fisher |
Cat#4392420 |
| NR2F1 siRNA#3: |
Millipore Sigma |
Cat#NM_005654 (SASI_Hs01_00095428) |
| NR2F1 siRNA#4: |
Millipore Sigma |
Cat#NM_005654 (SASI_Hs01_00095429) |
| SAMD4 siRNA: targeting sequence: GCAAUUGAAAGUUUGGUAA |
Horizon |
Cat#J-003902-09-0005 |
| SMAD4 sh1: clone ID: V3LHS_359402. Sequence: AACTCTGTACAAAGACCGC |
Horizon |
Cat#RHS4430-200305036 |
| SMAD4 sh2: clone ID: V3LHS_408444. Sequence: TAACTTTGAGAACTTCTCT |
Horizon |
Cat#RHS4430-200301270 |
| SMAd4 sh3: clone ID: V3LHS_359404. Sequence: TCCAGGTGATACAACTCGT |
Horizon |
Cat#RHS4430-200302670 |
| Scr sh: clone ID: E20200805A. Sequence: N/A |
Horizon |
Cat#RH4346 |
| Q-PCR primers |
IDT |
See supplementary table |
|
| Software and algorithms |
|
| ImageJ |
Version 1.8.0/1.53a |
https://ImageJ.nih.gov/ij/index.html; RRID:SCR_003070 |
| CaseViewer |
Version 2.4 |
https://www.3dhistech.com/solutions/caseviewer/; RRID:SCR_017654 |
| fastQC |
Version 0.11.8. Andrews, S.54
|
https://github.com/s-andrews/FastQC; RRID:SCR_014583 |
| STAR |
Version 2.7.5b. Dobin et al.55
|
https://github.com/alexdobin/STAR; RRID:SCR_004463 |
| Trim Galore |
Version 0.6.6 |
https://github.com/FelixKrueger/TrimGalore; RRID:SCR_011847 |
| Salmon |
Version 1.11 |
https://github.com/COMBINE-lab/salmon/releases; RRID:SCR_017036 |
| DEseq2 |
Version 1.34.0. Love et al.57
|
https://github.com/mikelove/DESeq2; RRID:SCR_015687 |
| Bowtie2 |
Version 2.2.8. Langmead et al.60
|
https://github.com/BenLangmead/bowtie; RRID:SCR_005476 |
| PICARD |
Version 2.2.4 |
https://github.com/broadinstitute/picard/releases; RRID:SCR_006525 |
| Samtools |
Version 1.11. Li et al.61
|
http://www.htslib.org/; RRID:SCR_002105 |
| MACS2 |
Version 2.1.0. Zhang et al.62
|
https://pypi.org/project/MACS2/; RRID:SCR_013291 |
| deepTools |
Version3.2.1. Ramirez et al.63
|
https://deeptools.readthedocs.io/en/develop/; RRID:SCR_016366 |
| Ranking Ordering of Super Enhancers algorithm (ROSE) |
Whyte et al.64; Loven et al.41
|
http://younglab.wi.mit.edu/super_enhancer_code.html; RRID:SCR_017390 |
| RStudio |
Version 1.1.46 |
https://rstudio.com/; RRID:SCR_000432 |
| R |
Version 4.1.0 |
https://www.r-project.org/; RRID:SCR_001905 |
| GE ImageQuant LAS 4010 |
GE Healthcare |
https://www.gehealthcare.com/
|
| GraphPad Prism |
Version 9 |
https://www.graphpad.com/; RRID:SCR_002798 |
