Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ; NSG | The Jackson Laboratory | Stock no. 005557; RRID:IMSR_JAX:005557 | |
| Cell line (Homo sapiens) | HEK293T | ATCC | CRL-3216; RRID:CVCL_0063 | |
| Cell line (H. sapiens) | MCF7 | ATCC | HTB-22; RRID:CVCL_0031 | |
| Cell line (H. sapiens) | WHIM12 | Li et al., 2013 | ||
| Cell line (H. sapiens) | SUM159 | Asterand | RRID:CVCL_5423 | |
| Cell line (H. sapiens) | SUM159T-Luciferase | Westcott et al., 2015 | ||
| Antibody | anti-HA (Rat monoclonal) | Roche | Cat #11867423001; RRID:AB_390918 | IB (1:1000), IP (1 μg) |
| Antibody | anti-c-Myc (Rabbit polyclonal) | Santa Cruz Biotechnology | sc-789; RRID:AB_631274 | IB (1:1000) |
| Antibody | anti-V5 (Rabbit monoclonal) | Cell Signaling Technology | Cat #13202; RRID:AB_2687461 | IB (1:1000) |
| Antibody | anti-SMAD3 (Rabbit polyclonal) | Abcam | ab28379; RRID:AB_2192903 | IB (1:1000), PLA (1:200), ChIP-qPCR (1.5 μg), ChIP-seq (10 μg) |
| Antibody | anti-phospho-SMAD3 (Rabbit monoclonal) | Cell Signaling Technology | Cat #9520; RRID:AB_2193207 | IB (1:1000), ChIP (5 μg) |
| Antibody | anti-SMURF2 (Mouse monoclonal) | Santa Cruz Biotechnology | sc-393848 | IB (1:500) |
| Antibody | anti-RRAD (Goat polyclonal) | Thermo Fisher Scientific | PA537885; RRID:AB_2554493 | IB (1:1000) |
| Antibody | anti-ZNF165 (Mouse monoclonal) | Novus Biologicals | H00007718-M02; RRID:AB_1717273 | IB (1:1000) |
| Antibody | anti-ZNF165 (Rabbit polyclonal) | Atlas Antibodies | HPA007247; RRID:AB_2797217 | IB (1:1000), PLA (1:200), IP (5 μg) |
| Antibody | anti-Tubulin (Rabbit monoclonal) | Cell Signaling Technology | Cat #2128; RRID:AB_823664 | IB (1:1000) |
| Antibody | anti-ZNF446 (Rabbit polyclonal) | Proteintech | 16218–1-AP | IB (1:1000), PLA (1:200) |
| Antibody | anti-TRIM27 (Rabbit monoclonal) | Cell Signaling Technology | Cat #15099; RRID:AB_2798707 | IB (1:1000) |
| Antibody | anti-V5 (Mouse monoclonal) | Thermo Fisher Scientific | R960-25; RRID:AB_2556564 | PLA (1:500), IP (1 μg) |
| Antibody | anti-SMAD3 (Mouse monoclonal) | Santa Cruz Biotechnology | sc-101154; RRID:AB_1129525 | PLA (1:200) |
| Antibody | anti-SMAD4 (Mouse monoclonal) | Santa Cruz Biotechnology | sc-7966; RRID:AB_627905 | PLA (1:200) |
| Antibody | anti-TRIM27 (Rabbit polyclonal) | Proteintech | 12205–1-AP; RRID:AB_2256660 | PLA (1:200), IHC (1:200) |
| Antibody | anti-H3K27ac (Rabbit polyclonal) | Abcam | ab4729; RRID:AB_2118291 | ChIP-qPCR (2 μg) |
| Antibody | Normal rabbit IgG (Rabbit polyclonal) | Cell Signaling Technology | Cat #2729; RRID:AB_1031062 | IP (1 μg), ChIP-qPCR (1.5–5 μg) |
| Antibody | anti-V5 (Rabbit polyclonal) | Abcam | ab9116; RRID:AB_307024 | ChIP-seq (5 μg) |
| Peptide, recombinant protein | Human Transforming Growth Factor-β1 | Cell Signaling Technology | Cat #8915 | |
| Chemical compound, drug | SB-431542 | Tocris Bioscience | Cat #1614 | |
| Commercial assay or kit | KAPA HyperPrep Kit | KAPA Biosystems | KK8502 | |
| Commercial assay or kit | Duolink In Situ PLA Probe Anti-Mouse PLUS | Sigma-Aldrich | DUO92001; RRID:AB_2810939 | |
| Commercial assay or kit | Duolink In Situ PLA Probe Anti-Rabbit MINUS | Sigma-Aldrich | DUO92005; RRID:AB_2810942 | |
| Commercial assay or kit | Duolink In Situ Detection Reagent Red | Sigma-Aldrich | DUO92008 | |
| Software, algorithm | ImageJ (Fiji) | Schindelin et al., 2012 | RRID:SCR_002285 | ver 2.0.0 |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | RRID:SCR_005476 | ver 2.3.2 |
| Software, algorithm | SAMtools | Li et al., 2009 | RRID:SCR_002105 | ver 1.6 |
| Software, algorithm | DeepTools | Ramírez et al., 2016 | RRID:SCR_016366 | ver 2.3.5 |
| Software, algorithm | Integrative Genomics Viewer | Robinson et al., 2011 | RRID:SCR_011793 | ver 2.3.93 |
| Software, algorithm | HOMER | Heinz et al., 2010 | RRID:SCR_010881 | ver 4.9 |
| Software, algorithm | GREAT | McLean et al., 2010 | RRID:SCR_005807 | ver 3.0.0 |
| Software, algorithm | MEME | Bailey et al., 2009 | RRID:SCR_001783 | ver 5.1.1 |
| Software, algorithm | GSEA | Subramanian et al., 2005 | RRID:SCR_003199 | ver 4.0.3 |