Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Homo sapiens) |
SMARCB1 | NA | ||
| Gene (Homo sapiens) |
PSMB5 | NA | ||
| Gene (Homo sapiens) |
CCNB1 | NA | ||
| Gene (Homo sapiens) |
UBE2C | NA | ||
| Strain, strain background (Mus musculus) |
CrTac:NCr-Foxn1nu | Taconic Biosciences |
RRID:IMSR_TAC:ncrnu | |
| Genetic reagent () | Luciferase | this paper | RRID:Addgene_117072 | Backbone: pXPR_BRD003 |
| Genetic reagent (Homo sapiens) |
UBE2C guide 1 | this paper | RRID:Addgene_117068 | Backbone: pXPR_BRD003 |
| Genetic reagent (Homo sapiens) |
UBE2C guide 2 | this paper | RRID:Addgene_117071 | Backbone: pXPR_BRD003 |
| Genetic reagent (Homo sapiens) |
PSMB5 guide 1 | this paper | RRID:Addgene_117073 | Backbone: pXPR_BRD003 |
| Genetic reagent (Homo sapiens) |
PSMB5 guide 2 | this paper | RRID:Addgene_117074 | Backbone: pXPR_BRD003 |
| Genetic reagent (Homo sapiens) |
pDONR223 SMARCB1 | this paper | RRID:Addgene_111181 | |
| Genetic reagent (Homo sapiens) |
pLXI_401 LacZ | this paper | RRID:Addgene_111183 | Backbone: pLXI_403 |
| Genetic reagent (Homo sapiens) |
pLXI_403 LacZ | this paper | RRID:Addgene_111184 | Backbone: pLXI_403 |
| Genetic reagent (Homo sapiens) |
pLXI_401 SMARCB1 | this paper | RRID:Addgene_111182 | Backbone: pLXI_401 |
| Genetic reagent (Homo sapiens) |
pLXI_403 SMARCB1 | this paper | RRID:Addgene_111185 | Backbone: pLXI_403 |
| Genetic reagent (Homo sapiens) |
CP1050 | PMID: 27329820 | Druggable Cancer Targets v1.0 library (shRNA) |
|
| Genetic reagent (Homo sapiens) |
CP1074 | PMID: 27329820 | Druggable Cancer Targets v1.0 library (CRISPR-Cas9) |
|
| Cell line (Homo
sapiens) |
CLF_PEDS0005_N | this paper | normal kidney cell line |
|
| Cell line (Homo
sapiens) |
CLF_PEDS0005_T1 | this paper | primary RMC cell line |
|
| Cell line (Homo
sapiens) |
CLF_PEDS0005_T2A | this paper | metastatic RMC cell line (adherent) |
|
| Cell line (Homo
sapiens) |
CLF_PEDS0005_T2B | this paper | metastatic RMC cell line (suspension) |
|
| Cell line (Homo
sapiens) |
CLF_PEDS9001_T1 | this paper | primary RMC cell line | |
| Cell line (Homo
sapiens) |
CLF_PEDS1012_T1 | this paper | Wilms tumor cell line | |
| Cell line (Homo
sapiens) |
G-401 | ATCC | CRL-1441 RRID:CVCL_0270 |
|
| Cell line (Homo
sapiens) |
RPMI 8226 | ATCC | CCL-155 RRID:CVCL_0014 |
|
| Cell line (Homo
sapiens) |
NCI-H2172 | ATCC | CRL-5930 RRID:CVCL_1537 |
|
| Cell line (Homo sapiens) |
A549 | ATCC | CCL-185 RRID:CVCL_0023 |
|
| Cell line (Homo sapiens) |
HA1E | other | Cell line maintained in W. C. Hahn lab |
|
| Cell line (Homo sapiens) |
JMSU1 | PMID: 30777879 | RRID:CVCL_2081 | |
| Antibody | anti-cytokeratin CAM5.2 |
BD Biosciences | 349205 RRID:AB_2134314 |
Immunohistochemistry |
| Antibody | anti-SMARCB1/BAF47 | BD Biosciences | 612110 RRID:AB_399481 |
Immunohistochemistry |
| Antibody | anti-ARID1A (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-373784 RRID:AB_10917727 |
1:500 |
| Antibody | antii-α-tubulin (mouse monoclonal) |
Sigma-Aldrich | T9026 RRID:AB_477593 |
1:5000 |
| Antibody | anti-β-actin (C-4) (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-47778 RRID:AB_2714189 |
1:10,000 |
| Antibody | anti-β-actin (D6A8) (rabbit monoclonal) |
Cell Signaling Technology |
#8457 RRID:AB_10950489 |
1:10,000 |
| Antibody | anti-BAF57/SMARCE1 (rabbit polyclonal) |
Bethyl Laboratories, Inc. |
A300-810A RRID:AB_577243 |
1:5000 |
| Antibody | anti-BAF60a (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-135843 RRID:AB_2192137 |
1:500 |
| Antibody | anti-SMARCC1/BAF155 (D7F8S) (rabbit monoclonal) |
Cell Signaling Technology |
#11956 | 1:1000 |
| Antibody | anti-BAF170 (G-12) (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-166237 RRID:AB_2192013 |
1:500 |
| Antibody | anti-SMARCA4 (G-7) (mouse monoclonal) |
Santa Cruz Biotechnology |
sc-17796 RRID:AB_626762 |
1:1000 |
| Antibody | anti-Cleaved Caspase-3 (Asp175) (5A1E) (rabbit monoclonal) |
Cell Signaling Technology |
#9664 RRID:AB_2070042 |
1:1000 |
| Antibody | anti-c-Myc (N-262) (rabbit polyclonal) |
Santa Cruz Biotechnology |
sc-764 RRID:AB_631276 |
1:200 |
| Antibody | anti-c-Myc (rabbit polyclonal) |
Cell Signaling Technology |
#9402 RRID:AB_2151827 |
1:1000 |
| Antibody | anti-cyclin B1 (V152) (mouse monoclonal) |
Cell Signaling Technology |
#4135 RRID:AB_2233956 |
1:1000 |
| Antibody | anti-cyclin B1 (rabbit polyclonal) |
Cell Signaling Technology |
#4138 RRID:AB_2072132 |
1:1000 |
| Antibody | anti-cyclin D1 (M-20) (rabbit polyclonal) |
Santa Cruz Biotechnology |
sc-718 RRID:AB_2070436 |
1:1000 |
| Antibody | anti-GAPDH (14C10) (rabbit monoclonal) |
Cell Signaling Technology |
#2118 RRID:AB_561053 |
1:1000 |
| Antibody | anti-GAPDH (D4C6R) (mouse monoclonal) |
Cell Signaling Technology |
#97166 RRID:AB_2756824 |
1:1000 |
| Antibody | anti-GRP78 (mouse monoclonal) |
Rockland Immunochemicals |
200–301 F37 RRID:AB_2611159 |
1:10,000 |
| Antibody | anti-IRE1α (14C10) (rabbit monoclonal) |
Cell Signaling Technology |
#3294 RRID:AB_823545 |
1:2000 |
| Antibody | anti-Lamin A/C (rabbit polyclonal) |
Cell Signaling Technology |
#2032 RRID:AB_2136278 |
1:1000 |
| Antibody | anti-PSMB5 (rabbit polyclonal) |
Abcam | ab3330 RRID:AB_303709 |
1:1000 |
| Antibody | anti-SMARCB1/SNF5 (rabbit polyclonal) |
Bethyl Laboratories, Inc. |
A301-087A RRID:AB_2191714 |
1:5000 |
| Antibody | anti-UBE2C (mouse monoclonal) |
Proteintech | 66087–1 RRID:AB_11232220 |
1:1000 |
| Commercial assay or kit |
QIAamp DNA Blood Midi Kit |
Qiagen | 51183 | |
| Commercial assay or kit |
QIAprep Spin Miniprep Kit |
Qiagen | 27106 | |
| Commercial assay or kit |
Rneasy Plus Mini Kit |
Qiagen | 74134 | |
| Commercial assay or kit |
Qubit RNA HS Assay Kit |
Thermo Fisher Scientific |
Q32852 | |
| Commercial assay or kit |
KAPA Stranded mRNA-Seq Kit |
Kapa Biosystems | KK8420 | |
| Commercial assay or kit |
KAPA Library Quantification Kit |
Kapa Biosystems | KK4835 | |
| Commercial assay or kit |
High-Capacity cDNA Reverse Transcription Kit |
Thermo Fisher Scientific |
4368814 | |
| Commercial assay or kit |
Power SYBR Green PCR Master Mix |
Thermo Fisher Scientific |
4368708 | |
| Commercial assay or kit |
Senescence β-Galactosidase Staining Kit |
Cell Signaling Technology |
9860S | |
| Commercial assay or kit |
CellTiter-Glo Luminescent Cell Viability Assay |
Promega | G7570 | |
| Commercial assay or kit |
Proteasome-Glo Chymotrypsin-Like Cell-based Assay |
Promega | G8660 | |
| Commercial assay or kit |
Annexin V: FITC Apoptosis Detection Kit |
Thermo Fisher Scientific |
BD 556547 | |
| Commercial assay or kit |
PI/Rnase Staining Buffer |
BD Pharmingen | 550825 | |
| Commercial assay or kit |
FxCycle PI/Rnase Staining Solution |
Invitrogen | F10797 | |
| Chemical compound, drug | bortezomib (PS-341) | Selleck Chemicals | S1013 | in vitro studies |
| Chemical compound, drug | ixazomib (MLN2238) | Selleck Chemicals | S2180 | in vitro studies |
| Chemical compound, drug | nocodazole | Selleck Chemicals | S2775 | in vitro studies |
| Chemical compound, drug | Ro-3306 | Selleck Chemicals | S7747 | in vitro studies |
| Chemical compound, drug | MLN2238 | MedChem Express | HY-10453 | in vivo studies |
| Software, algorithm | SvABA v0.2.1 | PMID: 29535149 | ||
| Software, algorithm | FlowJo v10.0 | RRID:SCR_008520 | ||
| Software, algorithm | ComBat | RRID:SCR_010974 | ||
| Software, algorithm | GraphPad Prism v8.0 | RRID:SCR_002798 | ||
| Software, algorithm | GSEA | Broad Institute | RRID:SCR_003199 | |
| Software, algorithm | GATK v.4.0.4.0 | PMID: 20644199 | RRID:SCR_001876 | |
| Software, algorithm | TopHat v2.0.11 | PMID: 22383036 | RRID:SCR_013035 | |
| Software, algorithm | DESeq2 | PMID: 25516281 | RRID:SCR_015687 |