Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brg1 (D1Q7F) | CST | Cat#49360; AB_2728743 |
| Recombinant Anti-BRG1 | Abcam | Cat#ab108318; AB_10889900 |
| Phospho-EGF Receptor (Tyr1068) (D7A5) | CST | Cat#3777; AB_2096270 |
| EGF Receptor | CST | Cat#2232; AB_901981 |
| GAPDH (14C10) | CST | Cat#2118; AB_561053 |
| E-Cadherin (24E10) (AF594 Conjugate) | CST | Cat#7687; AB_2797633 |
| Vimentin (D21H3) (AF488 Conjugate) | CST | Cat#9854; AB_10829352 |
| c-Raf (D4B3J) | CST | Cat#53745; AB_2799444 |
| MEK1/2 (L38C12) | CST | Cat#4694; AB_10695868 |
| Phospho-MEK1/2 (Ser217/221) (41G9) | CST | Cat#9154; AB_2138017 |
| p44/42 MAPK (Erk1/2) (137F5) | CST | Cat#4695; AB_390779 |
| P-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) | CST | Cat#4370; AB_2315112 |
| Lamin A/C | CST | Cat#2032; AB_2136278 |
| CRISPR-Cas9 Antibody (7A9–3A3) | Novus Biologicals | Cat#NBP2–36440 |
| Anti-Nrf2 | Abcam | Cat#ab137550; AB_2687540 |
| Anti-mouse IgG, HRP-linked Antibody | CST | Cat#7076; AB_330924 |
| Anti-rabbit IgG, HRP-linked Antibody | CST | Cat#7074; AB_2099233 |
| Rabbit monoclonal anti-EGF Receptor (D38B1) XP® | Cell Signaling Technology | Cat# 4267, RRID:AB_2246311 |
| Rabbit monoclonal anti-phospho-Akt (Ser473) (D9E) XP® | Cell Signaling Technology | Cat# 4060, RRID:AB_2315049 |
| Rabbit polyclonal anti-Akt | Cell Signaling Technology | Cat# 9272, RRID:AB_329827 |
| Rabbit monoclonal anti-phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (197G2) | Cell Signaling Technology | Cat# 4377, RRID:AB_331775 |
| Rabbit polyclonal p44/42 MAPK (Erk1/2) | Cell Signaling Technology | Cat# 9102, RRID:AB_330744 |
| Rabbit monoclonal HSP90 (C45G5) | Cell Signaling Technology | Cat# 4877, RRID:AB_2233307 |
| Rabbit monoclonal Vinculin (E1E9V) XP® | Cell Signaling Technology | Cat# 7074, RRID:AB_2099233 |
| Goat polyclonal anti-rabbit HRP-linked IgG | Cell Signaling Technology | Cat# 49360, RRID:AB_2728743 |
| Rabbit monoclonal Axl (C89E7) | Cell Signaling Technology | Cat# 8661, RRID:AB_11217435 |
| Rabbit monoclonal E-cadherin (24E10) | Cell Signaling Technology | Cat# 3195, RRID:AB_2291471 |
| Rabbit polyclonal Vimentin (R28) | Cell Signaling Technology | Cat# 3932, RRID:AB_2288553 |
| Rabbit monoclonal Brg1 (D1Q7F) | Cell Signaling Technology | Cat# 365062, RRID:AB_1084786 |
| Mouse monoclonal anti-GAPDH (G-9) | Santa Cruz | Cat# 11956, RRID:AB_2797776 |
| Rabbit monoclonal SMARCC1/BAF155 (D7FS8) | Cell Signaling Technology | Cat# 8173, RRID:AB_10949503 |
| CUTANA Rabbit IgG CUT&RUN Negative Control Antibody | Epicypher | Cat# 130042, RRID:AB_2923178 |
| Rabbit monoclonal Acetyl-Histone H3 (Lys27) (D5E4) XP® | Cell Signaling Technology | Cat# 2729, RRID:AB_1031062 |
| Bacterial and virus strains | ||
| MAX Efficiency® DH5α Competent Cells | Thermo Fisher | Cat#18258012 |
| Biological samples | ||
| EGFR-mutant tumors tissue micro array | Toki MI. et al, 2018 (PMID: 30267840) | YTMA-356 |
| Patient Derived Xenografts (PDXs) | This Paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Osimertinib | Selleckchem | Cat#S7297 |
| Trametinib | Selleckchem | Cat#S2673 |
| Osimertinib | MedChemExpress | Cat# HY-15772A |
| Osimertinib | AstraZeneca | AZD9291 |
| Compound14 | Jun Qi’s Laboratory | N/A |
| FHD-286 | Jun Qi’s Laboratory | N/A |
| High Sensitivity D100 ScreenTape | Agilent | Cat# 5067–5584 |
| High Sensitivity D100 Reagents | Agilent | Cat# 5067–5585 |
| BioMag Plus Concanavalin A beads | PolySciences | Cat# 8605 |
| AMPure XP Beads | Beckman Coulter | Cat# A6388 |
| Spermidine | Sigma-Aldrich | Cat# S2626 |
| pMD2.G | Addgene | Addgene_12259 |
| psPAX2 | Addgene | Addgene_12260 |
| pInducer10-mir-RUP-PheS | Meerbrey KL et al, 2011 (PMID: 21307310) | Addgene_44011 |
| TLCV2 | Addgene | Addgene_87360 |
| pLKO.1 puro | Addgene | Addgene_8453 |
| NRF2-sh1 | Sigma-Aldrich | TRCN0000007556 |
| NRF2-sh2 | Sigma-Aldrich | TRCN0000007557 |
| NRF2-sh2 | Sigma-Aldrich | TRCN0000007558 |
| Critical commercial assays | ||
| RPMI 1640 Medium | Thermo Fisher | Cat#A1049101 |
| Fetal Bovine Serum | Thermo Fisher | Cat#16140–071 |
| Penicillin-Streptomycin | Thermo Fisher | Cat#15140122 |
| 0.25% Trypsin with EDTA | Thermo Fisher | Cat#25200056 |
| TaqMan CNV Assay EGFR | Thermo Fisher | Cat#Hs02088787_cn |
| TaqMan CNV Assay EGFR | Thermo Fisher | Cat#Hs02190396_cn |
| TaqMan CNV Assay RAF1 | Thermo Fisher | Cat#Hs02614899_cn |
| TaqMan CNV Assay RAF1 | Thermo Fisher | Cat#Hs04252880_cn |
| Power SYBR Green Master mix | Thermo Fisher | Cat#4367659 |
| Protease and Phosphatase inhibitor cocktail | Thermo Fisher | Cat#78440 |
| SuperSignal West Pico PLUS | Thermo Fisher | Cat#34579 |
| SuperSigna West Femto Maximum Sensitivity Substrat | Thermo Fisher | Cat# 34096 |
| Triton X-100 | Sigma Aldrich | Cat#X-100 |
| Hoechst dye | Thermo Fisher | Cat#62249 |
| Tumor Dissociation Kit, human | Miltenyi Biotec | Cat#130–095-92 |
| Matrigel | Corning | Cat#356237 |
| Doxycycline diet | Envigo | Cat#TD.00426 |
| ProLong® Gold Antifade Mountant | Thermo Fisher | Cat#P10144 |
| CellROX® Deep Red Reagent | Thermo Fisher | Cat#C10422 |
| CellROX® Green Reagent | Thermo Fisher | Cat#C10444 |
| DNeasy Blood & Tissue kit | Qiagen | Cat#69504 |
| SuperScript III reverse transcriptase | Thermo Fisher | Cat#18080093 |
| RNeasy extraction kit | Thermo Fisher | Cat#74004 |
| MycoAlertTM Mycoplasma Detection Kit | Lonza | Cat#LT07–118 |
| CellTiter-Blue® Cell Viability Assay | Promega | Cat#G8081 |
| GenePrint 10 System | Promega | Cat#B9510 |
| Lipofectamine® RNAiMAX Transfection Reagent | Thermo Fisher | Cat#13778150 |
| TransIT®−293 Transfection Reagent | Mirus | Cat#MIR2704 |
| Antigen Unmasking Solution, Citrate-Based | Vector Laboratories | Cat#H-3300–250 |
| Antigen Unmasking Solution, Tris-Based | Vector Laboratories | Cat#H-3301–250 |
| VECTASTAIN® ABC-HRP Kit, Peroxidase (Mouse IgM ) | Vector Laboratories | Cat#PK-4010 |
| VECTASTAIN® ABC-HRP Kit, Peroxidase (Rabbit IgG) | Vector Laboratories | Cat#PK-4001 |
| Vector® NovaRED® Substrate Kit, Peroxidase (HRP) | Vector Laboratories | Cat#SK-4800 |
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | Cat# G7573 |
| CellEvent® Caspase-3/7 Green ReadyProbes® Reagent | Invitrogen | Cat# R37111 |
| CUTANA® ChIC/CUT&RUN Kit | Epicypher | Cat# 141048 |
| CUTANA® CUT&RUN Library Prep Ki | Epicypher | Cat# 141001 |
| RNAeasy Mini Kit | Qiagen | |
| MinElute PCR Purification kit | Qiagen | Cat# 28006 |
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | New England Biolabs | Cat# E7760L |
| Tagment DNA Enzyme and Buffer Large Kit | Illumina | Cat# 20034197 |
| NextSeq 500/550 High Output Kit v2.5 (75 cylcles) | Illumina | Cat# 20024906 |
| Deposited data | ||
| All sequencing data SuperSeries | GEO Database | GSE202864 |
| Whole Exome Sequencing | GEO Database | GSE202863 |
| RNA-sequencing | GEO Database | GSE202859 |
| ATAC-sequencing | GEO Database | GSE202857 |
| Cut&Run, ATAC-seq, RNA-seq | GEO Database | GSE227999 |
| Experimental models: Cell lines | ||
| PC9 | ATCC / This paper | CVCL_B260; N/A |
| PC9-OR | This paper | N/A |
| H1975 | ATCC | CVCL_1511 |
| H1975-OR | This paper | N/A |
| HCC827 | ATCC | CVCL_2063 |
| HCC827-OR | This paper | N/A |
| YU-005C | This paper | N/A |
| HEK293T | ATCC | CVCL_0063 |
| PC-9*; human EGFR-mutant NSCLC, male | Dr. Kazuto Nishio (Kindai University, Osaka, Japan) | RRID:CVCL_B26 |
| PC-9_OR*; human EGFR-mutant NSCLC, male | This paper | N/A |
| HCC4006; human EGFR-mutant NSCLC, male | ATCC | CRL-2871; RRID:CVCL_1269 |
| HCC4006_OR; human EGFR-mutant NSCLC, male | This paper | N/A |
| HCC827; human EGFR-mutant NSCLC, female | Dr. Adi Gazdar (UT Southwestern, Dallas, TX) | RRID:CVCL_2063 |
| HCC827GR6; human EGFR-mutant NSCLC, female | Engelman et al. 2007 Science | N/A |
| Experimental models: Organisms/strains | ||
| NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice | Jackson Labs | IMSR_JAX:005557 |
| Oligonucleotides | ||
| See Table S4 - Oligonucleotides | N/A | N/A |
| Software and algorithms | ||
| QuPath | Bankhead P. et al 2017 (PMID: 29203879) | SCR_018257 |
| ImageJ | Schneider et al., 2012 | SCR_003070 |
| ApE | https://jorgensen.biology.utah.edu/wayned/ape/ | SCR_014266 |
| Graphpad 9.1.1 | PRISM | SCR_000306 |
| FlowJo v10 | BD | SCR_008520 |
| Ingenuity Pathway Analysis | Qiagen | SCR_008653 |
| RStudio (1.3.1093) | N/A | SCR_000432 |
| Kent Tools | UCSC | https://github.com/ucscGenomeBrowser/kent |
| IGV (2.8.2) | Robinson JT et al. 2012 (PMID: 21221095) | SCR_011793 |
| HOMER (4.11) | Heinz S. et al. 2010 (PMID: 20513432) | SCR_010881 |
| Primer3 | https://primer3.ut.ee/ | SCR_003139 |
| Combenefit | Di Veroli et al. 2016 Bioinformatics | N/A |
| Graphpad Prism 9 | https://www.graphpad.com/scientific-software/prism/ | N/A |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| STAR | Dobin etal., 2013 | https://github.com/alexdobin/STAR |
| MACS2 | Zhang etal., 2008 | https://github.com/taoliu/MACS |
| ngsplot | Shen et al., 2014 | https://github.com/shenlab-sinai/ngsplot |
| EdgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| GSEA | Subramanian et al., 2005 | http://software.broadinstitute.org/gsea/index.jsp |
| Bedtools | Quinlan and Hall, 2010 | http://bedtools.readthedocs.io/en/latest/ |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Picard | Broad Institute | http://broadinstitute.github.io/picard |
| Trimmomatic | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| Gene Ontology | Gene Ontology Consortium, 2015 | http://geneontology.org/ |
| BWA-MEM | Li, 2013 | bio-bwa.sourceforge.net/ |
| Matplotlib | Hunter, 2007 | https://matplotlib.org/stable/ |
| Seaborn | Michael Waskom | https://seaborn.pydata.org/ |