Virus:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Recombinant:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Membrane:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Xenograft Assay:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Protease Inhibitor:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Gentle:Article Title: Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-ZFP36L2/TIS11D Abcam Cat#ab70775; RRID: AB_1271231 Anti-MDM2 Antibody (clone IF2) EMD Millipore Cat#MABE340; RRID: AB_2943329 Goat polyclonal anti-TP53 (HRPconjugated) R&D Systems Cat#HAF1355; RRID: AB_2303928 Mouse monoclonal anti-GAPDH (clone 0411, HRP-conjugated) Santa Cruz Biotechnology Cat#sc-47724 HRP; RRID: AB_3716894 Bacterial and virus strains Endura Competent cells Biosearch Technologies Cat#60242-2 E. coli NEB Stable competent cells New Englands Biolabs Cat#C3040I Biological samples Primary mammary tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Primary skin tumors from Pik3caH1047R/+;Cas9 mice (FMRE screen) This paper N/A Chemicals, peptides, and recombinant proteins Hydrocortisone Sigma-Aldrich H0888; CAS: 50-23-7 Cholera toxin Sigma-Aldrich C8052; CAS: 9012-63-9 Insulin Sigma-Aldrich I5500; CAS: 11061-68-0; GenPept: P01308 Horse serum (Gibco) Thermo Fisher Scientific Cat#16050122 Fetal Bovine Serum Wisent Cat#090-150 EGF (5 ng/mL) Wisent Cat#511-110-EU; GenPept: P01133 DMEM/F12 50/50 mix with L-Glutamine Wisent Cat#319-075 CL DMEM 1× with 4.5 g/L Glucose & L-Glutamine w/o Sodium Pyruvate Wisent Cat#319-015 CL Penicillin-Streptomycin (100×) Wisent Cat#450-201-EL Corning Matrigel Basement Membrane Matrix Corning Cat#354234 CorningTM MatrigelTM Matrix (xenograft) Fisher Scientific Cat#CB-40234 Nutlin-3a (MDM2 inhibitor, 10 μM) Sigma-Aldrich Cat#SML0580 CAS: 675576-98-4 Puromycin Wisent Cat#400-160-EM CAS: 58-58-2 Blasticidine HCL Solution Wisent Cat#450-190-XL Poly-L-lysine hydrobromide Sigma-Aldrich Cat#P2636 CAS: 25988-63-0 Polyethylenimine (PEI) Cedarlane Cat#23966-100 CAS: 9002-98-6 cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail (Roche) Millipore Cat#04693159001 BsmBI-v2 New Englands Biolabs Cat#R0739L SapI New Englands Biolabs CatR0569L Gentle Collagenase/Hyaluronidase in DMEM (10×) Stemcell Technologies Cat#07919 Fast Green FCF Sigma-Aldrich Cat#F7252-5G CAS: 2353-45-9 (Continued on next page) 18 Cell Reports 45, 118111, October 27, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzolTM Reagent Invitrogen Cat#15596018 PowerUpTM SYBRTM Green Master Mix for qPCR Applied BiosystemsTM Cat#A25778 TaqManTM Fast Advanced Master Mix for qPCR Applied BiosystemsTM Cat#4444557 Immobilon -P PVDF Membrane, 0.45 μm Millipore Cat#IPVH00010 Clarity Western ECL substrate, 500 mL Bio-Rad Cat#1705061 Critical commercial assays DNeasy Blood & Tissue Kit Qiagen 69504 Zymoclean Gel DNA Recovery Kit Zymo Research D4008 Zymo Oligo Clean and Concentrator Zymo Research D4060 Quick-RNA Miniprep Kit Zymo Research R1055 miRNeasy Tissue/Cells Advanced Micro Kit Qiagen 217684 RNA Qubit Fluorometric Quantitation Kit Invitrogen Q32852 SuperScriptTM IV VILOTM Master Mix Thermo Fisher Scientific 11766500 TaqManTM MicroRNA Reverse Transcription Kit Applied Biosystems 4366596 TaqManTMMicroRNA Assay – U6 snRNA Applied Biosystems 4440877; Assay ID 001973 TaqManTMMicroRNA Assay – hsa-miR-21a Applied Biosystems 4440877; Assay ID 000397 PierceTM BCA Protein Assay Kits Thermo Fisher Scientific 23225 Deposited data PCAWG WGS somatic mutation data ICGC/PCAWG https://dcc.icgc.org/ Hartwig Medical Foundation metastatic cancer WGS dataset Hartwig Medical Foundation https://www.hartwigmedicalfoundation.nl/ ENCODE regulatory element annotations (ChIP-seq peaks) ENCODE Project Consortium https://www.encodeproject.org/ Roadmap Epigenomics epigenetic annotations Roadmap Epigenomics Consortium https://www.roadmapepigenomics.org/ Experimental models: Cell lines Human: MCF10A-PIK3CAH1047R Horizon Discovery; acquired May 2018 Cat#HD 101-011; RRID: CVCL_LD55 Human: MCF10A-PIK3CAH1047R-Cas9: stable Cas9 clonal line This paper; derived from Horizon Cat#HD 101-011 N/A Human: HEK293T (293FT cell line) Invitrogen Cat#R700-07; RRID: CVCL_6911 Mouse: MEFs derived from R26-LSLtdTomato embryos (for lentiviral titration) This paper N/A Experimental models: Organisms/strains Mouse: Pik3caH1047R: Gt(ROSA)26Sortm1(Pik3ca*H1047R)Egan; FVB/N background Provided by S. Egan (SickKids, Toronto) MGI:5000472 Mouse: R26-LSL-Cas9-EGFP: Gt(ROSA)26Sortm1(CAG-xstpx-cas9− EGFP)Fezh/ J; C57BL/6 background The Jackson Laboratory JAX: 026175; RRID: IMSR_JAX:026175 Mouse: Pik3caH1047R/+;Cas9: F1 hybrid FVB/N × C57BL/6; used for all CRISPR screens This paper N/A Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/ SzJ; immunocompromised; xenograft host The Jackson Laboratory JAX: 005557; RRID: IMSR_JAX:005557 Mouse: R26-LSL-tdTomato (Ai14) The Jackson Laboratory JAX#007914; RRID:IMSR_JAX:007914 Oligonucleotides Pooled sgRNA library – human FMRE library (3,266 sgRNAs) GenScript (pooled chip synthesis) N/A (Continued on next page) Cell Reports 45, 118111, October 27, 2026 19
Purification:Article Title: ATM promotes nucleolytic processing of reversed replication forks during DNA interstrand cross-link repair
Article Snippet: .. Deproteinized replication intermediates were purified as described above, and 2 μL of recovered DNA was digested with either 2 UHincII or 2 U eachof HincII and SapI (NEB #R0569) in 1X NEBuffer rCutSmart at 37 °C for 3 h. Digestion products were resolved on a native 0.8% agarose gel and visualized by phosphorimaging. ..
Agarose Gel Electrophoresis:Article Title: ATM promotes nucleolytic processing of reversed replication forks during DNA interstrand cross-link repair
Article Snippet: .. Deproteinized replication intermediates were purified as described above, and 2 μL of recovered DNA was digested with either 2 UHincII or 2 U eachof HincII and SapI (NEB #R0569) in 1X NEBuffer rCutSmart at 37 °C for 3 h. Digestion products were resolved on a native 0.8% agarose gel and visualized by phosphorimaging. ..
Transferring:
other:Article Title: Coordination of sequential RNase activities in an ancient molecular machine
Article Snippet: All cloned constructs were sequenced either via Sanger sequencing or full plasmid sequencing at Microsynth Seqlab GmbH.
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