Virus:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
Recombinant:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
Transfection:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
Cryo-EM Sample Prep:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
Western Blot:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
Functional Assay:Article Title: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies OSR1 Rabbit Cell Signaling RRID:AB_2157610; #3729S BCL6B Polyclonal Antibody Invitrogen RRID:AB_2852838; #PA5-103502 Mouse beta-actin Antibody Cell Signaling RRID:AB_2242334; #3700 Vinculin Rabbit mAb Cell Signaling RRID:AB_2728768; #13901S Beta-Actin Rabbit mAb Cell Signaling RRID:AB_2223172; #4970S Bcl-6 mouse monoclonal antibody Santa Cruz RRID:AB_2063455; #sc-7388 Bacterial and virus strains Stbl3 Thermo Fisher Scientific Cat#C737303 Chemicals, peptides, and recombinant proteins Ethanol Fisher Bioreagents Cat#BP2818-500 LanthaScreen Eu-Streptavidin Invitrogen Cat#PV6025 TRIzol LS reagent Invitrogen Cat#10296028 Chloroform/isoamyl alcohol 24:1 (v/v) Thermo Scientific Cat#327155000 Isopropanol Fisher Bioreagents Cat#BP2618-1 Ethanol Fisher Bioreagents Cat#BP2818-500 Critical commercial assays T4 DNA Ligase New England Biolabs M0202S Quick CIP New England Biolabs M0525S BsmBI-v2 New England Biolabs R0739L NEBNext High Fidelity New England Biolabs M0541S TransIT-L-LT1 Transfection Reagent Mirus Cat#MIR 2300 Deposited data Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 EMDB EMD-49892 Cryo-EM map for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A EMDB EMD-49893 Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449 PDB 9NWS Structural Model for DDB1ΔB⋅CRBN⋅ mezigdomide⋅SALL4 392− 449;G416A PDB 9NWT crystal structure of DDB1 ΔB⋅CRBN⋅ALV1⋅IKZF2 ZF1–3 PDB 9E2U Uncropped Western blots Mendeley https://doi.org/10.17632/4ptft2dg4t.1 Proteomics PRIDE PXD056867; PXD056913 FASTQ files for functional genomics SRA PRJNA1295817, PRJNA1295818, PRJNA1295819, PRJNA1295549, PRJNA1296746 Experimental models: Cell lines HEK293T-L/HEK293T-Cas9 Broad Institute https://www.atcc.org/products/crl-3216 U937-Cas9 Broad Institute https://www.atcc.org/products/crl-1593.2 SYO1-Cas9 Broad Institute https://depmap.org/portal/cell_line/ACH-001275 KYO1-Cas9 Broad Institute https://www.dsmz.de/collection/ catalogue/details/culture/ACC-601 (Continued on next page) e1 Molecular Cell 85, 3184–3201.e1–e14, August 21, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER SuDHL4-Cas9 Broad Institute https://www.atcc.org/products/crl-2957 Trichoplusia ni (High Five) Gibco Cat#B85502 Spodoptera frugiperda (Sf9) Expression Systems Cat#94-001F Oligonucleotides Oligonucleotides used in this study.
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