Bicinchoninic Acid Protein Assay:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Western Blot:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Lysis:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Real-time Polymerase Chain Reaction:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Mass Spectrometry:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Stable Transfection:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Expressing:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Multiplex sample analysis:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Transfection:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Data-independent acquisition:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
RNA sequencing:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
Recombinant:Article Title: An interactome-based framework for DDB1- and CUL4-associated factor prioritization in targeted protein degradation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER GL-Tip SDB GL Sciences Cat# 7820-11200 BCA Protein Assay Kit Thermo Fisher Scientific Cat# 23250 ImmunoStar LD FUJIFILM Wako Pure Chemical Corporation Cat# 290-69904 Immobilon Western Chemiluminescent HRP Substrate Millipore Cat# WBKLS0500 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596026 QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) LEXOGEN Cat# 015.384 SuperPrep II Cell Lysis Kit TOYOBO Cat# SCQ-501 KOD SYBR qPCR Mix TOYOBO Cat# QKD-201 Deposited data Mass spectrometry data of biotinylated peptides in HEK293T cells stably expressing AirID-DCAF This paper Table S2; ProteomeXchange: PXD057875 TMT-based mass spectrometry of HEK293T cells transfected with siDCAF This paper Table S4; ProteomeXchange: PXD057876 DIA-based mass spectrometry of HEK293T cells treated with MLN4294 This paper Table S7: ProteomeXchange PXD064494 RNA-sequencing of HEK293T cells transfected with siDCAF This paper Table S6; DRA021433 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Oligonucleotides All oligonucleotides This paper Table S1 Recombinant DNA pcDNA3.1-AGIA-AirID Kido et al.,34 Addgene Cat# 182210 pCMV-VSV-G-RSV-Rev RIKEN Cat# RDB04393 pCAG-HIVgp RIKEN Cat# RDB04394 pCSII-CMV-MCS-IRES2-Bsd RIKEN Cat# RDB04385 pCSII-CMV-AirID-DCAF-IRES2-Bsd This paper Table S1 pCSII-CMV-DCAF3-FLAG-IRES2-Bsd This paper N/A pLVSIN-EF1α-MCS-puro Takara Bio Cat# 6186 pLVSIN-EF1α-AirID-DCAF-puro This paper Table S1 pCAGGS-MCS RIKEN #RDB08938 pCAGGS-FLAG-MCS This paper N/A pCAGGS-MCS-FLAG This paper N/A pCAGGS-FLAG-COP1 This paper N/A pCAGGS-DCAF3-FLAG This paper N/A pCAGGS-FLAG-DCAF1 This paper N/A pCAGGS-FLAG-DCAF2 This paper N/A pCAGGS-FLAG-DCAF8 This paper N/A pCAGGS-FLAG-DCAF8L2 This paper N/A pCAGGS-FLAG-DCAF9 This paper N/A pCAGGS-FLAG-DCAF10 This paper N/A pCAGGS-FLAG-DCAF11 This paper N/A pCAGGS-FLAG-DCAF12 This paper N/A pCAGGS-FLAG-DCAF14 This paper N/A pCAGGS-FLAG-DCAF15 This paper N/A (Continued on next page) Molecular Cell 86, 1397–1416.e1–e11, April 2, 2026 e3 .. Cell lines and cell culture HEK293T (#CRL-3216, American Type Culture Collection [ATCC]) cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37◦C under 5% CO2.
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