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cell lines 293t atcc cat  (DSMZ)
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cell lines hek293t atcc crl  (ATCC)
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ATCC cell lines hek293t atcc crl
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cell lines 293t cell line atcc n a hela cell line atcc n a u2os cell line atcc n a rpe1 cell line atcc n a u2os ha er asisi cell line gift  (ATCC)
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ATCC cell lines 293t cell line atcc n a hela cell line atcc n a u2os cell line atcc n a rpe1 cell line atcc n a u2os ha er asisi cell line gift
Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Cell Lines 293t Cell Line Atcc N A Hela Cell Line Atcc N A U2os Cell Line Atcc N A Rpe1 Cell Line Atcc N A U2os Ha Er Asisi Cell Line Gift, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cho human chromosome 6  (Coriell Institute for Medical Research)
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Coriell Institute for Medical Research cho human chromosome 6
Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Cho Human Chromosome 6, supplied by Coriell Institute for Medical Research, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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l b et al14 ft 293 t rex cells thermo fisher scientific r71007 experimental models  (Janvier Labs)
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Janvier Labs l b et al14 ft 293 t rex cells thermo fisher scientific r71007 experimental models
Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
L B Et Al14 Ft 293 T Rex Cells Thermo Fisher Scientific R71007 Experimental Models, supplied by Janvier Labs, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lines 293t human embryonic kidney cells atcc  (ATCC)
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ATCC cell lines 293t human embryonic kidney cells atcc
Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Cell Lines 293t Human Embryonic Kidney Cells Atcc, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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crl 11268 rrid cvcl 1926 experimental models  (ATCC)
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Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Crl 11268 Rrid Cvcl 1926 Experimental Models, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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experimental models hek293t 17 sf atcc acs 4500  (ATCC)
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Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Experimental Models Hek293t 17 Sf Atcc Acs 4500, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lines hela cells atcc ccl 2 lenti x 293t cells takara 632180 hela  (ATCC)
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ATCC cell lines hela cells atcc ccl 2 lenti x 293t cells takara 632180 hela
Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI <t>U2OS</t> cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.
Cell Lines Hela Cells Atcc Ccl 2 Lenti X 293t Cells Takara 632180 Hela, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lines hek293t cells atcc crl 11268 rrid cvcl 1926  (ATCC)
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ATCC cell lines hek293t cells atcc crl 11268 rrid cvcl 1926
Figure 7. PHF7-Mediated Histone Ubiquitination Attenuates the Ubiquitination of BRDT (A) Co-immunoprecipitation of BRDT with PHF7 from <t>HEK293T</t> cells. (B) In vitro pull-down assay of biotinylated nucleosome bearing H3ub and/or H4ac with GST-BRDT from E. coli using streptavidin beads. Relative ratio of pulled down GST-BRDT was indicated below immunoblot. (C) In vitro ubiquitination assay was performed with BRDT, SPOP-Cul3-Rbx1, and modified nucleosome. (D) Schematic model showing regulation of BRDT stability via PHF7-mediated H3ub in early condensing spermatids (step 12).
Cell Lines Hek293t Cells Atcc Crl 11268 Rrid Cvcl 1926, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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human embryonic kidney 293 cells  (ATCC)
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ATCC human embryonic kidney 293 cells
Figure 7. PHF7-Mediated Histone Ubiquitination Attenuates the Ubiquitination of BRDT (A) Co-immunoprecipitation of BRDT with PHF7 from <t>HEK293T</t> cells. (B) In vitro pull-down assay of biotinylated nucleosome bearing H3ub and/or H4ac with GST-BRDT from E. coli using streptavidin beads. Relative ratio of pulled down GST-BRDT was indicated below immunoblot. (C) In vitro ubiquitination assay was performed with BRDT, SPOP-Cul3-Rbx1, and modified nucleosome. (D) Schematic model showing regulation of BRDT stability via PHF7-mediated H3ub in early condensing spermatids (step 12).
Human Embryonic Kidney 293 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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cell lines raw 264 7 laboratory stock n a bmdms  (Proteintech)
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Figure 7. PHF7-Mediated Histone Ubiquitination Attenuates the Ubiquitination of BRDT (A) Co-immunoprecipitation of BRDT with PHF7 from <t>HEK293T</t> cells. (B) In vitro pull-down assay of biotinylated nucleosome bearing H3ub and/or H4ac with GST-BRDT from E. coli using streptavidin beads. Relative ratio of pulled down GST-BRDT was indicated below immunoblot. (C) In vitro ubiquitination assay was performed with BRDT, SPOP-Cul3-Rbx1, and modified nucleosome. (D) Schematic model showing regulation of BRDT stability via PHF7-mediated H3ub in early condensing spermatids (step 12).
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Image Search Results


Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI U2OS cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.

Journal: Cell reports

Article Title: NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step.

doi: 10.1016/j.celrep.2022.111600

Figure Lengend Snippet: Figure 4. NEIL3 is required for DSB end resection (A–D) Representative images and statistical analysis to show (A, B) RPA2 foci and (C, D) BrdU foci formation 24 h after 100 ng/mL MMC treatment in WT and NEIL3/ HeLa cells. Scale bar, 10 mm. A total of 100 cells from three independent experiments were analyzed for each group. ***p < 0.001, ****p < 0.0001, two- tailed Student’s t test. (E) The schematic of in vitro DSB end resection assay in ER-AsiSI U2OS cells. See STAR Methods for details. (F) Quantification and statistical analysis of the ssDNA level after depletion of NEIL3, CtIP, and BRCA1, respectively, in ER-AsiSI U2OS cells. Data are shown as mean ± SEM compiled from three independent experiments. **p < 0.01, ***p < 0.001, two-tailed Student’s t test. (G) The efficiency of knockdown of individual proteins was examined by western blot.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 4-Hydroxytamoxifen Sigma-Aldrich Cat# H7904 Ethidium Bromide Sigma-Aldrich Cat# E8751 Doxycycline Selleck Chemicals Cat# S5159 Hoechst 33,342 Beyotime Technology Cat# C1029 Doxycycline Selleck Chemicals Cat# S5159 Benzonase Sigma-Aldrich Cat# E8263 MG-132 Selleck Chemicals Cat# S2619 Olaparib (AZD2281) Selleck Chemicals Cat# S1060 Critical commercial assays CellTiter-Glo Luminescent Viability Assay Promega Cat# G7570 Subcellular Protein Fractionation Kit Life Technologies Cat# 78840 CometAssay Single Cell Gel Electrophoresis Assay Trevigen Cat# 4250-050-K Hieff Clone Plus One Step Cloning Kit Yeasen Cat# 10911ES20 Immunoprecipitation (IP/CoIP) Kit Absin Cat# abs955 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 PierceTM anti-HA magnetic beads Thermo Fisher Scientific Cat# 88836 PierceTM anti-c-Myc magnetic beads Thermo Fisher Scientific Cat# 88842 GFP-Trap magnetic beads Chromotek Cat# gtma-20 Experimental models: Cell lines 293T Cell Line ATCC N/A HeLa Cell Line ATCC N/A U2OS Cell Line ATCC N/A RPE1 Cell Line ATCC N/A U2OS-HA-ER-AsiSI Cell Line Gift from Dr. Gaëlle Legube N/A U2OS-FANCD2 / Cell Line Li et al., 2020 N/A HeLa-FANCA / Cell Line Li et al., 2020 N/A HeLa-NEIL3 / Cell Line Li et al., 2020 N/A HeLa-NEIL3-WT-Dox Cell line This paper N/A HeLa-NEIL3-del N term-Dox Cell line This paper N/A HeLa-NEIL3-del C term-Dox Cell line This paper N/A HeLa-NEIL3-del GRF2 -Dox Cell line This paper N/A HeLa-NEIL3-del GRF 1-2-Dox Cell line This paper N/A Oligonucleotides siRNA targeting sequence: negative Control: GGGTATCGACGATTACAAA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #1: GGGTGGATCATGTTATGGA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #2: GCTAATGGATCAGAACGTA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #50UTR: TGAGTTGCACAGCGGTATT This paper N/A siRNA targeting sequence: FANCA: TTTTTCCCTCTTGACCCTT Li et al., 2020 N/A siRNA targeting sequence: FANCD2: GGCTCAGGATTCTAATGTA Li et al., 2020 N/A siRNA targeting sequence: NBS1: CCAACTAAATTGCCAAGTA Sangon Biotech N/A (Continued on next page) e2 Cell Reports 41, 111600, November 8, 2022

Techniques: Two Tailed Test, In Vitro, Resection Assay, Knockdown, Western Blot

Figure 6. NEIL3 acts upstream of CtIP and MRN complex to promote their recruitment to DSBs (A) Western blots to validate the expression of GFP-tagged constructs of NEIL3, CtIP, and NBS1, respectively. (B) Representative time-lapse view to show the recruitment of indicated proteins to laser irradiation damaged sites in U2OS cells. Scale bar, 5 mm. (C) Normalized fluorescent intensity curve of indicated proteins at DNA damage sites. (legend continued on next page)

Journal: Cell reports

Article Title: NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step.

doi: 10.1016/j.celrep.2022.111600

Figure Lengend Snippet: Figure 6. NEIL3 acts upstream of CtIP and MRN complex to promote their recruitment to DSBs (A) Western blots to validate the expression of GFP-tagged constructs of NEIL3, CtIP, and NBS1, respectively. (B) Representative time-lapse view to show the recruitment of indicated proteins to laser irradiation damaged sites in U2OS cells. Scale bar, 5 mm. (C) Normalized fluorescent intensity curve of indicated proteins at DNA damage sites. (legend continued on next page)

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER 4-Hydroxytamoxifen Sigma-Aldrich Cat# H7904 Ethidium Bromide Sigma-Aldrich Cat# E8751 Doxycycline Selleck Chemicals Cat# S5159 Hoechst 33,342 Beyotime Technology Cat# C1029 Doxycycline Selleck Chemicals Cat# S5159 Benzonase Sigma-Aldrich Cat# E8263 MG-132 Selleck Chemicals Cat# S2619 Olaparib (AZD2281) Selleck Chemicals Cat# S1060 Critical commercial assays CellTiter-Glo Luminescent Viability Assay Promega Cat# G7570 Subcellular Protein Fractionation Kit Life Technologies Cat# 78840 CometAssay Single Cell Gel Electrophoresis Assay Trevigen Cat# 4250-050-K Hieff Clone Plus One Step Cloning Kit Yeasen Cat# 10911ES20 Immunoprecipitation (IP/CoIP) Kit Absin Cat# abs955 TIANamp Genomic DNA Kit TIANGEN Cat# DP304 PierceTM anti-HA magnetic beads Thermo Fisher Scientific Cat# 88836 PierceTM anti-c-Myc magnetic beads Thermo Fisher Scientific Cat# 88842 GFP-Trap magnetic beads Chromotek Cat# gtma-20 Experimental models: Cell lines 293T Cell Line ATCC N/A HeLa Cell Line ATCC N/A U2OS Cell Line ATCC N/A RPE1 Cell Line ATCC N/A U2OS-HA-ER-AsiSI Cell Line Gift from Dr. Gaëlle Legube N/A U2OS-FANCD2 / Cell Line Li et al., 2020 N/A HeLa-FANCA / Cell Line Li et al., 2020 N/A HeLa-NEIL3 / Cell Line Li et al., 2020 N/A HeLa-NEIL3-WT-Dox Cell line This paper N/A HeLa-NEIL3-del N term-Dox Cell line This paper N/A HeLa-NEIL3-del C term-Dox Cell line This paper N/A HeLa-NEIL3-del GRF2 -Dox Cell line This paper N/A HeLa-NEIL3-del GRF 1-2-Dox Cell line This paper N/A Oligonucleotides siRNA targeting sequence: negative Control: GGGTATCGACGATTACAAA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #1: GGGTGGATCATGTTATGGA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #2: GCTAATGGATCAGAACGTA Li et al., 2020 N/A siRNA targeting sequence: NEIL3 #50UTR: TGAGTTGCACAGCGGTATT This paper N/A siRNA targeting sequence: FANCA: TTTTTCCCTCTTGACCCTT Li et al., 2020 N/A siRNA targeting sequence: FANCD2: GGCTCAGGATTCTAATGTA Li et al., 2020 N/A siRNA targeting sequence: NBS1: CCAACTAAATTGCCAAGTA Sangon Biotech N/A (Continued on next page) e2 Cell Reports 41, 111600, November 8, 2022

Techniques: Western Blot, Expressing, Construct, Irradiation

Figure 7. PHF7-Mediated Histone Ubiquitination Attenuates the Ubiquitination of BRDT (A) Co-immunoprecipitation of BRDT with PHF7 from HEK293T cells. (B) In vitro pull-down assay of biotinylated nucleosome bearing H3ub and/or H4ac with GST-BRDT from E. coli using streptavidin beads. Relative ratio of pulled down GST-BRDT was indicated below immunoblot. (C) In vitro ubiquitination assay was performed with BRDT, SPOP-Cul3-Rbx1, and modified nucleosome. (D) Schematic model showing regulation of BRDT stability via PHF7-mediated H3ub in early condensing spermatids (step 12).

Journal: Cell reports

Article Title: PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis.

doi: 10.1016/j.celrep.2020.107950

Figure Lengend Snippet: Figure 7. PHF7-Mediated Histone Ubiquitination Attenuates the Ubiquitination of BRDT (A) Co-immunoprecipitation of BRDT with PHF7 from HEK293T cells. (B) In vitro pull-down assay of biotinylated nucleosome bearing H3ub and/or H4ac with GST-BRDT from E. coli using streptavidin beads. Relative ratio of pulled down GST-BRDT was indicated below immunoblot. (C) In vitro ubiquitination assay was performed with BRDT, SPOP-Cul3-Rbx1, and modified nucleosome. (D) Schematic model showing regulation of BRDT stability via PHF7-mediated H3ub in early condensing spermatids (step 12).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Rabbit monoclonal anti-ubiquitin (FK2) StressMarq Biosciences SMC-550D; RRID:AB_2728859 Rabbit polyclonal anti-BRD4 Bethyl Laboratories A301-985A; RRID:AB_1576498 Mouse monoclonal anti-HA Covance MMS-101R; RRID:AB_291263 Rabbit polyclonal anti-Tubulin AbFrontier LF-PA0146A; RRID:N/A Mouse monoclonal anti-Xpress Invitrogen R910-25; RRID:AB_2556552 Bacterial and Virus Strains DH5-a Escherichia coli Enzynomics CP010 Rossetta Escherichia coli Novagen 70954-3CN Chemicals, Peptides, and Recombinant Proteins TOPreal qPCR 2X PreMIX Enzynomics RT500 MG132 A.G. Scientific M-1157 DMSO (Vehicle) Sigma-Aldrich D2650 3X Flag peptide Sigma-Aldrich F4799 cOmplete Protease Inhibitor Cocktail Roche Cat#11697498001 TALON Metal Affinity Resin Clontech Cat#635501 Streptavidin agarose Thermo Fisher Cat#20353 Glutathion Sepharose High Performance GE healthcare Cat#17-5279-01 UbcH5a BostonBiochem E2-616 UbcH5b BostonBiochem E2-622 UbcH5c BostonBiochem E2-627 UbcH13/Ube1a BostonBiochem E2-664 Ubiquitin BostonBiochem U-100H Biotinylated nucleosome Epi Cypher Cat#16-0006 Biotinylated H4ac nucleosome Epi Cypher Cat#16-0313 His-UBE1 protein (His-tagged purification) This paper N/A GST-PHF7 protein (GST purification) This paper N/A GST-BRDT protein (GST purification) This paper N/A His-SPOP protein (His-tagged purification) This paper N/A Flag-Cul3 / HA-Rbx1 protein (Flag-tagged purification) This paper N/A Critical Commercial Assays PTMSCan Ubiquitin Remnant Motif (K-ε-GG) Kit Cell Signaling Technology Cat#14482 Orbitrap Fusion Lumos mass spectrometer Thermo Fisher IQLAAEGAAPFADBMBHQ Chromium Single Cell 30 Library & Gel Bead Kit v2 10X Genomics PN-120237 Chromium Single Cell A Chip Kit 10X Genomics PN-1000009 Chromium i7 Multiplex Kit 10X Genomics PN-120262 NextSeq 500/550 Mid-Output v2.5 Kit (150 cycles) Illumina Cat#20024904 NovaSeq 6000 S4 Reagent Kit (300 cycles) Illumina Cat#20012866 Deposited Data Raw and analyzed data This paper GEO: GSE136752 Raw data Mendeleys https://doi.org/10.17632/7h6grmkwhg.1 Experimental Models: Cell Lines HEK293T cells ATCC CRL-11268 RRID:CVCL_1926 (Continued on next page) e2 Cell Reports 32, 107950, July 28, 2020

Techniques: Ubiquitin Proteomics, Immunoprecipitation, In Vitro, Pull Down Assay, Western Blot