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human embryo kidney hek293 cells  (ATCC)


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    Structured Review

    ATCC human embryo kidney hek293 cells
    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
    Human Embryo Kidney Hek293 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 27813 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human embryo kidney hek293 cells/product/ATCC
    Average 99 stars, based on 27813 article reviews
    human embryo kidney hek293 cells - by Bioz Stars, 2026-02
    99/100 stars

    Images

    1) Product Images from "Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation"

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    Journal: bioRxiv

    doi: 10.1101/2025.05.27.656291

    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
    Figure Legend Snippet: (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Techniques Used: Ubiquitin Proteomics, Knock-In, Lysis, SDS Page, Control

    A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.
    Figure Legend Snippet: A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Techniques Used: Knock-In

    (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.
    Figure Legend Snippet: (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Techniques Used: Knock-In

    (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).
    Figure Legend Snippet: (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Techniques Used: Lysis, SDS Page, Control

    A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.
    Figure Legend Snippet: A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Techniques Used: Control



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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
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    Image Search Results


    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Ubiquitin Proteomics, Knock-In, Lysis, SDS Page, Control

    A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Knock-In

    (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Knock-In

    (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Lysis, SDS Page, Control

    A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Control