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Anti ubiquitin

Manufactured by Santa Cruz Biotechnology
Sourced in United States, Japan, United Kingdom

Anti-ubiquitin is a lab equipment product manufactured by Santa Cruz Biotechnology. It is used to detect and analyze ubiquitin, a small regulatory protein found in eukaryotic cells. Anti-ubiquitin can be utilized in various research applications, such as Western blotting, immunoprecipitation, and immunohistochemistry, to study the role of ubiquitin in cellular processes.

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129 protocols using anti ubiquitin

1

Quantification of Huntingtin and Ubiquitin

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Striatal tissue was processed as described previously (Ochaba et al., 2016 (link)). Antibodies: Anti-HTT (Millipore, #MAB5492; RRID: AB_347723) and anti-ubiquitin (Santa Cruz Biotechnology, #sc-8017; RRID: AB_628423). Quantification of bands was performed using software from the NIH program ImageJ and densitometry application.
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2

Antibody Validation for Western Blot

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Anti-HA monoclonal and polyclonal antibodies were purchased from Covance and GenScript, respectively. Anti-SUMO2 was from Life Technologies, anti-ubiquitin was from Santa Cruz Biotechnology, and anti-GAPDH antibody was from Millipore.
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3

Immunoblotting for Autophagy Markers

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The primary antibodies used were the anti‐Ubiquitin (Santa Cruz Biotechnology, Inc., sc‐8017), anti‐foxo (COSMO BIO CO, CAC‐THU‐A‐DFOXO), anti‐26S proteasome α (Santa Cruz Biotechnology, Inc., sc‐65,755), anti‐26S Proteasome p54 (Rpn10) (Santa Cruz Biotechnology, Inc., sc‐65,746), anti‐pAMPK (Cell Signaling Technology, #2535), anti‐GABARAP (Atg8a) (Cell Signaling Technology, #13733), anti‐Lamp1 (Abcam, ab30687), anti‐ATP5A (Abcam, ab14748), anti‐Actin (Cell Signaling Technology, #8457), and anti‐Gapdh (Sigma‐Aldrich, G9545). The anti‐ref(2)P/p62 antibody was kindly donated from Prof. G. Juhász. The secondary antibodies Peroxidase AffiniPure Donkey anti‐Mouse IgG (715‐035‐150) and Peroxidase AffiniPure Donkey anti‐Rabbit IgG (711‐035‐152) were purchased from Jackson ImmunoResearch Laboratories, Inc. The anti‐Rabbit‐IgG Alexa Fluor 647 (711‐605‐152), anti‐Rabbit‐IgG Alexa Fluor 488 (111‐545‐003), anti‐Mouse‐IgG Rhodamine (TRITC) AffiniPure (715‐025‐151), anti‐Mouse‐IgG Alexa Fluor 488 (115‐545‐003), and anti‐Mouse IgG DyLight™ 405 (715‐475‐151) antibodies were also from Jackson ImmunoResearch Laboratories, Inc. Ponceau S solution (6226–79) was from Sigma‐Aldrich.
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4

In Vitro Ubiquitination Assay

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Recombinant proteins were expressed in E. coli BL21(DE3) and purified by affinity chromatography using amylose resin (New England Biolabs). Recombinant His‐UBA1 and His‐UBC8 were purified using Ni‐Ted resin (Macherey‐Nagel). Purified proteins were used for in vitro ubiquitination assays. Each reaction of 30 ml final volume contained 25 mM Tris–HCl, pH 7.5, 5 mM MgCl2, 50 mM KCl, 2 mM ATP, 0.6 mM DTT, 2 μg ubiquitin, 200 ng E1 His‐ AtUBA1, 1.2 μg E2 His‐AtUBC8, 2 μg of E3s, and 0.3 µg of MBP‐AtSH3P2. Samples were incubated for 1 h at 30°C, and the reaction was stopped by adding SDS loading buffer and incubated for 10 min at 68°C. Samples were separated by SDS–PAGE electrophoresis using 4–15% Mini‐PROTEAN® TGX™ Precast Protein Gels (BioRad) followed by detection of the ubiquitinated substrate by immunoblotting using anti‐MBP (New England Biolabs), anti‐GST and anti‐ubiquitin (Santa Cruz Biotechnology) antibodies.
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5

Western Blotting for Protein Analysis

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Western blotting was performed as described previously with some modifications18 (link). Briefly, cells were lysed with RIPA buffer (Wako) containing a protease inhibitor mixture (Roche Diagnostics, Basel, Switzerland). Equal amounts of protein (10 μg) were electrophoresed using 10% sodium dodecyl sulphate–polyacrylamide gels. Proteins were transferred to polyvinylidene difluoride membranes, washed with Tris-buffered saline containing 0.05% Triton X-100, and incubated with BlockingOne solution (Nacalai Tesque, Kyoto, Japan) for 60 min. Anti-p62 (1:1,000; MBL) and anti-ubiquitin (1:1,000; Santa Cruz Biotechnology) antibodies were used as the primary antibodies. Horseradish peroxidase-conjugated anti-rabbit or anti-mouse IgG antibodies (Promega, Madison, WI, USA) were used as the secondary antibodies. As a control, β-actin was detected with anti-β-actin pAb-HRP-DirecT (1:2000; MBL). Blots were visualized using Chemi-Lumi One L (Nacalai Tesque). Stained membranes were scanned with ImageQuant LAS 4000 (GE Healthcare, Menlo Park, California, USA). Quantification was performed using ImageJ software (https://imagej.nih.gov/ij/).
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6

Cisplatin-Induced Cell Viability Assay

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The reagents used in this study include the following: cisplatin (Sigma‐Aldrich, St. Louis, MO), 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) (Sigma‐Aldrich) and ViaFect™ transfection reagent (Promega, Madison, MI). Antibodies used in this study include anti‐p62 (Abcam, Cambridge, MA, USA), anti‐LC3 (Abcam), anti‐Caspase 8 (Proteintech, Chicago, IL), anti‐actin (Proteintech) and anti‐ubiquitin (Santa Cruz, CA).
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7

Comprehensive Antibody Panel for Cell Signaling Analysis

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Catalog numbers and dilution fold are listed in parentheses. The following antibodies were purchased from Cell Signaling Technology: Anti-Bak (3792; 1:1000), anti-Bax (2772; 1:1000), anti-Bcl-2 (2870; 1:1000), anti-Bcl-xL (2764; 1:500), anti-CHK1 (2360; 1:1000), anti-phospho-CHK1 (S345; 2348; 1:1000), anti-cleaved caspase-3 (9661; 1:1000), anti-cleaved caspase-7 (9491; 1:1000), anti-cleaved caspase-8 (9496; 1:500), anti-cleaved caspase-9 (9501; 1:1000), anti-cytochrome c (4272; 1:500), anti-H2A.X (7631; 1:1000), anti-phospho-H2A.X (S139; 9718; 1:1000), anti-p53 (2524; 1:1000), anti-p53 (2527; 1:1000), anti-phospho-p53 (S6; 9285; 1:1000), anti-phospho-p53 (S15; 9284; 1:1000), anti-p21 (2946; 1:1000), and anti-voltage-dependent anion channel (VDAC; 4866; 1:1000). The following antibodies were purchased from Santa Cruz Biotechnology: Anti-CD95 (1023; 1:500), anti-cyclophilin 40, also known as anti-CYPD (137157; 1:400), anti-His tag (803; 1:500), anti-lamin A (20680; 1:1000), anti-MDM2 (965; 1:500), and anti-ubiquitin (8017; 1:200). Anti-PEPD (Ab86507; 1:500) and anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH; MAB374; 1:5000) were purchased from Abcam and EMD Millipore, respectively. Anti-mouse IgG-horseradish peroxidase (IgG-HRP; NA931V; 1:4000–5000) and anti-rabbit IgG-HRP (NA934V; 1:5000) were purchased from GE Healthcare.
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8

RIPK1-Mediated Necroptosis Signaling

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Stimulated T cells were incubated in lysis buffer. For signaling complex analyses, cell lysates were pre-cleared with Protein G beads prior to immunoprecipitation with anti-RIPK1 antibody. Antibodies and reagents used for immunoprecipitation and immunoblotting studies included: anti-RIPK1, anti-Bim, anti-Bclx, (BD Biosciences), nec1, anti-Bcl2, β-actin (Merck chemicals), anti-RIPK3 (ProSci Incorporated), anti-ubiquitin, anti-Bax, anti-RIPK3 (Santa Cruz Biotechnology), anti-RIPK1, anti-A20 (Cell signaling Technology), QVD, ZVAD (Enzo Life Science).
Signaling studies in MEFs were performed as described19 (link). RIPK1 immunoprecipitations were performed using anti-RIPK1 (Cell Signaling) and Dynabeads M270 Epoxy (Invitrogen). K63-ubiquitin immunoprecipitations were performed using anti-K63 (Millipore) and Dynabead Protein A (Invitrogen). Studies of RIPK3 mutants in A20−/−Ripk3−/− MEFs were performed by generating RIPK3 lysine mutants, introducing mutant RIPK3-encoding cDNAs into GFP expressing lentiviral constructs, and infecting A20−/−Ripk3−/− MEFs with these viruses. Productively infected cells were FACS-sorted to obtain pure populations of RIPK3-expressing cells prior to being tested in necroptosis assays. Cell survival of MEFs was quantitated using the CellTiter-Glo Luminescent Cell Viability Assay per manufacturer’s instructions (Promega).
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9

Antibody-based Protein Analysis Workflow

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The following commercial antibodies were used: HRP-conjugated anti-mouse I gG (NA931), and anti-rabbit IgG (NA941) from GE Healthcare (Pittsburgh, PA), HRP-conjugated anti-rat IgG (AP136P), and anti-ubiquitin Lys63 specific (05–1313) from EMD Millipore (Billerica, MA), anti-TAK1 (sc-7162), anti-IKKα/β.(sc-7607), anti-IκBα.(sc-371), anti-JNK (sc-7345), anti-p38 (sc-728), anti-Tab1 (sc-6052), anti-β-actin (sc-69879), and anti-ubiquitin (sc-8017) from Santa Cruz (Dallas, Texas), anti-p-TAK1 (4531), anti-p-IKKα/β.(2078), anti-p-IκBα.(9246),.anti-p-JNK (9251), and anti-p-p38 (9211) from Cell Signaling (Beverly, MA), anti-HA (11867423001) from Roche (Indianapolis, IN), and anti-Flag (M2, F3165) from Sigma (St. Louis, MO). LPS, TNF, IL-1β,.5Z-7-oxozeaenol, dithiothreitol (DTT), iodoacetamide (IAA), and formic acid were obtained from Sigma. Acetonitrile (ACN) and ammonium bicarbonate were obtained from Aldrich (Milwaukee, WI). Sequencing-grade trypsin was purchased from Promega (Madison, WI).
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10

Antibody Panel for Protein Analysis

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Antibodies used in the study were as follows: anti-Flag (F3165/F7425, Sigma), anti-Myc (9B11/71D10, Cell Signaling Technology (CST)), anti-HA (16B12, Biolegend and H6908, Sigma), anti-TRAF2 (sc-136999, Santa Cruz), anti-Rab5 (sc-46692, Santa Cruz), anti-Rab7 (sc-376362, Santa Cruz), anti-Sprouty 2 (sc-100862, Santa Cruz/ab85670, Abcam), anti-EGFR (sc-373746, Santa Cruz), anti-p-Tyr (9411, CST), anti-p-Ser/Thr (ab9344, Abcam and 05-368, Sigma), anti-Ser (sc-81514, Santa Cruz), anti-Thr (sc-5267, Santa Cruz), anti-Ubiquitin (sc-8017, Santa Cruz), anti-β-Actin (AC026, Abclonal), anti-GFP (AE011, Abclonal), anti-glutathione S-transferase (GST) (2622 S, CST), anti-V5 (R960-25, Thermo Fisher and 30801ES10, Yeasen), anti-Mouse/Rabbit IgG-peroxidase secondary antibody (A0545/A9044, Sigma), anti-Mouse IgG (light chain specific)-peroxidase secondary antibody (115-005-174, Jackson), and anti-DYRK1A polyclonal antibody has been previously described [30 (link)].
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