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18 protocols using sumo2 3

1

Antibodies for SARS-CoV-2 Interactome Analysis

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The antibodies used in this study include: rabbit monoclonal anti-SUMO-2/3 (Cell Signaling, 4971; 1:1000 for IB), mouse monoclonal anti-SARS2-NP (ABclonal, A20142; 1:2000 for IB, 1:200 for PLA), rabbit monoclonal anti-SARS2-NP (Abcam, ab271180; 1:200 for IP), rabbit monoclonal anti-ACE2 (Abcam, ab108252; 1:1000 for IB), rabbit monoclonal anti-TRIM28 (ABclonal, A19568; 1:2000 for IB, 1:100 for IP/PLA), mouse monoclonal anti-Flag (M2) (Sigma, F3165; 1:2000 for IB, 1:200 for PLA), rabbit polyclonal anti-HA (Y11) (Santa Cruz, sc-805; 1:2000 for IB, 1:200 for PLA), rabbit monoclonal anti-HA (12CA5) (Santa Cruz, sc-57592; 1:2000 for IB), rabbit polyclonal anti-Myc (A-14) (Santa Cruz, sc-789; 1:2000 for IB, 1:200 for PLA), mouse monoclonal anti-Myc (9E10) (Santa Cruz, sc-40; 1:2000 for IB, 1:200 for IP), mouse monoclonal anti-His (H-3) (Santa Cruz, sc-8036; 1:2000 for IB), mouse monoclonal anti-β-actin (Sigma, A1978; 1:2000 for IB), rabbit monoclonal anti-β-tubulin (Cell Signaling, 2146; 1:2000 for IB), rabbit polyclonal anti-VSV-G (ABGENT, AP1016a; 1:1000 for IB), and HRP-conjugated secondary antibodies (Cell Signaling, 7076 (anti-mouse IgG) or 7074 (anti-rabbit IgG); 1:10,000 for IB).
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2

Western Blotting for SUMO Pathway Proteins

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Whole cell lysates or tumor extracts were fractionated by non-reducing SDS–PAGE and immunoblotted with antibodies to SAE2 (for cell lysates: polyclonal rabbit antibody generated by Millennium, antibody was validated on cell lines overexpressing SAE2; for tumor extract: epitomics T0083, rabbit), Ubc9 (epitomics 2426–1, rabbit), SUMO1 (epitomics S2227, rabbit), SUMO2/3 (Cell Signaling Technologies 4971, rabbit), RanGAP1 (abcam ab2081, goat), p53 (Cell signaling Technologies 9282, rabbit), p21 (Santa Cruz sc-397, rabbit), cleaved caspase 3 (Cell Signaling Technologies 9661, rabbit), TopoIIα (Cell signaling Technologies 12286, rabbit). All primary antibodies were used 1:1000 dilution. Secondary HRP-labeled antibodies to goat IgG (Millipore, 1:2000 dilution) were used for RanGAP1 primary antibody and blots were developed with ECL reagent (Amersham). For other primary antibodies, the secondary antibody was Alexa-680-labelled antibody to rabbit/mouse IgG (Invitrogen, 1:5000 dilution) and the blots were imaged using the Li-Cor Odyssey Infrared Imaging system. Tubulin (Sigma) was blotted for a loading control.
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3

Western Blot Analysis of Protein Modifications

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Cells from different groups were collected, lysed in RIPA Lysis Buffer (Beyotime Biotechnology), and centrifuged at 12,000 g for 10 min at 4°C. The supernatants were collected, and the cellular protein concentrations were determined with a BCA protein assay kit. Protein samples were denatured at 95°C for 5 min, separated by SDS-PAGE, and electrophoretically transferred to polyvinylidene difluoride membranes (Millipore). The blots were incubated with primary antibodies against SUMO1 (1:1,000, rabbit anti-human, Cell Signal Technology), SUMO2/3 (1:1,000, rabbit anti-human, Cell Signal Technology), p53 (1:1,000, mouse anti-human, Cell Signal Technology), cyclin D1 (1:200, rabbit anti-human, Abcam), LC3 (1:1,000, rabbit anti-human, Cell Signal Technology), p62 (1:1,000, rabbit anti-human, Proteintech), or β-actin (1:1,000, mouse anti-human, Abcam) overnight at 4°C. Subsequently, the blots were incubated with an HRP-conjugated secondary antibody (goat anti-rabbit IgG H&L and goat anti-mouse IgG H&L) at room temperature for 1 h, and then, enhanced chemiluminescence was used to visualize the bands.
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4

Antibody Dilutions for Western Blot

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Antibodies used in this study are listed below where respective dilutions are mentioned in the parentheses:
α-actinin, mouse monoclonal, Sigma-Aldrich (1:400); SUMO2/3, rabbit monoclonal, Cell signaling (1:1000); SUMO2 + 3, mouse monoclonal, Abcam (1:1000); Calcineurin A, mouse monoclonal, BD Bioscience (1:250); GAPDH, mouse monoclonal, Sigma-Aldrich (1:20,000); Histone H3, rabbit polyclonal, Cell-signaling (1:1000); α-Tubulin, mouse monoclonal, Sigma-Aldrich (1:8000); Ubiquitin, mouse monoclonal, Millipore (1:1000); STAT1, rabbit monoclonal, Cell signaling (1:1000); p-STAT1, rabbit monoclonal, Cell signaling (1:1000); STAT3, rabbit monoclonal, Cell signaling (1:1000); p-STAT3, rabbit monoclonal, Cell signaling (1:1000); F4/80, rat monoclonal, Dianova (1:500); HA, mouse monoclonal, Sigma-Aldrich (1:20,000); HectD3, rabbit polyclonal, Mybiosource (1:1000); V5, mouse monoclonal, Biozol (1:1000).
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5

Immunoblot Analysis of Cellular Proteins

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Lysate, IP or His‐PD Samples were resolved by SDS–PAGE (10–15% gels) and transferred to Immobilon‐P membranes (Millipore Inc.), which were then immunoblotted with the following antibodies against: β‐actin (Sigma), CHIP (Cell Signaling), Drp1 (Cell Signaling), Fis1 (Proteintech), Flag (Proteintech), FTH1 (Cell Signaling), GAPDH (Santa Cruz biotechnology), GST (GE Healthcare), LC3 (Cell Signaling), p62 (Cell Signaling), SENP3 (Cell Signaling), SENP5 (Proteintech), SUMO‐1 (Santa Cruz biotechnology), SUMO‐2/3 (Cell Signaling; MBL) or Tom20 (Santa Cruz biotechnology). Immune complexes were detected using either HRP‐conjugated secondary antibodies (Sigma) followed by enhanced chemiluminescence (GE Healthcare) or using fluorescent secondary antibodies (LI‐COR).
Each immunoblot presented is representative of at least three experiments carried out using different cell populations.
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6

Cloning and Characterization of Aim2 and Ube2i

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Plasmids of mouse Aim2 and Ube2i were cloned from cDNA of bone marrow derived macrophages (BMDMs), ligated to pcDNA4.0. Sumo1, sumo2 and sumo3 plasmids were kindly provided by Dr. Jinke Cheng (Shanghai Jiao Tong University). Blots were stained with anti-FLAG (Sigma), anti-V5 (InvivoGen), anti-HA (Santa Cruz), anti-sumo1, -sumo2/3, -Ube2i, -Aim2, -Stat1, -P-Stat1, and -GAPDH antibodies (Cell Signaling Technology).
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7

VSMC Protein Immunoblotting Assay

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Primary VSMCs were homogenized and lysed in RIPA buffer supplemented with protease inhibitor tablets (Roche). Protein was separated (10 μg, for each sample) on gradient (4–12%) SDS-PAGE, followed by semi-dry transfer onto PVDF membranes (Millipore, Bedford, MA). Membranes were immunoblotted with primary antibody and the appropriate horseradish peroxidase-conjugated secondary antibody (Bio-Rad). Immunoblots were analyzed by enhanced chemiluminescence technique (Thermo Fisher). Primary antibodies to IRE1α, TG2, GAPDH, SUMO1, SUMO2/3, HA, and K48 ubiquitin were from Cell Signaling Technology (Beverly, MA).
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8

Quantification of SUMO Pathway Proteins

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Cells were lysed directly into 1x Laemmli sample buffer, collected in eppendorfs and heated to 95 °C for 10 min prior to SDS-PAGE. Western blots were immunoblotted with the following antibodies: SUMO1 (Cell Signaling Technology, 1:1000), SUMO2/3 (Cell Signaling Technology, 1:1000), SENP3 (Cell Signaling Technology, 1:1000), Ubc9 (Cell Signaling Technology, 1:1000), PIAS1/2 (Abcam, 1:1000), UBA2 (Santa Cruz Biotechnology, 1:500), Drp1 (BD Biosciences, 1:2000), Mff (Santa Cruz Biotechnology, 1:500), Fis1 (ProteinTech, 1:1000), Mfn2 (Cell Signaling Technology, 1:2000), OPA1 (Abcam, 1:1000), AMPKα (Cell Signaling Technology, 1:1000), p-AMPKα (Cell Signaling Technology, 1:1000) and cleaved caspase-3 (Cell Signaling Technology, 1:1000). Horseradish peroxidase-conjugated anti-mouse and anti-rabbit IgG (Sigma, 1:10000) were used as secondary antibodies and GAPDH (Abcam, 1:20000) was used as loading control. Each immunoblot is representative of at least three experiments carried out using different cell populations and analysed using ImageJ software (NIH, USA).
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9

Western Blot Analysis of Cellular Proteins

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Transfected cells were washed with PBS and lysed in RIPA buffer containing protease and phosphatase inhibitor cocktails. The supernatant was collected and preserved at –80 °C. Protein samples were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), transferred to polyvinylidene fluoride (PVDF) membranes, and incubated with 5% skim milk for 1 h. The membranes were incubated overnight at 4 °C with the following specific primary antibodies: human DAXX (diluted 1:200), SUMO-2/3 (Cell Signaling Technology (CST), Danvers, MA, USA; #4971), α-Tubulin (CST; #3873), Lamin A/C (CST; #4777), HA-Tag (CST; #3724) (diluted 1:1000), and GAPDH (diluted 1:1000, Proteintech, Chicago, USA; 60004-1-Ig). The membranes were then incubated with secondary horseradish peroxidase (HRP)-conjugated antibodies (dilution 1:5000, Cell Signaling Technology) for 2 h at 25 °C. Proteins were then detected using enhanced chemiluminescence reagent and observed using a Biorad Imaging System (Biorad). The grayscale value represents the amount of target protein and was calculated by gray scanning using ImageJ software (NIH, Bethesda, USA). All protein expression levels were evaluated relative to GAPDH expression.
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10

Quantitative Analysis of SUMOylation Patterns

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The above prepared cell lysates or immunoprecipitates were separated on 10% (vol/vol) polyacrylamide gels and transferred onto PVDF membranes. The lysates and imminoprecipitates were probed with primary antibodies, including SUMO1, SUMO2/3 (Cell Signaling, Danvers, MA, USA), SUMO-specific protease 3 (SENP3), SUMO-specific protease 7 (SENP7) and beta-actin (Santa Cruz, Delaware, California, USA), and UBC9 (Cell Signaling, Danvers, MA, USA) for quantitative Western blot analysis, respectively, to confirm that the CSE insulted HBEs underwent a change in terms of total SUMOylation levels or patterns [14 (link)]. Similarly, to verify that CYP1A1 was SUMOylated by SUMO1, the above precipitates were probed with a CYP1A1 antibody (13241–1-AP) (Proteintech Group, Inc., Wuhan, China) and the reactive bands were developed using the established techniques [17 (link)]. Briefly, the membranes were incubated with an indicated primary antibody at 4 °C overnight. After washes with TBST (0.5% Tween) five times, the membranes were probed with an appropriate HRP-conjugated secondary antibody for 1 h, and the reactive bands were visualized using the ECL reagents (Servicebio, Wuhan, China) as instructed. Quantitative analysis of relative intensity of each band was conducted using the Image J software and β-actin was used for normalization.
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