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11 protocols using ha tag

1

Molecular Cloning and Mutagenesis Protocols

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The coding regions of H2B, CBP, HDAC1, MDM2 and wild-type K-Ras (RasWT) were amplified by using PCR. These PCR products were sub-cloned into pEGFP-N1 plasmid and HA-tag (Invitrogen, Carlsbad, CA, USA). The pEGFP-K-RasG12V/T35S was mutated using pEGFP-K-RasG12V construct as a template. The siRNAs that were specific for MDM2 and HDAC1 were synthetized from GenePharma (Shanghai, China). The pEGFP-H2BK12Q was constructed using the TaKaRa MutanBEST Kit (TaKaRa, Dalian, China) based on the kit instructions.
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2

Profiling Epithelial-Mesenchymal Transition Markers

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The cervical cancer cell pellets were washed twice with PBS, lysed in RIPA buffer, and quantified by Bradford protein assay (Bio-Rad, Hercules, CA, USA; #500-0006). Firstly, 30 μg of quantified total protein lysate was loaded into each well of the gel, analyzed in 10% SDS-PAGE under reducing conditions, and then transferred to a nitrocellulose blotting membrane (PALL Corpo., Pansacola, FL, USA) followed by blocking in 5% skim milk. The membrane was stained with primary antibody as follows: HA Tag (1:2000 dilution, Invitrogen); E-cadherin (MW: 135 kDa, 1:1,000 dilution); vimentin (MW: 57 kDa; 1:1,000 dilution, Cell signaling, #3932), snai1 (MW: 29 kDa; 1:500 dilution, Cell signaling) and internal control GAPDH (MW: 37 kDa, 1:2,000 dilution, Cell signaling), prepared in 1% BSA in TBST at 4 ℃ overnight. Then the membrane was washed and incubated with secondary antibody at room temperature for 1 h. Signals were detected for 1 min using an enhanced chemiluminescence solution (Advansta, Menlo Park, CA, USA) and a ChemiDoc XRS imaging system (Bio-Rad Laboratories Inc., Heracles, CA, USA). Quantification was performed using ImageJ 2.0 software (Fiji), all experiments were performed in duplicate.
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3

CK2 Protein Interaction Analysis

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HEK293A cells were transfected with ps14-Mock 35 (link), an rTA expression construct to later induce CK2 expression, utilizing Lipofectamine 3000 (Invitrogen; L3000008). 16 hours later cells were sorted for GFP+ cells and plated. After 32 hours cells were transfected with an equimolar mix of CK2α/β plasmid (Addgene; #27093) and the relevant MCAM tail variant. Following another 16-hour incubation cells were treated with DOX. After 24 hours cells were washed with PBS+EDTA, collected, resuspended in IP Lysis buffer (Pierce; 87787) with the Halt Protease & Phosphatase inhibitor cocktail (Thermo Fisher Scientific, #78440) and allowed to rotate at 4°C for 1 hour. 10ug of rabbit anti-FLAG antibody (Invitrogen; #740001) was added and allowed to incubate overnight at 4°C. The following day, magnetic Protein A/G beads (Pierce; 88802) were added according to the manufacturer’s instructions and samples were rotated at 4°C for 1 hour prior to magnetic separation, washing the A/G beads, and sample preparation for western blot analysis. Westerns were probed for HA-Tag (Invitrogen; #26183) and Myc (Invitrogen; #MA1–980) for CK2 α and β respectively.
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4

Immunoprecipitation and Western Blot

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S2 cells were transfected with the indicated plasmids and lysed after 48 hours, whereas third instar larval imaginal discs were dissected and lysed directly. Lysates were immunoprecipitated, or directly subjected to SDS-PAGE and transferred to PVDF (Millipore). Membranes were immunoblotted with antibodies specific for HA tag (Invitrogen), Flag tag (Sigma), V5 tag (Invitrogen), GFP (Roche), phospho-T195-Hpo (Cell Signaling) or Tubulin (Sigma).
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5

Quantitative Analysis of Subcellular Protein Localization

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IF slides and cover slips were prepared as described in Rausch et al (2019) (link). Primary antibodies recognising YAP (EP1674Y), YAP/TAZ (63.7/sc-101199), AR (N-20/sc-816), and HA Tag (6E2/2367S), and Alexa Flour 488- and 594- conjugated secondary antibodies (Invitrogen) were used. Cover slips were mounted on slides using ProLong Diamond Antifade Mount with DAPI stain (Thermo Fisher Scientific). Image acquisition was performed using Leica TCS SP8 confocal laser scanning microscope utilising the HC PL AP Oil 63x1.4 CS2 objective. The nuclear-to-cytoplasmic signal intensity ratio was quantified in 5–15 cells of each population from between 8–15 images. The nucleus was identified in the DAPI channel and used to draw the region of interest. The channel of interest was picked, and the signal intensity of the nucleus was measured and tabulated. The region of interest was further moved to the cytoplasm, measured, and tabulated to determine the signal intensity outside the nucleus. The value obtained from the nucleus was excluded from the latter images and the nuclear-to-cytoplasmic ratio was quantified in Microsoft Excel and plotted as a scatterplot in GraphPad Prism.
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6

Western Blot Analysis of Protein Expression

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Cells were lysed using RIPA buffer (sigma) with a phosphatase inhibitor cocktail (GenDEPOT). The concentration of extracted proteins was determined using NanoDrop One (Thermo Scientific, Waltham, MA, USA). Samples were heated at 95°C for 5mins and cooled down with ice. Each 80 μg protein was electrophoresed on 4-12% SDS-polyacrylamide gel (Invitrogen, Basel, Switzerland). The gel was transferred onto PVDF membrane. Blots were blocked with PBS containing 0.05% Tween 20 and 5% nonfat dry milk for 2 h, then incubated with GAPDH (Santa Cruz, CA, USA) or HA-Tag (Invitrogen) antibody for 1 h at room temperature. After washing with PBS containing 0.05% Tween 20, blots were incubated with peroxidase-conjugated secondary antibody for 1 h at room temperature. Finally, blots were visualized by enhanced chemiluminescence procedures (Bio-rad, Hercules, CA) according to the manufacturer's instructions (Figure S1).
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7

Detecting HA-tagged Anti-PD-L1 Antibody

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To determine the expression of the HA-tagged PD-L1 antibody coded by XVir-N-31-anti-PD-L1, 48 h after infection (30 MOI), the cell lysates were prepared. For the detection of anti-PD-L1 secretion, cells were infected as described above. One hour later, the medium was changed to a serum-deprived medium. The supernatants were collected after 48 or 72 h, and the proteins were acetone precipitated and prepared for immunoblotting using the following antibodies: HA-tag (1:500, No. 14-6756-81, Thermo Fisher Scientific) and GAPDH (1:1000, sc-25778, Santa Cruz, Heidelberg, Germany). The detection was performed using Clarity ECL substrates on a ChemiDocTM MP Imaging System and ImageLab 5.1 software (all Bio-Rad Laboratories, Feldkirchen, Germany).
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8

Validating Proteomic Data with Western Blot

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To validate proteomic data, the experiments were replicated and analyzed using immunoblotting with a standard protocol. In short, all samples were separated on 4–12% SDS-PAGE (Life Technologies, Carlsbad, CA, USA), transferred to PVDF membrane (Amersham), and blocked using 5% BLOTTO milk. Primary antibodies for immunoblots: MDC1 (Bethyl), HA-tag (ThermoScientific), ACTB, CBR1 (Sigma Aldrich), EIF4A1 PHB (GeneTex, Irvine, CA, USA). The membrane was then incubated with species-appropriate secondary antibodies conjugated to horseradish peroxidase (HRP). Immune complexes were then identified using enhanced chemiluminescence (ECL, GE Healthcare, Chicago, IL, USA) and an Amersham Imager 680 system. Western blot quantification was performed with GE-ImageQuant TL and Image J software (1.53t), using red Ponceau staining as a loading control or human beta-actin.
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9

Comprehensive Protein Quantification Protocol

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Total protein extracts according to our previous study [13 (link)]. The primary antibodies used are as follows: ARHGEF3 (PA598942; Thermofisher), ACLY (67166-1-lg; Proteintech), HA-tag (26183; Thermofisher), Flag-tag (20543-1-AP; Proteintech), β-Actin (TA811000; Origene), ubiquitin (10201-2-AP; Proteintech), acetylation (06-933; Millipore), and GAPDH (TA802519; Origene).
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10

Western Blot Analysis of Protein Expression

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Cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS), 1 mM EDTA, 1 mM EGTA) supplemented with protease inhibitors (1 mM phenylmethylsulfonyl fluoride, 1μg/ml leupeptin, and 1 μg/ml pepstatin), and a phosphatase inhibitor cocktail (Sigma). Protein concentrations were determined as above. Equal amounts of protein (25 μg) from each lysate was resolved on an 8% SDS-polyacrylamide gel (SDS-PAGE) and transferred to a PVDF membrane (BioRad). Membranes were blocked for 1h in 5% milk in Tris-buffered saline (TBS) with 0.1% Tween 20 (TBST) and incubated overnight with primary antibody at 4°C. Primary antibodies were diluted in 3% BSA-TBST. Membranes were washed in TBST four times (15min each) and incubated for 1h in appropriate horseradish peroxidase-conjugated secondary antibody (Thermo Fisher) diluted in 2% milk-TBST. Membranes were washed in TBST four times and probed with an ECL chemiluminescence kit (Pierce). Densitometry was performed using Image J software. Membranes were probed with following antibodies: rabbit polyclonal against IFIT1 (1:1000, Sigma), goat polyclonal against TGTP (1:250, Santa Cruz) and mouse monoclonal against actin (1:5000, Millipore) and HA-tag (1:1000, Thermo Scientific).
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