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136 protocols using anti ha antibody

1

Western Blotting and Reporter Assay for Virus Particles

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Western blotting and reporter assay were performed as previously described [12 (link)–14 (link), 45 (link)–47 (link), 52 (link)]. For the Western blotting of virus particles, 340 μl of the culture supernatant was ultracentrifuged at 100,000×g for 1 h at 4 °C using a TL-100 instrument (Beckman), and the pellet was lysed with 1 × SDS buffer. For the Western blotting of transfected cells, the cells were lysed with RIPA buffer (50 mM Tris–HCl buffer [pH 7.6], 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.1% SDS) with protease inhibitor cocktail (Roche). The following antibodies for Western blotting: anti-His polyclonal antibody (OGHis; Medical and Biological Laboratories), anti-HA antibody (3F10; Roche), anti-FIV p24 Capsid antibody (PAK3-2C1; Santa Cruz Biotechnology); anti-alpha-tubulin (TUBA) antibody (DM1A; Sigma), and anti-VSVg antibody (P5DA; Roche). For FIV reporter assays, HEK293T cells were used for the target of infection. Ten microliter of the culture supernatant of transfected cells was inoculated into HEK293T cells in a 96-well plate (Nunc), and the firefly luciferase activity was measured by using the BrillianStar-LT assay system (Toyo-b-net) and the 2030 ARVO X multilabel counter instrument (PerkinElmer) according to the manufacturers’ procedures.
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2

Western Blot Analysis of HA-Tagged Proteins

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50 mL yeast cultures in S.D. media were harvested and disrupted using acid-washed glass beads [23 (link)]. The cell lysates were separated by SDS-PAGE and proteins were transferred to polyvinylidene fluoride membranes (Amersham Hybond-P 0.45, GE Healthcare Life Sciences, München, Germany). Chemiluminescence detection (ECL Chemostar, Intas Science Imaging Instruments, Göttingen, Germany) was carried out using a monoclonal mouse Anti-HA antibody (1:5000, Roche; cat. no. 11583816001, Mannheim, Germany), a horseradish peroxidase secondary goat anti-mouse antibody (1:5000, Jackson ImmunoResearch/Dianova; cat. no. 115-035-174, Hamburg, Germany), and the Clarity Western ECL substrate (Bio-Rad, Feldkirchen, Germany).
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3

Immunofluorescence Analysis of Reporter Proteins

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Preparation of chemically fixed cells for immunofluorescence and analysis of subcellular distribution of reporter proteins by wide-field and confocal microscopy were done as described previously [42 (link),54 (link)]. Nuclear labelling was performed with 4',6-diamidino-2-phenylindole (DAPI). The HA epitope tag was detected with a monoclonal anti-HA antibody coupled to FITC (dilution 1:50; Roche) whereas GlIscU was detected with a self-made antibody (dilution 1:300) followed by an anti-mouse antibody coupled to Alexafluor 594 (dilution 1:300; Molecular Probes). To avoid any possibility for cross reaction, co-labelling experiments for IFA were performed by incubating first with the anti-GlIscU antibody, followed by the AF594-conjugated anti-mouse secondary antibody, and direct detection of the HA epitope tag with a FITC-conjugated rat anti-HA monoclonal antibody as a final step.
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4

Comprehensive Antibody Inventory for Cell Organelle Labeling

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Anti-HA antibody (#3F10) was purchased from Roche Diagnostics; anti-CERT (#ab72536) from Abcam; chicken antibody against VAP (Kumagai et al., 2014 (link)) anti-TGOLN2/TGN46 (#A304-434A) from Bethyl Laboratories; anti-TOMM20 (#WH0009804M1) from Sigma-Aldrich; anti-Lamp2 (#sc-18822) from Santa Cruz; anti-LBPA (#z-PLBPA) from Echelon Bioscience; anti-EEA1 (#610457) from BD Transduction Laboratories; anti-catalase (#D4P7B) and anti-Rab11a (#2413) from Cell Signaling Technology; anti-Hrs (#10390-1-AP) from Proteintech; anti-GFP (#04404-84) from Nacalai Tesque, and anti-GAPDH (016-25523) from Fujifilm Wako Pure Chemical Corporation. 2-Bromohexadecanoic acid (2-BP, #M1177) was purchased from Sigma-Aldrich. Lipid dye II (#LD02) was from Dojindo Laboratories. Lysenin was a gift from Dr. Sekizawa (Zenyaku Kogyo). GFP-lysenin was a gift from Dr. Kobayashi (Riken). [14C(U)]L-serine (156 mCi/mmol, #MC265) was from Moravec.
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5

GST Pull-down Assay for HNF4 Interactions

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The bacteria expression plasmids pGEX-HNF4/1–127, pGEX-HNF4/128–370 and pGEX-HNF4/371–465, which produce the GST-tagged HNF4 derivatives, were transformed and expressed in E. coli BL21 (DE3). The GST pull down assay was conducted in accordance with the procedure described previously18 (link). In brief, 20 μl glutathione Sepharose resins (GE Healthcare) prebound GST fusion proteins (3 μg) were incubated with nuclear extracts (200 μg, prepared as described previously18 (link)) of HuH7 or HepG2 cells expressing either HA-tagged SHP or HA-tagged HNF4 in the presence or absence of 100 μg/ml RNAse A. After incubation at 4 °C for 5 hr, the beads were washed thrice with cold PBS containing 0.5% NP40. The associated proteins were eluted and separated by SDS-PAGE, then subjected to Western blot analysis with anti-HA antibody (Roche).
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6

Interaction Analysis of Transcription Regulators

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HEK293T cells were grown in DMEM + 10% FBS and transfected with pCI-Neo-GFP-CTCF and pCI-Neo-HA-BORIS along with pCI-Neo-myc-TAF7L, pReceiver-myc-BRD4 (Genecopoeia), or pReceiver-myc-RFX2 (Genecopoeia). For co-IP analysis, 1.5 mg of total protein was incubated with anti-Myc antibody (Sigma), anti-HA antibody (Roche), or anti-GFP antibody (Abcam ab290) overnight at 4 °C with gentle agitation, followed by incubation with 50 μl of a 1:1 mixture of Protein A and Protein G Dynabeads (Life Technologies) for 1 h at room temperature. The immunoprecipitates were collected using a magnetic rack and washed and analyzed by SDS-PAGE and western blotting.
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7

HA-tagged Protein Immunoprecipitation

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Immunoprecipitation was performed as described previously [111 (link)]. Transfected 293T cells were lysed in the buffer containing 10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 4 mM EDTA, 0.1% NP-40, 10 mM NaF, 1 mM DTT, and 1 mM PMSF. The lysates were pre-cleared with Protein-G-Sepharose (GE Healthcare), and incubated with anti-HA antibody (3F10; Roche) at 4 °C for 1 h. After the incubation with Protein-G-Sepharose for 1 h, the resin was washed five times with the lysis buffer. Proteins eluted were then subjected to western blot.
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8

Creation of pcDNA3.1(+) Peatar1b Construct

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An expression-ready construct of Peatar1b in pcDNA3.1(+) vector was generated by PCR. Specifically, receptor encoding cDNA was modified in a PCR with primers Peatar1b-expr-F (5′-TTTAAGCTTCCACCATGGCGACTGACTGGAGAAATATG-3′) and Peatar1b-expr-R (5′-TTTGAATTCTGGTTTGATGTGGAGTAATTTTTTG-3′). In front of the start codon, a HindIII restriction site (AAGCTT) and a Kozak consensus motif (CCACC; [109 (link)]) were inserted. The stop codon was replaced by an EcoRI recognition sequence (GAATTC). We reused the pcAm5-ht1A-HA construct [110 (link)] and exchanged the Am5-ht1A cDNA for the Peatar1b cDNA by ligation into the HindIII and EcoRI sites. The resulting construct (pcPeatar1b-HA) is extended in frame at the 3′ end with a sequence encoding the hemagglutinin A (HA) tag (YPYDVPDYA) which allowed us to monitor receptor protein expression using a specific anti-HA antibody (Roche Applied Science, Mannheim, Germany). The correct insertion was confirmed by DNA sequencing.
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9

Detecting SNAIL Ubiquitination

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Whole cell lysates were prepared as described previously [17 (link)]. Primary antibodies used were SNAIL, COPS5, Vimentin from Cell Signaling Technology (Beverly, MA, USA), α-tubulin from Santa Cruz Biotechnology (Santa Cruz, CA, USA), anti-FLAG antibody (Sigma-Aldrich, St. Louis, MO, USA), and anti-HA antibody from Roche (Indianapolis, IN, USA). The ubiquitination of SNAIL was assessed by Ubiquitin Enrichment Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The immunoprecipitation lysates were subjected to Western blotting. The band intensities were measured by ImageJ and normalized to that of each control lane.
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10

Assessing DispHA and DispCSHA Complexes

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NIH3T3 cells were transfected with pCDNA-DispHA, pCDNA-DispCSHA or empty vector control. Lysates were processed as previously described (Etheridge et al., 2010 (link)) with slight modifications. Approximately 48 hr post transfection cells were lysed for 30 min on ice in 1x NativePAGE sample buffer containing protease inhibitor cocktail (Roche) and 1% n-dodecyl-B-d-maltoside (DDM). Lysates were treated with Benzonase nuclease (Sigma) for 30 min at room temperature followed by centrifugation at 12,000xg for 30 min at 4°C. Supernatants were collected and run on a 4–20% NativePAGE Bis-Tris gel and transferred to PVDF membrane. A fraction of the lysates was run on a 7.5% Tris-HCl gel (BioRad) using denaturing settings and transferred to nitrocellulose membrane. Blots were probed using anti-HA antibody (Roche) and protein sizes were determined using NativeMark on native gels and Precision plus protein standard (Biorad) on denaturing gels. NativePAGE sample buffer, DDM, NativePAGE gels and NativeMark molecular weight standard were purchased from Life Technologies.
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