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7 protocols using anti ha

1

Antibody Sources for Protein Detection

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Antibody against FABP5 was purchased from R&D systems (Minneapolis, MN, USA); anti-p-AKT, anti-p-mTOR, and anti-Ki-67 from Cell Signaling (Danvers, MA, USA); anti-Flag from Sigma-Aldrich (St. Louis, MO, USA); anti-B-tubulin and anti-Lamin B from Santa Cruz Biotechnology (Santa Cruz, CA, USA); anti-GFP from Thermo Fisher Scientific (Waltham, MA, USA); anti-HA from GeneTex (Irvine, CA, USA). Anti-HIF-1α was generated against human HIF-1α in rabbits, and a monoclonal anti-hydroxylated Asn 803 of HIF-1α was raised in mouse as described previously61 (link),62 (link).
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2

Immunoprecipitation and Immunoblotting of Influenza Viral Proteins

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Cells were harvested in lysis buffer (50 mM Tris pH 8.0, 5 mM NaCl, 0.5% NP-40, and 1X protease inhibitor), frozen and thawed three times, and then the proteins were recovered. Immunoprecipitation (IP) proceeded overnight at 4 °C in IP buffer containing antibodies against Grail or Flag. The IP mixture was then incubated with Dynabeads Protein G (Invitrogen) for 1 h prior to isolation using a DynaMag magnet and washing three times with SNNTE buffer (5% sucrose, 1% NP-40, 0.5 M NaCl, 50 mM Tris pH 7.4, and 5 mM EDTA). The immunoprecipitates were resuspended in SDS-PAGE sample buffer, boiled, and loaded onto a gel. Following separation, the proteins were transferred to a nitrocellulose membrane and the blot was probed with antibodies diluted in PBS/Tween 20 with 5% non-fat milk. Antibody detection was carried out using enhanced chemiluminescence reagents (GE Healthcare), as described by the manufacturer. The primary antibodies used for immunoblotting were: anti-PA (GeneTex), anti-PB1 (GeneTex), anti-PB2 (GeneTex), anti-HA (GeneTex), anti-NA (GeneTex), anti-NP (GeneTex), anti-M1 (GeneTex), anti-M2 (GeneTex), anti-NS1 (GeneTex), anti-HA (81B8, Cell Signaling, USA), anti-beta actin (MAb1501, Chemicon), and anti-Grail antibodies.
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3

Western Blot Analysis of Cellular Proteins

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Cells were lysed with RIPA buffer containing a cocktail of protease (Sigma). Protein samples were separated by SDS-PAGE and transferred to a polyvinylidene difluoride (PVDF) transfer membrane (Hybond-P; GE Healthcare). The nonspecific antibody binding sites were blocked with milk in Tris-buffered saline–Tween 20 and then reacted with the primary antibodies anti-HA (GTX29110 [GeneTex] or 3724 [Cell Signaling]), anti-Ubc9 (4786; Cell Signaling), anti-actin (A5441; Sigma), anti-GFP (GTX26556GeneTex), anti-STAT1 (9175; Cell Signaling), anti-STAT2 (05-693; Upstate), and anti-RIG-I (3743; Cell Signaling). Anti-NS5 and -NS3 antibodies are gifts from Huey-Nan Wu. Blots were treated with horseradish peroxidase-conjugated secondary antibody (Thermo Scientific), and signals were detected by enhanced chemiluminescence (ECL; Millipore).
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4

Western Blot for Protein Expression

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Cells were washed with ice-cold PBS, harvested in ice-cold PBS, and pelleted by centrifugation at 500 g for 5 minutes. Cell pellets were resuspended with Radioimmunoprecipitation assay (RIPA) buffer (Sigma Aldrich, Saint Louis, MO) and rotated at 4 °C for 1 hour. Lysates were cleared by centrifugation at 16,000 g for 10 minutes and supernatants were analyzed for total protein concentration using a BCA kit (Pierce, Rockford, Illinois). 30 μg of total protein lysate was taken from each sample and fractionated on a 4–12% gradient Novex® Bis-Tris Bolt® SDS-PAGE gel via electrophoresis. Proteins were transferred onto 0.45 μm nitrocellulose membranes and incubated for 1hr in Odyssey® PBS blocking buffer (Li-Cor Biosciences, Lincoln, NE). Membranes were probed with anti-HA (1:5,000, GeneTex, Irvine, CA) and anti-NaK-ATPase (1:2,500, GeneTex, Irvine, CA) primary antibodies in Odyssey® PBS blocking buffer overnight at 4 °C. anti-HA and anti-NaK-ATPase signals were detected using IRdye 800 donkey anti-rabbit (1:20,000, Li-Cor Biosciences, Lincoln, NE) and IRdye 680 donkey anti-mouse (1:20,000, Li-Cor Biosciences), respectively. The Li-Cor Odyssey® imaging system and software was used for antibody detection and quantification.
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5

Protein Expression and Immunostaining Protocol

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All DNA constructs were transfected into 293T cells using Fugene 6 (Promega) and harvested 48 h later. An anti-Flag M2 affinity gel (Sigma, A2220) and an HA clone 16B12 monoclonal antibody (Covance, MMS-101R) were used for immunoprecipitation. The following primary antibodies were used for immunoblotting: mouse anti-TWIST1 2c1a (Santa Cruz Biotechnology), mouse anti-E-cadherin (BD, 610182), mouse anti-vimentin V9 (Thermo Scientific, MS-129-P), chicken anti-actin (Abcam, ab13822), anti-Flag (Sigma, F3165), anti-HA (Genetex, GTX115044), and anti-Myc hybridoma supernatant (clone 9E10).
Immunofluorescence was performed in eight-chamber slides by seeding 10,000 cells per well. Cells were fixed with 4% paraformaldehyde for 30 min and blocked in 5% goat serum/PBS-Tween for 1 h. Both primary and secondary antibodies were incubated in 5% goat serum/PBS-Tween overnight and for 1 h, respectively. The primary antibodies used were mouse anti-TWIST1 2c1a (Santa Cruz Biotechnology), rabbit anti-E-cadherin (Cell Signaling, 3195S), mouse anti-vimentin V9 (Thermo Scientific, MS-129-P), and nuclear DAPI staining (VectorShield). All images were imaged with an Olympus FV-1000 confocal microscope.
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6

Immunoblotting and Immunofluorescence Antibody Protocols

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Primary antibodies used for immunoblotting: anti-ACTB (MBL, #M177-3, 1:3000), anti-EGFR (MBL, #MI-12-1, 1:3000), anti-LC3 (MBL, #PM036, 1:3000), anti-VPS41 (SCBT, #sc-377118, 1:1000), anti-VPS8 (Proteintech, 15079-1-AP, 1:2000), anti-VPS39 (SCBT, sc-514762, 1:1000), anti-VPS3 (TRAP-1) (SCBT, #sc-13134, 1:1000), anti-VPS18 (Proteintech, #10901-1-AP, 1:2000), anti-VPS11 (SCBT, sc-515094, 1:2000), anti-VPS16 (Proteintech, # 17776-1-AP, 1:2000), anti-VPS33A (NovusBio, #NBP2-20872, 1:1000), anti-FLAG (Sigma-Aldrich, #F1804, 1:1000), anti-HA (Gene Tex, #GTX18181, 1:2000), anti-His (MBL, #PM032, 1:1000), anti-Myc (MBL, #M192-3, 1:10000), anti-V5 (MBL, #M215-3, 1:2000), anti-FLAG HRP-conjugated (FUJIFILM-Wako, # 019-22394, 1:10000), anti-Myc HRP-conjugated (MBL, #M192-7, 1:10000), anti-HA HRP-conjugated (MBL, #M180-7, 1:10000). Secondary antibodies used for immunoblotting: HRP-conjugated anti-rabbit IgG (Invitrogen, #31460, 1:3000 or 1:10000) and anti-mouse IgG (Invitrogen, #31430, 1:3000 or 1:10000).
Primary antibodies used for immunofluorescence staining: anti-LC3 (MBL, #PM036, 1:500. Secondary antibodies used for immunofluorescence staining: Alexa Fluor 488 anti-rabbit IgG (H + L) (Molecular Probes, #A21206).
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7

Western Blot Antibody Panel for Protein Analysis

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The commercial antibodies used for Western blot analysis are as follows: anti-Twist1 (1:1000, sc-81417, Santa Cruz Biotechnology), anti-USP13 (1:3000, ab109264, Abcam), anti-RNF8 (1:1000, sc-271462, Santa Cruz Biotechnology), anti-FBXL14 (1:1000, HPA053889, Sigma-Aldrich), anti-βTrcp1 (1:1000, sc-390629, Santa Cruz Biotechnology), anti-E-cadherin (1:1000, sc-8426, Santa Cruz Biotechnology), anti-N-cadherin (1:1000, sc-59987, Santa Cruz Biotechnology), anti-Vimentin (1:1000, sc-6260, Santa Cruz Biotechnology), anti-MMP9 (1:1000, sc-21733, Santa Cruz Biotechnology), anti-Ubiquitin (1:1000, sc-8017, Santa Cruz Biotechnology), anti-Flag (1:3000, GTX115043, GeneTex), anti-GFP (1:3000, GTX113617, GeneTex), anti-HA (1:3000, GTX115044, GeneTex), anti-c-Myc (1:3000, PLA0001, Sigma), anti-GST (1:3000, sc-138, Santa Cruz Biotechnology), anti-GAPDH (1:3000, GTX627408, GeneTex), anti-tubulin (1:3000, bs-0715R, Bioss), and anti-Ubiquitin K48-specific antibody (1:1000, ZRB2150, Sigma-Aldrich). anti-Flag Affinity Gel (B23102), Poly Flag Peptide (B23111) and Protein A/G mix magnetic beads (B23202) were obtained from Bimake Chemicals. Cycloheximide (S7418) and MG132 (S2619) were obtained from Selleck Chemicals. TGF-β1 (100–21) was obtained from Peprotech.
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