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11 protocols using anti flag

1

Western Blot Analysis of Cellular Proteins

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The antibodies included the following: anti-SQSTM1/p62 (M162-3, Medical Biological Laboratories, Japan), anti-SQSTM1/p62 (ab109012, Abcam, USA), anti-p53 (sc-126, Santa Cruze Biotechnology, USA), anti-p53 (10,442–1-AP, Proteintech, China), anti-mutant p53 (ab32049, Abcam), anti-NRF2 (M200-3, Medical Biological Laboratories), anti-NRF2 (16,396–1-AP, Proteintech), anti-ubiquitin (10,201–2-AP, Proteintech), anti-GAPDH (#5174, Cell Signaling Technology), anti-β-actin (#4970, Cell Signaling Technology), anti-HA (M180-3 and M561, Medical Biological Laboratories), anti-His (D291-3, Medical Biological Laboratories), anti-Flag (M185, Medical Biological Laboratories), anti-Flag (20,543–1-AP, Proteintech), anti-SLC7A11 (NB300-318, Novus, USA), anti-SLC7A11 (26,864–1-AP, Proteintech) anti-HO1 (ab68477, Abcam), anti-HO1 (10,701–1-AP, Proteintech), anti-NQO1 (ab80588, Abcam), anti-Keap1 (10,503–2-AP, Proteintech).
The reagents included the following: Erastin (S7242, Selleck, USA), APR-246 (HY-19980, MCE, USA), Pifithrin-α (HY-15484, MCE), Nutlin-3 (S1061, Selleck).
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2

Immunostaining of MEF Cells with GSNO

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For immunostaining, MEF cells were cultured in 24 wells plate with coverslips. After cell seeding for 24 hours, the cells were further treated with GSNO donor (Sigma Aldrich, 10uM) for 24 hours. Cells were fixed with 4% paraformaldehyde (Sigma Aldrich), and blocked with a blocking solution (normal goat serum) accompanied with 0.1% saponin for permeabilization. After blocking, the cells were incubated in 0.1% saponin with primary antibody: anti-FLAG (Medical & Biological Laboratories), secondary antibody and fluorescence-probe: Alex Flour 633 goat anti-mouse, ProteoStat Dye (1:1000), DAPI (1ug/ml). Images were taken in multi-tracking mode on a laser scanning confocal microscope (LSM710, Carl Zeiss) with a 63 plan apochromat 1.4 NA objective.
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3

Separation and Analysis of Protein Complexes

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Protein complexes of anthers or crude mitochondria were separated by Blue Native polyacrylamide gel electrophoresis (BN-PAGE) according to [21 (link)]. A NativePAGE Novex BisTris Gel system (Thermo Fisher Scientific, Waltham, MA, USA) was used. Separated complexes were blotted onto a Hybond-P PVDF membrane (GE Healthcare, Little Chalfont, UK) according to the manufacturer’s instruction manual. Primary antisera were anti-preSATP6 [10 (link)], anti-COXI [10 (link)], and anti-FLAG (Medical and Biological Laboratories, Nagoya, Japan). Antisera were diluted as described in [25 (link)]. The secondary antibody was HRP-conjugated goat anti-mouse IgG and HRP-conjugated goat anti-rabbit IgG (Jackson ImmunoResearch, West Grove, PA, USA). Conditions for quantification were modified as previously described [25 (link)]. Uncropped images are provided in Additional file 8.
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4

Immunoblotting Analysis of Protein Lysates

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The primary tissue lysates and whole cell lysates were prepared for immunoblotting as described previously 25 (link). Equal amounts of total proteins (30 µg) were subjected to SDS-PAGE and immunoblotting analysis with specific antibodies. The primary antibody against Cyclin D1 was purchased from Cell Signaling Technology (Danvers, MA). Anti-USP5 antibody was obtained from Proteintech Group (Wuhan, China). Anti-TUFM and anti-EBF1 antibodies were purchased from ABclonal Biotechnology (Hubei, China). Anti-Flag, Myc and HA antibodies were purchased from Medical & Biological Laboratories (Tokyo, Japan). Anti-GAPDH antibody was purchased from Abgent Biotechnology (Suzhou, China). Horseradish peroxidase-conjugated anti-mouse and anti-rabbit IgG antibodies were purchased from Beyotime Biotechnology (Nantong, China).
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5

ChIP Assay for Protein-DNA Interactions

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The ChIP kit (Millipore, Burlington, MA, USA, 17-295) was employed according to the manufacturer’s instructions and the ChIP assay was performed as described previously25 (link). Briefly, cells (1 × 107 per assay) were bathed in 1% formaldehyde at 25°C for 10 min for cross-linking of proteins and DNA and then lysed in sodium dodecyl sulfate buffer containing protease inhibitors. DNA was sheared by sonication using a Sonic Dismembrator Model 500 (Fisher Scientific, Pittsburgh, PA, USA). Immunoprecipitation was carried out by incubating with 1 μg of anti-FLAG (Medical & Biological Laboratories, M185-3L), anti-NANOG (Bethyl Laboratories, A300-379A) antibodies or rabbit IgG (Millipore, Billerica, MA, USA, PP64) for 16 h and then the immunoprecipitated DNA was quantified by real-time qPCR using the following primer set: 5′-GCAGGACTTGAGAAGCCTCTC-3′ (forward) and 5′-GACGCAGCTGCACACATG-3′ (reverse). Each sample was assayed in triplicate, and the amount of precipitated DNA was calculated as the percentage of the input sample.
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6

Co-immunoprecipitation Assay for TaMOR-GFP and ARF5-Flag

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The coding sequence of TaMOR was cloned into vector pCAMBIA1300‐GFP to form TaMOR‐GFP. The coding sequence of ARF5 was cloned into vector to pCAMBIA1300‐Flag to form ARF5‐Flag. They were introduced into Agrobacterium tumefaciens strain EHA105 and infiltrated into N. benthamiana leaves. After 48 h, the infiltrated leaves were ground to powder in liquid nitrogen and resuspended in 500 μl protein extraction buffer. The Co‐IP assay was performed as previously described (Cai et al., 2021 (link)). Anti‐GFP mAb magnetic beads (Medical Biological Laboratories, D153‐11), Anti‐GFP (Medical Biological Laboratories, 598‐7) and anti‐Flag (Medical Biological Laboratories, M185‐7) antibodies were used in the assay.
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7

Quantification of Vif and A3G Proteins in HIV-1 Virions and Cells

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Western blotting analysis was performed as described previously [37 (link),38 (link)]. Briefly, pro-viral clones or pcNLmini-RI-based clones were transfected into HEK 293T cells by Lipofectamine2000, and unless otherwise noted, on day 1, post-transfection cell lysates were prepared with 1 × TNE buffer. Analyses of Vif and A3G expression levels in virions and cells were carried out similarly as described previously [43 (link),44 (link)]. Briefly, HEK 293T cells were co-transfected with pro-viral clones along with a FLAG-tagged A3G expression vector by the calcium phosphate coprecipitation method. On day 1 post-transfection, virions were collected by ultracentrifugation, and the lysates of virions and cells were prepared with 1 × TNE buffer. Anti-HIV-1 Vif 319 (catalog no. ab66643; Abcam, Tokyo, Japan), anti-Gag-p24 (#3537, NIH Research and References Reagent Program), anti-FLAG (FLA-1, MEDICAL & BIOLOGICAL LABORATORIES), and anti-β-actin clone AC-15 (Sigma-Aldrich, Burlington, MA, USA) antibodies were used for immunoblotting analyses.
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8

Comprehensive Biochemical Assay Protocol

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DMSO was purchased from Servicebio (GC203005). The AKT inhibitor SC66 was obtained from MedChemExpress (HY-19832). TMZ was purchased from Selleck (S1237).
The following antibodies were used: anti-RND1 (GTX83709, GeneTex), anti-GAPDH (#5174, Cell Signalling Technology, CST), anti-Flag (M185, Medical Biological Laboratories), anti-E-cadherin (20874–1-AP, Proteintech), anti-N-cadherin (22018–1-AP, Proteintech), anti-Vimentin (10366–1-AP, Proteintech), anti-Snail1 (sc -28,199, Santa Cruz), anti-mmp2 (10373–2-AP, Proteintech), anti-AKT (GTX121937, GeneTex), anti-Phospho-AKT (#4060, CST), anti-GSK-3β (#12456, CST), anti-Phospho-GSK-3β (#9323, CST), anti-β-catenin (51067–2-AP, Proteintech), anti-MAPK (#4511, CST), anti-Phospho-MAPK (#9212, CST) and anti-Smad3 (66516–1-Ig, Proteintech).
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9

Immunostaining of MEF Cells with GSNO

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For immunostaining, MEF cells were cultured in 24 wells plate with coverslips. After cell seeding for 24 hours, the cells were further treated with GSNO donor (Sigma Aldrich, 10uM) for 24 hours. Cells were fixed with 4% paraformaldehyde (Sigma Aldrich), and blocked with a blocking solution (normal goat serum) accompanied with 0.1% saponin for permeabilization. After blocking, the cells were incubated in 0.1% saponin with primary antibody: anti-FLAG (Medical & Biological Laboratories), secondary antibody and fluorescence-probe: Alex Flour 633 goat anti-mouse, ProteoStat Dye (1:1000), DAPI (1ug/ml). Images were taken in multi-tracking mode on a laser scanning confocal microscope (LSM710, Carl Zeiss) with a 63 plan apochromat 1.4 NA objective.
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10

Antibody Characterization Protocol

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Anti‐USP11 (catalog no. sc‐365528), anti‐Ub (catalog no. sc‐166553) and anti‐NONO (catalog no. sc‐376865) antibodies were purchased from Santa Cruz. Anti‐USP11 (EPR4346) and anti‐Myc (2276S) antibodies were provided by Abcam. Three antibodies against NONO were obtained from Sangon Biotech (catalog no. D199144), MBL Life science (catalog no. RN092PW), Proteintech Group, Inc (catalog no. 11058‐1‐AP). Anti‐Flag (catalog no. M185‐3L), anti‐HA (catalog no. M180‐3) and anti‐Myc (catalog no.M192‐3) were purchased from Medical & Biological Laboratories. Anti‐GAPDH (catalog no. KC‐5G4) antibody was bought from Kangchen Biotech.
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