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24 protocols using nb300 221

1

Western Blot Analysis of VEGF-A

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Protein fractions were isolated using the active motif kit (Active Motif, Carlsbad, CA, USA). Total protein lysates were quantified by Bradford assay. Proteins were separated by 10% SDS-PAGE, transferred onto a nitrocellulose membrane, and blocked overnight in blocking solution (1× TBS, pH 7.6, 0.1% Tween-20, and 5% w/v nonfat dry milk). The membrane was then incubated with antibodies specific for VEGF-A (Ab105846, 1:500; Abcam; Cambridge, MA, USA). As a loading control, the membrane was probed for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (1:1,000, NB300-221; NOVUS Biological; Littleton, CO, USA). The membrane was then incubated with horseradish peroxidase-conjugated secondary antibody (1:1,000) in blocking solution for 1 hour at room temperature. Horseradish peroxidase activity was detected by incubating the membrane in chemiluminescence solution (Bio-Rad, Hercules, CA, USA). The exposure time was adjusted to keep the integrated optical densities within a linear and nonsaturated range. Densitometric analysis was carried out using a UVP Bioimaging system (UVP, Minneapolis, MN, USA).
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2

GFP-Tagged Protein Complex Isolation

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GFP-tagged protein complexes were isolated by immunoaffinity chromatography using a polyclonal goat anti-GFP antibody that was generated in house as previously described (Poser et al., 2008 (link)) and analyzed by mass spectrometry or western hybridization using the following primary antibodies: Ctr9 (Abcam, Cat# ab84487, RRID: AB_1860992), Tox4 (Sigma-Aldrich, Cat# HPA017880, RRID: AB_1845573), and Gapdh (Novus Biologicals, Cat# NB300-221, RRID: AB_10077627). See Supplemental Information for details.
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3

Arp2/3 Complex Inhibitor CK-66633 Protocol

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The Arp2/3 complex inhibitor CK-66633 (link) was purchased from Tocris Bioscience and dissolved in DMSO. BSA, β-Lactoglobulin and Pluronic F127 were purchased from Sigma and dissolved in 1x PBS. pLL-PEG was from Surface SolutionS and diluted in 10~mM HEPES. GFP-FAK was provided by Ekaterina Papusheva/ Carl-Philipp Heisenberg. Speckle GFP-Vinculin was a gift from Alan Rick Horwitz. MRLC-GFP was a gift from Rex Chisholm. siRNAs were Stealth Select RNAi siRNAs from Invitrogen with the following sequences: TLN1 siRNA (RSS320275): 5'-GGGCAUAUCCAUGUCUUCGAGCAAA-3'; TLN2 siRNA (RSS321623): 5'-GAGAGGAGCCGAGAAGCGAAUAUUU-3'. Knockdown efficiency was quantified by Western blotting with antibodies for TLN1 (monoclonal, clone 8d4, Sigma #T3287, 1:2000), TLN2 (GeneTex, #EPR2536(2), 1:1000) and GAPDH (clone 1D4, NovusBiologicals #NB300-221, 1:20000). Representative images of immunoblots are based on at least 2 experiments.
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4

Arp2/3 Complex Inhibitor CK-66633 Protocol

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The Arp2/3 complex inhibitor CK-66633 (link) was purchased from Tocris Bioscience and dissolved in DMSO. BSA, β-Lactoglobulin and Pluronic F127 were purchased from Sigma and dissolved in 1x PBS. pLL-PEG was from Surface SolutionS and diluted in 10~mM HEPES. GFP-FAK was provided by Ekaterina Papusheva/ Carl-Philipp Heisenberg. Speckle GFP-Vinculin was a gift from Alan Rick Horwitz. MRLC-GFP was a gift from Rex Chisholm. siRNAs were Stealth Select RNAi siRNAs from Invitrogen with the following sequences: TLN1 siRNA (RSS320275): 5'-GGGCAUAUCCAUGUCUUCGAGCAAA-3'; TLN2 siRNA (RSS321623): 5'-GAGAGGAGCCGAGAAGCGAAUAUUU-3'. Knockdown efficiency was quantified by Western blotting with antibodies for TLN1 (monoclonal, clone 8d4, Sigma #T3287, 1:2000), TLN2 (GeneTex, #EPR2536(2), 1:1000) and GAPDH (clone 1D4, NovusBiologicals #NB300-221, 1:20000). Representative images of immunoblots are based on at least 2 experiments.
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5

Western Blotting of Cell Signaling Proteins

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Proteins were extracted from cells in RIPA lysis buffer with protease inhibitors (S8820, Sigma, Saint-Louis, MO, USA). Antibodies against CDC20 (1:1000; sc-13162, Santa Cruz, Dallas, TX, USA), hnRNP-U (1:1000; sc-32315), pH3 (1:1000; 06-570; EMD Millipore, Burlington, MA, USA), MPM-2 (1:1000; 05-368; EMD Millipore), cyclin B1 (1:1000; sc-245), cyclin A (1:1000; sc-271682), cyclin E (1:1000; sc-247), PARP (1:1000; 9532; CST), GAPDH (1:1000; NB300-221, Novus Biologicals, Centennial, CO, USA), HSP90 (1:1000; 4877, CST, Beverly, MA, USA), H3 (1:1000; 4499; CST), Myc (1:1000; sc-40), Ubiquitin (1:1000; 43124, CST), CTCF (1:1000; 3418; CST), RAD21 (1:1000; ab992; Abcam, Boston, MA, USA), V5 (1:2000; 80076; CST), Flag (1:1000; 14793; CST), and HA (1:1000; 3724; CST) were used in this study. Antibody against actin (1:5000; A5441, Sigma) was used as a loading control.
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6

Western Blot Analysis of Sox18 Protein

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Total protein lysates were isolated and quantified by Bradford assay. The lysates were separated by 10% SDS-PAGE and transferred onto a nitrocellulose membrane (BioRad, Hercules, CA). The membrane was incubated in blocking solution (1x TBS, pH 7.6, 0.1% Tween-20, and 5% w/v of nonfat dry milk) and then incubated with a primary antibody to detect Sox18 (Abcam ab23342). The membrane was probed for GAPDH (NOVUS Biological, NB300-221) to normalize the protein loading. The membrane was then incubated with HRP-conjugated secondary antibody (1 : 1000) in blocking solution for 1 hour at room temperature. HRP activity was detected by incubating the membrane in chemiluminescence solution (Bio-Rad, Hercules, CA). The exposure time was adjusted to keep the integrated optical densities within a linear and nonsaturated range. Densitometric analysis was done using a UVP Bioimaging system (UVP, Minneapolis, MN).
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7

Quantification of STAT5 and GAPDH Proteins

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Total protein was extracted in RIPA buffer (50 mM Tris-HCl (PH7.5), 150 mM NaCl, 10% Glycerol, 50 mM NaF, 0.5 mM EDTA and 1% NP-40) and 20 μg of proteins was loaded on 7.5% Mini-PROTEAN® TGX™ Precast Gel (Bio-Rad, #4561023EDU) for STAT5 and in NuPAGE® Novex 4–12% Bis-Tris Gel (Invitrogen, NP0321BOX) for GAPDH. Primary antibodies were incubated overnight at 4°C (anti-STAT5A (Santa Cruz Biotechnology, sc-1081X, 1:1000) and GAPDH (Novus Biologicals, NB300-221, 1:10000)).
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8

Tissue Homogenization and Western Blot Analysis

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Protein samples were prepared by homogenizing snap frozen tissue in 1× RIPA (ThermoFisher) buffer containing protease inhibitors (Roche). Protein concentrations were determined using the Bradford assay (BioRad protein assay reagent). Aliquots of total protein (10 μg for aorta and liver; 50 μg for all other tissues) resolved by SDS–PAGE and electro-transferred to nitrocellulose membranes. Blots were blocked with 5% nonfat dry milk in TBST for 1 h at room temperature and then incubated overnight with primary antibody. After rinsing, the membranes were incubated with HRP-conjugated secondary antibodies (BioRad) for 1 h at room temperature followed by chemiluminescent detection (BioRad ChemiDoc). Antibodies used were TG2 polyclonal (PA5-95256; ThermoFisher) and GAPDH (1D4; NB300-221; Novus Biologicals). ImageLab (BioRad) was used for densitometry analysis.
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9

Antibodies for Immunofluorescence and Immunoblotting

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Mouse monoclonal antibodies used in the study included those against PSF (for immunofluorescence, P2860, Sigma-Aldrich; and for immunoblotting, sc-101137, Santa Cruz), SC35 (S4045, Sigma-Aldrich), FLAG tag (F1804, Sigma-Aldrich) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH, NB300-221, NOVUS). Rabbit polyclonal antibodies included those against CoAA (A300-331A, Bethyl), FLAG tag (F7425, Sigma-Aldrich) and RBM4 (2 (link)). The anti-hnRNP K rabbit monoclonal antibody was from Abcam (ab52600). Alexa Fluor 488- and 568-conjugated secondary antibodies were from Invitrogen.
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10

Western Blot Analysis of Polycystins

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Cells were lysed in RIPA buffer boiled at 95 °C for 5 min. And after quantification loaded to 4-15% mini-Protean TGX gel (4568086, Bio-Rad) and transferred to PVDF membranes (162-0177, Bio-Rad). The membranes were blotted for polycystin-1, rabbit polyclonal antibody (1:2,000, ABT128, Millipore) or polycystin-2, mouse monoclonal antibody (1:1,000, sc-47734, Santa Cruz Biotechnology). GAPDH was used for loading control, mouse monoclonal antibody (1:2,000, NB300-221, NovusBio). For full details see Supplementary Methods.
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