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13 protocols using mini protein tgx precast gel

1

Western Blot Analysis of Protein Interactions

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Protein extracts were separated on 7.5 or 10% Mini-PROTEIN TGX Precast Gels (Bio-Rad) and then transferred onto nitrocellulose membranes with the Trans-Blot Turbo Transfer System (Bio-Rad). The following primary antibodies and dilutions were used: rabbit anti-PRDM9 polyclonal (Grey et al. 2017 (link)), 1:500; rabbit anti-CTCF monoclonal (Cell Signaling Technology, D31H2), 1:2000; rabbit anti-CXXC1 polyclonal (Millipore, ABE211), 1:5000; rat anti-tubulin α monoclonal (Abcam, ab6161), 1:3000; rabbit anti-PIH1D1 polyclonal (Proteintech, AP19427), 1:5000; rabbit anti-CEP70 polyclonal (Abnova, PAB17658), 1:1000; mouse anti-MCRS1 polyclonal (Abnova, H00010445-B01P), 1:250; anti-Gal4 AD (Millipore, 06-283), 1:3000; and anti-Gal4 BD (Sigma, G3042), 1:2000. Signals were detected with the horseradish peroxidase (HRP)-conjugated secondary antibodies, donkey anti-rabbit IgG HRP (Jackson ImmunoResearch Laboratories), goat anti-rat IgG HRP (GE Healthcare), and sheep anti-mouse IgG HRP (GE Healthcare), and then visualized with SuperSignal West Pico Chemiluminescent Substrate (Thermo Fisher Scientific). ImageJ 1.49m was used to quantify signal intensities of western blot images captured by ChemiDoc™ XRS+ Imager with the Image Lab 5.1 software.
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2

Protein extraction and western blotting

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Cells were lysed using RIPA buffer (Pierce) supplemented with Complete Mini EDTA-free protease inhibitor (Roche diagnostics GmbH). Cell lysis was further aided by passing cells through 18-gauge needles attached to 2mL syringes. Diluted Laemmli buffer solution (Bio-Rad), mixed with 0.1M DTT (ThermoFisher Scientific), was mixed with equal amounts of supernatant from centrifuged cell solution for western blotting analysis.
Blotting was done using BIORAD mini-protein TGX precast gels and Trans-Blot Turbo 0.2μm (pore size) Mini Nitrocellulose membranes utilising a BIORAD Trans-Blot Turbo System. Blocking was performed in TBST buffer supplemented with 3% BSA (SIGMA life science). Detection was carried out using SuperSignal West Pico PLUS Chemiluminescent Substrate, followed by imaging with a BIORAD ChemiDoc MP imaging system.
The following primary antibodies were used: anti-Pol II, clone F-12 (Santa Cruz, Santa Cruz sc-55492), anti-Dendra2, clone OTI1G6 (ThermoFisher, TA180094), Anti-HaloTag (Promega, G9211) anti-GAPDH, clone 1E6D9 (ThermoFisher, 60004-1-IG). The following secondary antibodies were utilised during western blotting and imaging: m-IgGK BP-HRP (Santa Cruz, sc-516102). Abcam Broad Molecular Weight ladder (ab116028) was used to visualise bands following imaging.
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3

Notch1 Protein Detection in iPSCs

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25ug protein from NCHi014-A and control iPSC were separated on 10 % Mini-PROTEIN TGX Precast Gels (Bio-Rad, #4561034), transferred into a polyvinylidene difluoride membrane (Bio-Rad, #1620177), blocked with 5 % milk solution for 1 h, probed against NOTCH1 (Abcam, #Ab-52627) at 1–1000 dilution overnight at 4C⁰. Membrane was further probed with LiCore secondary antibody for 1 h before imaging.
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4

Collagen Degradation by Hydrogen Peroxide

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Purified collagen type I (from human placenta, Sigma-Aldrich) was dissolved in 0.5M acetic acid at 1mg/ml and then mixed with either 25%, 12.5%, 6% and 3% H 2 O 2 (final concentration) for 1, 12 or 24h at room temperature. Samples were mixed with equal volume of sample buffer (0.062M Tris-HCl, pH 6.8, 10% glycerol, 2% SDS, 5% 2-âmercapthoethanol, 0.002% bromophenol blue; final concentration) and 30µL samples were separated by SDS-PAGE using 4-15% mini Protein TGX Precast gels (Bio-Rad, Hemel Hempstead, UK), 0.025M Tris, 0.192M glycine, 0.1% SDS, pH 8.3 running buffer, 200v for 40 min. Evidence of degradation was visualised using a silver stain plus kit (Bio-Rad) following manufacturer's instructions. Gels were scanned using a Gel-Doc TM EZ Imager (Bio-Rad).
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5

SDS-PAGE Analysis of SRV Extracts

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Comparative protein profiles of the different SRV extract samples were obtained using SDS-PAGE with 4–20% Mini-PROTEIN TGX Precast gels (Bio-Rad Laboratories, Hercules, CA, USA). Prior to electrophoresis, protein concentrations of the SRV extracts were determined using the Bradford assay (BioRad). SRV samples were loaded at 25 µg protein per lane after denaturation for 5 min at 95 °C. Samples were run at 200 volts and the gels subsequently stained using Coomassie blue for visual analysis.
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6

Western Blot Analysis of IDH1 and HIF-1α

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Cells were lysed in a Laemmli sample buffer (Bio-Rad) supplemented with 2-mercaptoethanol (Sigma-Aldrich). The lysates were centrifuged at 14,000 rpm for 10 min at 4° C. The supernatants were collected and denatured at 95°C for 10 min. Equal protein lysates were separated on 4-20% Mini-PROTEIN TGX precast gels (Bio-Rad) and transferred to nitrocellulose membranes (Pall Corporation). The following antibodies were used: anti-IDH1 (1 : 1000, Abcam, ab172964), anti-HIF-1α (0.5 μg/ml, RD Systems, NB100-105), and anti-β-actin (1 : 5000, Cell Signaling).
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7

SDS-PAGE Protein Visualization and Western Blotting

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Protein
samples were loaded onto 4–15% Mini-protein TGX precast gel
(Biorad) in Tris/glycine buffer. After migration, protein bands were
visualized by Coomassie blue staining (Biorad). For Western blotting,
the proteins in the SDS–PAGE gel were transferred onto nitrocellulose
membranes (Biorad) using a Trans-Blot Turbo Transfer system (Biorad).
Membranes were blocked with 3% bovine serum albumin (BSA) in TBS for
1 h at room temperature and incubated with anti His-tag antibody (1:2000,
Qiagen) for 1 h. The membranes were washed and incubated with an HRP-conjugated
anti-mouse secondary antibody (1:2000, Invitrogen) in 10% nonfat dried
milk. After washing, the protein bands were imaged with the ChemiDoc
MP system (Biorad) after incubation with Immobilion Western HRP Chemiluminescent
Substrates (Millipore).
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8

Murine Splenic CD4+ T Cell Proteome

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The lysates of murine splenic CD4+ T cells were prepared by homogenization with CelLytic M, supplemented with a protease inhibitor cocktail (Sigma-Aldrich). Protein concentration was determined using the Pierce BCA protein Assay kit (Thermo Fisher Scientific). The samples were run on a 4–20% Mini-PROTEIN TGX Precast Gel (Bio-Rad) electrophoresis (SDS-PAGE) and blotted on Amersham Hybond P 0.45 µm PVDF (GE Healthcare Life Sciences). Primary antibodies against CTSE at 1:2,000 dilution (NB400-152, NOVUS) and beta-Actin at 1:1,000 dilution (ab8227; abcam) in 5% bovine serum albumin in TBS supplemented with 0.1% Tween 20 (TBS-T) were incubated overnight at 4 °C. Then, the blots were washed with TBS-T and incubated with donkey anti-rabbit IgG-HRP (1:5,000; SANTA CRUZ) for 45 minutes at room temperature. After three-time washes with TBS-T, bands were visualized with enhanced chemiluminescence using the Pirece Western Blotting Substrate Plus (Thermo Fisher Scientific). Protein bands were semiquantified by densitometry using ImageQuant TL software (GE Healthcare Life Sciences).
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9

Western Blot Analysis of Midkine-a in Zebrafish

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Western blot analyses were performed as previously described (Calinescu et al., 2009a (link)). Briefly, proteins were extracted from the heads of 30–50 WT and mdkami5001 embryos or adult retinas (6 retinas from 3 animals per sample) in cold RIPA lysis buffer containing protease and phosphatase inhibitor mixture (Cell Signaling Technology). Proteins were separated in 12% Mini-PROTEIN TGX Precast gel (Bio-Rad) and were transferred to PVDF membranes (GenHunter). After blocking in 5% nonfat dry milk in Tris-buffered saline containing 0.3% Tween 20, membranes were incubated with rabbit anti-Midkine-a antisera or rabbit anti-STAT3 (Nelson et al., 2012 (link)) followed by HRP-conjugated secondary antibody (1:1000) (Calinescu et al., 2009a (link)). Immunolabeled proteins were detected using the enhanced ECL detection system for chemiluminescence assay (GE Healthcare). Actin was used as a loading control.
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10

Western Blot Analysis of Total Proteins

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Whole cell lysates were collected using urea lysis buffer containing 6.6M urea, 10mM Tris-HCl, 1% SDS, 5mM DTT, 1% Triton X-100, 10% Glycerol and 1 × protein inhibitor mix. Protein concentrations were determined by using Bio-Rad Protein Assay Kit I. The same amounts of total proteins were loaded onto a Mini-protein TGX precast gel (Bio-Rad, Hercules, CA) and electrophoresis was performed. The separated proteins were transferred onto PVDF membrane (Bio-Rad), blocked with 5% non-fat dry milk powder in TBST buffer (50mM Tris, pH 8.0, 150mM NaCl, 0.2% Tween-20), and probed with the appropriate antibody. Bands were visualized using chemiluminescence system (Thermo Scientific, Rockford, IL). Western blots were stripped in buffer containing 62.5mMTris-HCl, pH 6.7, 2% SDS, and 100mM 2-mercaptoethanol at 50°C for 1 h, washed 4–6 times in TBST buffer, and re-probed when needed. Western blot quantification was performed using Quantity One (Bio-Rad); the bands were automatically analyzed by the software. Signals were calculated by subtracting the detected intensity × mm2 by background. Signal from control was arbitrarily set as 1.00, while the signals of treated groups were denoted as the fold compared to the control.
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