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14 protocols using anti rabbit sc 2004

1

Western Blot Analysis of COPZ1 in Cancer Cells

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PLC/PRF/5 and Huh7 cells were collected, washed twice with pre-cooled PBS, and then lysed for 30 min on ice using a cell lysis buffer (Beyotime, P0013, Haimen, China), containing 1 percent protease inhibitor (PMSF), and 1 percent phosphokinase inhibitor. The supernatant protein lysate was then collected. Protein concentration was measured by a Pierce BCA Protein Assay kit (Thermo Scientific, Waltham, MA, USA). A PVDF membrane was then used to transfer the separated cellular lysates that had been separated using a 10% SDS-PAGE gel. The chosen primary antibodies were probed with the PVDF membrane overnight at 4 °C after it had been masked with 5% BSA buffer for an hour at room temperature. The primary antibodies against COPZ1 (1:1000; Proteintech, 20440-1-AP, Sankt Leon-Rot, Germany) and GAPDH (1:5000; AM102013) were used. After that, 1×TBST (washing buffer) washed the mem-brane 3 times for 10 min each time. After being incubated with a secondary antibody for an hour at room temperature, the protein membrane was washed with 1×TBST three times for a total of ten minutes. The secondary anti-mouse (sc-2005) and anti-rabbit (sc-2004) antibodies were purchased from Santa Cruz Biotechnology. An ECL chemiluminescence hypersensitive colorimetric kit and a chemiluminescent imaging system were used for signal generation and detection.
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2

GLUT1 Protein Expression Analysis

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Western blot analysis was performed in LOVO and SW480 cells using the following primary antibodies: GLUT1 (21829-1-AP, Proteintech) and α-tubulin (T 6074, Sigma-Aldrich). Briefly, the cell pellet was mixed with LDS sample buffer (Life Technologies) and sample reducing agent (Life Technologies), according to the manufacturer’s protocol. Proteins extracted were loaded onto a SDS-PAGE (Novex 4–12% Bis–Tris gel, Life Technologies), transferred to a nitrocellulose membrane by iBlot (Life Technologies), and blocked 1 h with 1× TBST buffer (Fisher Scientific) with 5% w/v nonfat dry milk. The membranes were incubated in blocking buffer at 4 °C overnight with primary antibody against GLUT1 (1:1000) or 1 h at room temperature for α-tubulin (1:3000). Subsequently, the membranes were washed three times with Tris-buffered saline with Tween-20 (TBST) and incubated 1 h with secondary antibodies (1:5000; anti-rabbit sc-2004, Santa Cruz Biotechnology; or 1:3000; anti-mouse A9044, Sigma-Aldrich). The signal was obtained using the Novex ECL Chemiluminescent Substrate Reagent kit (WP 20005, Invitrogen) and the images were developed and quantified using the Chemidoc System (Bio-Rad).
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3

Western Blot Analysis of Cell Lysates

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Western blot analysis in protein lysates derived by cell lines was performed as previously described 19 (link). Briefly, SDS-PAGE was conducted using 8%-12% gradient Tris-Glycine gels (Invitrogen) and loaded with 30ugs of total protein lysates. Membranes were blocked in TBS + 5% nonfat milk, primary and secondary antibodies were incubated overnight at 4° C or for 2h at RT, respectively, in TBS + 0.1% Tween-20 + 5% nonfat milk (pStat3 was incubated in TBS + 0.1% Tween-20 + 5% BSA). Primaries used were: β-actin ms (1:1000, 130065; Santa Cruz Biotech, Inc), pStat3 (Tyr705) rb (1:1000, 9145S; Cell Signaling, Inc), b-catenin rb (1/3000, ab6302; Abcam, Cambridge, MA), vimentin ms (1/2000, ab8069; Abcam), E-cadherin rb (1/500, ab53033; Abcam), ZEB1 rb (1/500, SAB3500514; Sigma-Aldrich, Saint Louis, MO), CRHR2 (1/1000, ABN433; Millipore, Temecula, CA). Horseradish peroxidase (HRP)-tagged IgG secondary antibodies were anti-mouse (sc2005; Santa Cruz Biotech, Inc) or anti-rabbit (sc2004; Santa Cruz Biotech, Inc) used at 1/2000 dilution. Chemiluminescence was detected with enhanced reagent (34080; ThermoScientific, Rockford, IL) using an Eastman Kodak Co. 440 Imaging System (Kodak, Rochester, NY). Beta-actin was used as a loading control.
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4

Immunoblotting of proteasome subunits

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EndoC-βH1 cells were lysed in RIPA buffer supplemented with a protease inhibitor cocktail (Roche Applied Science, Germany). Protein quantification was performed using the BCA protein assay kit (Thermo Fisher Scientific, USA). A total of 25 µg of protein was subjected to electrophoresis on 12% acrylamide/bis acrylamide SDS page gels. After electrophoresis, proteins were transferred onto nitrocellulose membranes (GE Healthcare, USA). Membranes were stained with primary antibodies overnight at 4°C and secondary HRP-conjugated antibodies (Santa Cruz Biotechnology, USA) for 1h at room temperature. Primary antibodies were from Enzo Life Sciences (Switzerland) and were used at a dilution of 1:1000 (β1i: BML-PW8345; β5i: BML-PW8355; β2i: BML-PW8350). The loading control was β-actin (MAB1501, EMD Millipore, USA) and was used at 1:1000 dilution. Secondary antibodies were anti-mouse (#G21040) or anti-rabbit (#sc-2004) antibodies from Santa Cruz Biotechnology and were used at a dilution of 1:5000. Western ECL substrate was used for imaging (1705062, BioRad, USA).
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5

Protein Extraction and Western Blot Protocol

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Cells were lysed in buffer containing 50 mM Tris-HCl pH = 7.5, 120 mM NaCl, 1 mM EGTA, 6 mM EDTA, 15 mM Na4P2O7, 20 mM NaF, and 1% Triton X-100 protease inhibitor cocktail. Lysates were clarified by centrifugation at 10,000× g for 15 min at 4 °C, and supernatants were quantified for protein content (Coomassie Blue reagent, Bio-Rad, Hercules, CA, USA). All passages were carried out on ice as described by Rapizzi et al. (Rapizzi et al., 2014). Proteins were separated by 8% or 12% sodium dodecyl sulfate polyacrylamide (SDS/PAGE) gels and transferred to PVDF membranes (Fisher Scientific or Immobilon, Millipore, MA, USA). Primary antibodies against alpha-tubulin (#3873), cyclin D1 (#55506), phospho-AMPK (Thr172) (#2535), phospho-Erk1/2 (#9106s), Erk1/2 (#9102s), N-Cadherin (#14215s), and E-Cadherin (#14472s), were from Cell Signaling Technology. Phospho-Akt (Ser473) (sc7985), Akt (sc8312), and all the secondary HRP conjugated antibodies (anti-mouse, sc-2005, and anti-rabbit, sc-2004) were obtained from Santa Cruz Biotechnology (Dallas, Texas, USA).
Protein bands were detected with ECL reagents (Immobilon Crescendo, Millipore, Burlington, MA, USA). ImageJ software was used for the densitometric analysis of the bands.
The original whole blot (uncropped blots) showing all the bands are reported in the Supplementary Materials.
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6

Quantitative Western Blot Analysis of MACC1 Protein

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Total protein samples from control and octreotide treated GH3 cells were extracted by RIPA buffer (50 mM Tris-HCl; pH 8.0, 150 mM NaCl, 5 mM EDTA, 1% Igepal CA-630, 0.5% sodium deoxycholate, 0.1% SDS, and supplemented with Halt™ protease inhibitor cocktail; Thermo Fisher Scientific). Protein concentration was quantified with BCA Protein Assay reagent (Thermo Fisher Scientific), according to the manufacturer’s instructions. Lysates (45 µg) were electrophoresed through a 10% SDS-PAGE gel and transferred to Hybond-C-extra nitrocellulose membranes (Amersham Biosciences) for 45 min in a semi-dry transfer system. Membranes were blocked with 5% non-fat milk in TBS-T buffer (20 mM Tris, pH 7.6, 137 mM NaCl, and 0.05% Tween 20) for 1 h at room temperature. Membranes were incubated with 1 µg/ml MACC1(PA5-20758, Thermo Fisher Scientific) and 1 µg/ml β-actin (ab8224, Abcam) primary antibodies for 1 h at room temperature and incubated with horseradish peroxidase-conjugated anti-mouse IgG (sc-2005, Santa Cruz Biotechnology) and anti-rabbit (sc-2004, Santa Cruz Biotechnology) secondary antibodies for 1 h at room temperature. Membranes were then washed in TBS-T buffer three times and developed with Pierce ECL western blotting substrate (Thermo Fisher Scientific). UVP software VisionWorks LS (Thermo Fisher Scientific) was used to capture signals.
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7

Cardiac Protein Expression Analysis

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The protein extraction buffer contained 100 mmol/L Tris‐HCl (pH 8.0), 0.1% sodium dodecyl sulphate, 1% Triton X‐100, 150 mmol/L NaCl and protease inhibitor cocktail (Roche). The cardiac protein extracts were separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis and then transferred to polyvinylidene difluoride membranes (Millipore) that were incubated with the listed antibodies: Cav1.2 (1:1000, AACC‐033, rabbit polyclonal antibody; Alomone Labs, Jerusalem, Israel), CaMKII (1:1000, sc‐5306, mouse monoclonal antibody; Santa Cruz Biotechnology, Dallas, USA), NCX (1:1000, mouse monoclonal antibody, ab2869; Abcam), SERCA2a (1:5000, sc‐376235, mouse monoclonal antibody; Santa Cruz Biotechnology, Dallas, USA) and α‐tubulin (1:10 000, sc‐5286, mouse monoclonal antibody; Santa Cruz Biotechnology, Dallas, USA). Subsequently, the membranes were incubated with anti‐mouse (sc‐2056; Santa Cruz Biotechnology, Dallas, USA or anti‐rabbit (sc‐2004; Santa Cruz Biotechnology, Dallas, USA) secondary IgG antibodies at a dilution of 1:10 000. Immunoreactive proteins were detected by enhanced chemiluminescence (GE Healthcare, Chicago, USA) and quantified using the ImageJ software.
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8

Analyzing Integral Membrane Proteins

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Protein extracts from cell lines and tissues were prepared and analysed as previously reported.32 (link) Antibodies to calreticulin (ab2907), TAPBP (ab140982), ERP57 (ab13506) and MHC class I (ab70328) were from Abcam (Cambridge, MA, USA); PPARγ (sc-7273), TRAP1 (sc-9134), GRP78 (sc-13968), anti-mouse (sc-2031) and anti-rabbit (sc-2004) were from Santa Cruz Biotechnology (Dallas, TX, USA); ANXA1 (71–3400) from Thermo Fisher, β-Actin (F-3022) from Sigma-Aldrich (Milan, Italy); E-cadherin (BD 610405) from BD transduction (BD Biosciences, San Jose, CA, USA). To analyse surface proteins, we used an extraction method based on a published procedure. Positivity for E-cadherin, a plasma membrane protein, and negativity for β-Actin, a cytosolic protein, proved that the identified proteins were truly integral membrane components. Comassie blue staining was also used for assessing equivalent protein load. Proteins were then analysed by western blotting as previously reported.32 (link), 33 (link)
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9

Protein Extraction and Western Blot Analysis

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Total cellular protein was extracted using Pierce RIPA Buffer (Thermo Scientific) supplemented with PhosSTOP Protease Inhibitor Cocktail Tablets (Roche Life Science). For the placenta, frozen tissues were thawed for several minutes in pre-chilled RIPA buffer and homogenized with a Polytron (Kinematica). Western blotting was performed by using AnykD Mini-PROTEAN TGX Gels (Biorad, Hercules, CA, USA) and nylon/nitrocellulose membranes (Biorad). Primary and secondary antibodies used were: rabbit anti-IRS1 (1:500, sc-559, Santa Cruz Biotechnology), rabbit anti-GLUT4 (1:1,000, 07-1404, Millipore), mouse anti-β-Actin (1:5,000, Sigma-Aldrich), goat anti-Mouse (sc-2005, Santa Cruz Biotechnology), and/or anti-Rabbit (sc-2004, Santa Cruz Biotechnology), human anti-HRP (1:2,000, Santa Cruz Biotechnology). HRP activity was detected by using SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific). Densitometric analysis and protein quantification of the western blots was performed by using Image Lab Software (version 5.2.1). Blots were stripped briefly in 0.2 M sodium hydroxide and reprobed for mouse anti-β-Actin (Sigma-Aldrich) as a loading control.
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10

Coimmunoprecipitation and E-cadherin Cleavage Analysis

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Coimmunoprecipitation was performed as described [7] (link). Cell lysates and coimmunoprecipitates were analyzed as previously described [20] (link). Blots were incubated with relevant primary antibodies (as detailed in Supplementary Methods) in Tris-buffered saline and 5% non-fat dry milk. Hybridized filters were washed in TBS, 0.1% Tween-20. Antibody binding was revealed by chemiluminescence, using horseradish-peroxidase-conjugated anti-mouse (#401215; Calbiochem), anti-rabbit (sc-2004; Santa Cruz Biotechnology) or anti-goat (sc-2020; Santa Cruz Biotechnology) pAbs. Cleavage of E-cadherin was assessed by comparing the signals from the antibodies recognizing the extracellular and intracellular domains of human E-cadherin. Ponceau red staining was routinely used as control of protein loading [21] (link). Signal intensity was quantified with ImageJ 1.47, using as reference a Kodak gray-scale standards power curve.
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