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145 protocols using intercept blocking buffer

1

Quantitative Western Blot Analysis of RPE65

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Total protein content in cell lysate was estimated by Pierce Coomassie Protein Plus assay reagent (Thermo Fisher Scientific) with bovine serum albumin (Sigma-Aldrich) as a standard. Samples were combined with 4 × LDS sample buffer, denatured samples were separated by SDS–PAGE using 4–12% gradient BisTris NuPAGE (Invitrogen) and electro-transferred to nitrocellulose membrane using an iBlot2 gel transfer device (Thermo Fisher Scientific). Membranes were blocked with Intercept blocking buffer (LI-COR Biosciences) for fluorescent Western blotting and then probed with primary antibodies in Intercept blocking buffer for overnight at 4°C. The membranes were washed three times for 5 min each with 1 × TBS containing 0.1% Tween 20, incubated with IRDye 680RD and 800CW secondary antibodies (LI-COR Biosciences, NE; 1: 15,000) in Intercept blocking buffer for 1 h at room temperature and then washed three times with 1 × TBS containing 0.1% Tween 20. For detection, membranes were scanned on an Odyssey CLx Infrared Imager (LI-COR Biosciences) in the 700- and 800-nm channels. The primary antibody used was rabbit polyclonal anti-RPE65 antibody (1:2,000; custom made) (Redmond & Hamel, 2000 (link)).
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2

Mouse Brain Protein Extraction and Analysis

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Whole-cell lysates were prepared from mouse whole brains (E12.5 and E13.5) and cortices (E14.5 to P2). Cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (50mM Tris-HCl pH7.5, 150mM 5M NaCl, 0.5% Sodium Deoxycholate monohydrate, 0.1% sodium dodecyl sulfate (SDS) and 1% TritonX-100) supplemented with Protease Inhibitor (Roche, 11873580001). Extracted proteins were boiled for 10 min with 2X Laemmeli buffer (100mM Tris-HCl pH6.8, 4% SDS, 0.2% Bromophenol blue, 20% Glycerol and 5% β-mercaptoethanol) at 100°C. Proteins were separated by SDS-polyacrylamide gel electrophoresis (PAGE) electroblotted onto a polyvinylidene difluoride (PVDF) membrane (Millipore, IPFL00010). PVDF membrane was masked with Intercept Blocking Buffer (LI-COR, 927-70001) for 2 hrs at 4°C, incubated with primary antibodies in Intercept Blocking Buffer overnight at 4°C, washed with PBST (137 mM NaCl, 2.7mM KCl, 11.9 mM phosphates and 0.1% Tween20) and incubated with secondary antibodies in Intercept Blocking Buffer for 1 h at RT. After the final washes, fluorescence signals were detected using Odyssey DLx Imager (LI-COR).
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3

Western Blot Analysis of MLH1 Protein

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Cells were lysed in a buffer containing 50 mM Tris-HCl (pH 7.5), 200 mM NaCl, 1% Tween-20, 0.2% NP-40, 2 mM PMSF, and 50 mM β-glycerophosphate and protease inhibitor cocktail tablet (Roche). 40μg of protein lysates were loaded into SDS-PAGE mini-gels (Bio-Rad). The gel was then transferred onto nitrocellulose membranes for 2 hours at 100mV. Anti-MLH1 (1:1000) (BD Pharmingen) and anti-β-ACTIN (1:10000) (Sigma Aldrich) antibodies were diluted in Intercept Blocking Buffer (LI-COR Biosciences) and incubated overnight at 4°C. Fluorescent secondary antibody anti-mouse IgG-AlexaFluor488 (LI-COR Biosciences) was diluted (1:10000) in Intercept Blocking Buffer and incubated for 1 hour at room temperature. Image acquisition was perfomed using a Odyssey Clx machine (LI-COR Biosciences).
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4

Western Blot Analysis of Cell Signaling

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Nitrocellulose membranes containing the transferred proteins were blocked in Intercept Blocking Buffer (LI-COR Bioscience) for 1-hour at room temperature. Membranes were probed with primary antibodies, including mouse anti-mTOR (1:1000; Cat# 4517), mouse anti-Akt (1:1000; Cat# 2920), mouse anti-GSK3β (1:1000; Cat# 9832), mouse anti-ERK (1:1000; Cat# 9107), rabbit anti-phospho mTOR (1:1000; Cat# 5536 S), rabbit anti-phospho Akt (1:1000; Cat# 4060 S), rabbit anti-phospho GSK3β (1:1000; Cat# 5558), rabbit anti-phospho ERK (1:1000; Cat# 4376) (all antibodies were purchased from Cell Signaling Technologies) diluted in Intercept Blocking Buffer + 0.2% Tween-20 and incubated overnight at 4 °C, before being exposed to secondary antibody (IRDye® 680RD Donkey anti-Mouse IgG and IRDye® 800CW Donkey anti-Rabbit IgG) (LI-COR Biosciences) for 1-hour at room temperature in the dark.
Membranes were scanned on the LI-COR Bioscience Odyssey CLx imaging system and imaged using LI-COR Image Studio software version 2.1.10. All densitometry analyses were performed using Image Studio Light version 5. The region of interest encircling each band was defined automatically. All bands at the correct molecular weight were analyzed as the signal for that target protein. Values for each protein were normalized to loading control β-tubulin (Abcam).
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5

Xanthine Oxidase Protein Detection

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Electrophoresis used 4–12% Bis Tris gradient Criterion™ XT Precast Gels (Bio Rad, #3450123). Samples were resolved by SDS-PAGE and transferred to nitrocellulose. Membranes were blocked with Tris-Buffered Saline (TBS)-based LiCOR Intercept blocking buffer (LiCOR, 927–80001). The primary antibody was xanthine oxidase A-3 mouse monoclonal antibody (Santa Cruz, #398548), 1:500 dilution. Secondary antibody was LiCOR, 926–32210. Blots were imaged with the LiCOR Odyssey CLX.
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6

Western Blot Analysis of TGF-β1 Signaling

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Cells were seeded at 10 x 104 cells/well into 6-well plates and incubated in presence or absence of 10 ng/ml TGF-ß1 with or without terfenadine, ebastine, and solifenacin at 10 μM for 72h. Protein was isolated using RIPA buffer (Sigma Aldrich, UK). 20 μg of protein mixed with Li-Cor 4x protein loading buffer (Li-Cor, UK) and heat denaturated at 95°C under reducing conditions. Samples were then loaded onto Any kD Mini-PROTEAN® TGX Precast Protein Gels (Bio-Rad) along with a protein ladder (Bio-Rad). After gel electrophoresis, the separated protein was transferred onto a methanol-activated PVDF membrane (Millipore) by wet blotting at 350 mA for 1h. The membrane was washed and left to dry for 1h before being blocked with Li-Cor Intercept Blocking Buffer (Li-Cor) for 1h. The membranes were incubated overnight with primary antibodies (anti–α-SMA antibody, 1:3000 (Sigma-Aldrich); anti-fibronectin antibody, 1:1000 (ThermoFisher); anti-GAPDH, 1:10,000 (Abcam)) at 4°C on a shaker. Membranes were washed 4x with Tris-buffered saline containing 0.1% Tween 20 before incubation with secondary antibodies (Li-Cor, 1:10,000) for 1h on a shaker in darkness. This was followed by 4 washes with Tris-buffered saline containing 0.1% Tween 20. Blots were visualised using an infrared imaging system (Odyssey CLx imager; LI-COR) at 700 and 800 nm wavelengths simultaneously.
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7

Western Blotting for EV Protein Markers

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Western blotting was used to assess the presence of EV and non-EV protein markers. Equal protein amounts of EV samples were mixed with 4X Laemmli buffer (Bio-Rad), denatured for 5 min at 95 °C, and loaded onto 4–20% Mini-PROTEAN TGX Stain-Free Protein Gels (Bio-Rad). SDS-PAGE was run for 1.5 h at 90 V; then, proteins were transferred to nitrocellulose membranes (Cytiva) at 100 V for 1 h. Membranes were blocked with LI-COR Intercept Blocking Buffer (LI-COR Biosciences, Bad Homburg, Germany) for 1 h at RT. Blocked membranes were incubated overnight at 4 °C with primary antibodies diluted in LI-COR blocking buffer with 0.1% Tween-20. Membranes were washed with TBS-T (TBS with 0.1% Tween-20) three times for 5 min and then incubated with secondary antibodies for 1 h at RT. Incubation was followed by three additional washes with TBS-T of 5 min each. Blots were imaged using the Odyssey Infrared Imaging System (LI-COR Biosciences). The detailed list of primary and secondary antibodies used is provided in Supplementary Table S5. Original images shown in File S1.
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8

Comprehensive Western Blotting for EV Characterization

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Western blotting was used to assess the presence of EV and non-EV protein markers. Equal protein amounts of EV samples were mixed with 4X Laemmli buffer (Bio-Rad, Herculaes, CA, USA), denatured for 5 min at 95 °C, and loaded onto 4–20% Mini-PROTEAN TGX Stain-Free Protein Gels (Bio-Rad). SDS-PAGE was run for 1.5 h at 90 V, and then proteins were transferred to nitrocellulose membranes (Cytiva) at 100 V for 1 h. Membranes were blocked with LI-COR Intercept Blocking Buffer (LI-COR Biosciences) for 1 h at RT. Blocked membranes were incubated overnight at 4°C with primary antibodies diluted in LI-COR blocking buffer with 0.1% Tween-20. Membranes were washed with TBS-T (TBS with 0.1% Tween-20) 3 times for 5 min, and then incubated with secondary antibodies for 1 h at RT. Incubation was followed by 3 additional washes with TBS-T, 5 min each. Blots were imaged using the Odyssey Infrared Imaging System (LI-COR Biosciences). The detailed list of primary and secondary antibodies used is provided in Supplementary Table S1.
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9

Histone H3 acetylation analysis

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Western Blot was analyzed on protein extracted from experiment 1 using method from our previously published study (Claycombe-Larson et al., 2022). Proteins (25 μg) were resolved on Novex WedgeWell 4–20 % Tris-Glycine Gel (Invitrogen, Thermo Fisher Scientific, Carlsbad, CA, USA) and then transferred to a 0.45 μM Immobilon-FL transfer membrane (Millipore, Burlington, MA, USA) and incubated in Li-Cor Intercept Blocking Buffer (Li-Cor Biosciences, Lincoln, NE, USA) with primary antibodies anti-Histone H3 (acetyl K9) antibody ab10812 (Abcam, Cambridge, MA, USA), anti-acetyl-Histone H3 (Lys14) antibody 07–353 (Millipore, Burlington, MA, USA), and anti-acetyl-Histone H3 (Lys18) antibody 07–354 (Millipore, Burlington, MA, USA) with anti-histone H3 antibody ab10799 (Abcam, Cambridge, MA, USA) as an endogenous control. Images were developed with the Odyssey M (Li-Cor Biosciences, Lincoln, NE, USA) and analyzed with Empiria Studio Software (Li-Cor Biosciences, Lincoln, NE, USA).
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10

Western Blot Analysis of SARS-CoV-2 Proteins

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Cells were lysed with phosphate‐buffered saline (PBS) containing 0.1% Triton X‐100 (Merck Millipore) according to a standard procedure (Lozach et al, 2011b (link)). Cell lysates were then diluted in LDS sample buffer (Thermo Fisher Scientific) and analyzed by SDS–PAGE (Nu‐PAGE Novex 10% Bis‐Tris gels; Thermo Fisher Scientific). Proteins were subsequently transferred to polyvinylidene difluoride membranes (iBlot transfer stacks; Thermo Fisher Scientific). The membranes were first blocked with intercept blocking buffer (LI‐COR) and then incubated with primary antibodies against the SARS‐CoV‐2 spike, TMPRSS2, cathepsin L, EF2, actin, and α‐tubulin, all diluted in Tris‐buffered saline containing 0.1% Tween and intercept blocking buffer (1:1,000, 1:1,000, 1:400, 1:1,000, 1:5,000, and 1:2,000, respectively). After extensive washing, the membranes were incubated with the corresponding secondary antibodies conjugated to IRDye 700 or 800CW (both at 1:10,000) or HRP (1:1,000). Proteins were analyzed with a LI‐COR Odyssey CLx scanner, or alternatively, detected with SuperSignal West Pico PLUS chemiluminescent substrate (Thermo Fisher Scientific) and an Intas ChemoStar ECL analyzer.
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