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Loading buffer

Manufactured by Thermo Fisher Scientific
Sourced in United States, Germany, China, United Kingdom

Loading buffer is a laboratory solution used to prepare samples for gel electrophoresis. It adjusts the density of the sample and allows it to sink into the gel. The buffer may also contain tracking dyes to visually monitor the progress of the electrophoresis.

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104 protocols using loading buffer

1

DNA Origami Assembly with QD Labeling

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To assemble Pep-biotin-streptavidin-QD655, pentagonal pyramid wireframe DNA origami objects with a biotin domain at the inner center or outer edge were incubated with Streptavidin QD655 (molar ratio was 1:4) at room temperature for 2 h. The mixture (15 μL) was then combined with 3 μL of 6× loading buffer (NEB) and loaded to a 0.8% agarose gel with 1× TAE and 12 mM MgCl2 and 1× SYBR Safe (Thermo Fisher Scientific, Waltham, MA). Each gel was run at 65 V for 2 h in 1× TAE with 12 mM MgCl2 at 4 °C. Gels were then visualized under blue light. To assemble Pep-30 nt A*-QD630, pentagonal pyramid wireframe DNA origami objects with ps-backbone-based ssDNA wrapping domain at the inner center or outer edge were incubated with QD630 (molar ratio was 1:4 or 4:1) at room temperature overnight. The mixture (15 μL) was then combined with 3 μL of 6× loading buffer (NEB) and loaded to a 0.8% agarose gel with 1× TAE and 12 mM MgCl2 and 1× SYBR Safe (Thermo Fisher Scientific, Waltham, MA). Each gel was run at 65 V for 1 h in 1× TAE with 12 mM MgCl2 at 4 °C. Gels were then visualized under blue light. All DNA sequences are summarized in Supplementary Tables 6 and 8.
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2

Phospho-Signaling Pathway Profiling of Naïve T Cells

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Naïve T cells were isolated from PBMCs, activated in the presence or absence of FTY720, and collected after 15, 30, 60, or 120 min. Cells were lysed with RIPA assay buffer (Thermo Scientific) supplemented with protease and phosphatase inhibitors (Thermo Scientific). Total protein concentration was determined by BCA assay (Thermo Scientific). Samples were prepared with 20 μg of protein, loading buffer (Life Technologies), and reducing agent (Life Technologies) and then heated for 10 min at 70 °C before use. Samples were run on a 10 % bis-tris gel (NOVO, Life Technologies), transferred to PVDF membrane, and detected by immunoblot. The following antibodies were used: p-AKT (Cell Signaling Technology), p-GSK3β (Cell Signaling Technology), pan-AKT (Cell Signaling Technology), pan-GSK3β (Cell Signaling Technology), beta actin (Cell Signaling Technology), and anti-rabbit IgG HRP (Cell Signaling Technology). The membrane was blocked with 5 % bovine serum albumin followed by primary and secondary antibody incubations as per the manufacturers’ instructions. Immunoblots were developed using ECL Prime (GE Healthcare).
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3

Western Blot Analysis of Protein Lysates

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Total cell lysates were prepared from biopsy protein following Qiazol (QIAGEN) RNA extraction. Briefly, protein pellets were resuspended in Laemmli buffer, incubated at 37°C for 30 minutes, vortexed briefly, and heated to 95°C for 5 minutes before electrophoresis. Cells were lysed using MPER lysis buffer (Sigma-Aldrich, St. Louis, MO) supplemented with protease inhibitors (Roche) and sodium orthovanadate (10 mM) (Sigma-Aldrich). Loading buffer (Life Technologies) was added and samples were heated to 95°C for 5 minutes, subjected to electrophoresis on 4-12% NuPAGE Bis-Tris gels (Life Technologies), transferred to nitrocellulose membranes (Life Technologies), and visualized using the Odyssey CLx system (LI-COR Biosciences, Lincoln, NE) with IRDye 800RD goat anti-rabbit (LI-COR) and IRDye 680RD goat anti-mouse (LI-COR Biosciences) secondary antibodies. Primary antibodies were: anti-LRRC31 (ab100379; Abcam PLC, Cambridge, UK) and anti-HSP90 (AF7247; R&D Systems, Minneapolis, MN). Blots were quantified using Image Studio (LI-COR).
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4

Western Blot Analysis of Protein Lysates

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Total cell lysates were prepared from biopsy protein following Qiazol (QIAGEN) RNA extraction. Briefly, protein pellets were resuspended in Laemmli buffer, incubated at 37°C for 30 minutes, vortexed briefly, and heated to 95°C for 5 minutes before electrophoresis. Cells were lysed using MPER lysis buffer (Sigma-Aldrich, St. Louis, MO) supplemented with protease inhibitors (Roche) and sodium orthovanadate (10 mM) (Sigma-Aldrich). Loading buffer (Life Technologies) was added and samples were heated to 95°C for 5 minutes, subjected to electrophoresis on 4-12% NuPAGE Bis-Tris gels (Life Technologies), transferred to nitrocellulose membranes (Life Technologies), and visualized using the Odyssey CLx system (LI-COR Biosciences, Lincoln, NE) with IRDye 800RD goat anti-rabbit (LI-COR) and IRDye 680RD goat anti-mouse (LI-COR Biosciences) secondary antibodies. Primary antibodies were: anti-LRRC31 (ab100379; Abcam PLC, Cambridge, UK) and anti-HSP90 (AF7247; R&D Systems, Minneapolis, MN). Blots were quantified using Image Studio (LI-COR).
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5

Protein Extraction and Analysis from Esophageal Biopsies

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Total cellular protein was extracted from esophageal biopsies with TRIzol (Invitrogen) according to the manufacturer’s instructions. Cell cultures were lysed with RIPA buffer with protease inhibitor cocktail. Loading buffer (Life Technologies) was added, and samples were sonicated, heated to 95°C for 10 minutes, and spun at 15,294 g for 10 minutes to separate the desired supernatant from the insoluble pellet. Samples were subjected to electrophoresis on 4% to 12% NuPAGE Bis-Tris gels (Life Technologies) and transferred to nitrocellulose membranes using the novex iblot system (Life Technologies) and a LICOR Odyssey CLx imager (LI-COR). Primary antibodies were used at a 1:1,000 dilution and included the following: anti-DSG1 (sc-20114, Santa Cruz Biotechnology), anti-CAPN14 (HPA035720, Sigma-Aldrich), anti-HSP-90 (61014, BD Biosciences), anti-CAPN1 (HPA005992, Sigma-Aldrich), and anti–β-actin (A5441, Sigma-Aldrich). Secondary antibodies were used at 1:10,000 and included the following: goat anti-mouse (926–68070, LI-COR) and goat anti-rabbit (926–3221, LI-COR). Blots were visualized using the Odyssey CLx system (LI-COR) and were quantified using Image Studio (LI-COR).
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6

Western Blot Analysis of NF-kB Activation

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Total PBMCs were Lysed with RIPA buffer (Pierce) containing HALT protease inhibitors (Pierce). Total protein was determined by BCA assay (Pierce) and 10 ug total protein run/lane. Samples were prepared with Loading buffer (Life technologies), and heated for 10 minutes at 72°C prior to running on Western. Samples were run on a 10% Bis-Tris gel and transferred to nitrocellulose by XCELL western blot transfer apparatus (Life Technologies). Blots were blocked with 1X TBS, 0.1% Tween-20 with 5% w/v nonfat dry milk overnight. P105/p50 NFκB and actin (Cell Signaling Technology) were stained overnight, washed 3 times with 1x TBS and 0.1% Tween-20, and labeled with HRP linked anti-mouse IgG (Cell Signaling Technologies). Blots were developed using ECL Prime (GE Healthcare). Densitometry was performed using ImageJ analysis software (NIH)
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7

Western Blot Analysis of DSP, PPL, and FLAG

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Proteins from cell cultures were extracted with RIPA Lysis and Extraction Buffer (Thermo Fisher Scientific) with protease and phosphatase inhibitors unless otherwise noted. Loading buffer (Life Technologies) was added, and samples were heated to 95 °C for 5 min, subjected to electrophoresis on 4–12% NuPAGE Bis-Tris gels (Life Technologies), transferred to nitrocellulose membranes (Life Technologies), subjected to western blot analysis and visualized using the Odyssey CLx system (LI-COR Biosciences). The primary antibodies were anti-DSP (MAB9080, R&D Systems) (1:2000 dilution), anti-PPL (ab131269, Abcam) (1:2000 dilution) and anti-FLAG (F3165, Sigma-Aldrich) (1:2000 dilution). Anti-GAPDH antibodies (ab181602, Abcam; TA802519, Origene) (1:2000 dilution) and anti-HSP90 antibodies (ab13495, Abcam; TA500494, Origene) (1:2000 dilution) were used as loading controls. The secondary antibodies used were IRDye 680RD goat anti-mouse (LI-COR Biosciences) (1:10,000 dilution) and IRDye 800CW goat anti-rabbit (LI-COR Biosciences) (1:10,000 dilution). Blots were quantified using the Image Studio software (LI-COR Biosciences).
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8

Western Blot Analysis of TMPRSS2 Expression

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Protein lysates of HEK-293T cells were extracted with RIPA buffer (PIERCE) and protease inhibitor cocktail (Roche). Loading buffer (Life Technologies) was added, and samples were heated to 95°C for 5 minutes and subjected to electrophoresis in 12% NuPAGE Bis-Tris gels (Life Technologies). Gels were transferred to nitrocellulose membranes (Life Technologies) and probed with the primary antibodies rabbit anti-V5 (Bethyl Laboratories), mouse anti-TMPRSS2 (Santa Cruz), and rabbit anti-human GAPDH (ABCAM) and subsequently with the secondary antibody IRDye 800RD goat anti-rabbit and IRDye 680RD goat anti-mouse (LI-COR Biosciences). Membranes were visualized and analyzed using the Odyssey CLx system (LI-COR Biosciences). For TMPRSS2 quantity estimations, recombinant TMPRSS2 was subjected to gel electrophoresis with protein lysates from TMPRSS2-overexpressing cells.
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9

IGF1R Expression in Cancer Cell Lines

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Whole cell lysates from S2VP10L, MiaPaCa-2, S2013, and SCC-1 cells were collected to determine IGF1R expression. The cells were plated at a density of 5x105 cells per well in a 6-well plate 24 h prior to protein harvest. Cells were then lysed in a solution containing 1 % NP-40, 1 % protease inhibitor, and 1 % phosphatase inhibitor (Thermo) in deionized water. The lysates were centrifuged at 13,000×g for 10 min. Total protein concentration was determined via Bradford assay (Bio-Rad, Hercules, CA, USA).
Approximately 50 µg of total protein was dissolved in deionized water, loading buffer, and reducing agent (Life Technologies, Carlsbad, CA, USA). Proteins were separated using NuPage 4–12 % Bis–Tris gel and transferred onto a nitrocellulose membrane by iBlot (Life Technologies). The membrane was blocked in blocking buffer (Li-Cor) for 30 min and then incubated overnight at 4 °C with IGF1R antibody (Abcam, Cambridge, England) at a concentration of 1 µg/mL and β-Actin antibody (Thermo) at a concentration of 1:3000. The membrane was then washed 3× with TBS (20 mM Tris–HCl, 150 mM NaCl in diH2O) for 10 min each, incubated with donkey anti-mouse IRDye 680RD and donkey anti-rabbit IRDye 800CW secondary antibodies (Li-Cor) for 1 h, washed 3× with TBS for 10 min each, and scanned using Li-Cor Odyssey infrared scanner. Dosimetry was performed using Li-Cor software.
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10

Western Blot Analysis of Exosomal Proteins

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RIPA lysate (Pierce) was added to the tissues/cells to obtain the protein that was mixed with the loading buffer (Life Technologies) at a ratio of 3:1, and boiled at 100°C for 8‐10 min. Protein samples were added to the gel well and the target protein was separated by electrophoresis. The protein was transferred to a PVDF membrane (Millipore), and non‐specific antigens blocked with 5% skim milk. The membranes were incubated with corresponding primary antibodies: anti‐CD9 (1:500; Proteintech), anti‐CD63 (1:500; Proteintech), anti‐CD81 (1:500; Proteintech), anti‐NEDD8 (1:500; CST), anti‐cullin 1 (1:500; Abcam), anti‐IκB (1:500; CST), anti‐NF‐κB (1:500; Abclonal), anti‐P‐NF‐κB (1:500; Abclonal), anti‐PCNA (1:500; Abcam), and anti‐β‐actin (1:500; SAB) overnight at 4°C. After washing with 1× TBS/T buffer, the membranes were incubated with the secondary antibody for 30 min at 37°C. Pictures were taken with a chemical gel imaging system (GE).
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