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221 protocols using ab7291

1

Quantification of Spinal Cord Proteins

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For each group, three rat L4–L5 spinal cord segments were selected and stored in liquid nitrogen; 600 mL of RIPA lysis solution (P0013C, Beyotime, China) was added for total protein extraction. After extracting proteins from rat spinal cord tissue, the protein concentration was adjusted to 1 μg/μL using the SDS-PAGE protein sample loading buffer (B1012, Applygen, China). Protein samples (10 μg) were separated by SDS-PAGE and transferred to PVDF membranes (R1DB92455, Millipore, Germany), which were then incubated with primary antibodies at 4 °C overnight. The primary antibodies used were toll-like receptor 4 (TLR4) (1:1000, ab13556, Abcam), IKBα (1:1000, ab12134, Abcam), p-IKBα (1:1000, ab133462, Abcam), and α-tubulin (1:5000, ab7291, Abcam). The electroporated membrane was washed with TBST, incubated with the secondary antibody for 1 h at room temperature, and developed. Quantitative analysis of the protein bands was performed using ImageJ software. All western blots represent data from three independent replicates.
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2

Reagents and Antibodies for Protein Detection

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Unless otherwise stated, all (bio)chemicals and reagents were from Sigma-Aldrich (Dorset, UK). Tissue culture reagents and buffers were from Thermo Fisher Scientific (Paisley, UK). Molecular biology enzymes and reagents were from New England BioLabs (Hitchin, UK). Primers were ordered at Eurofins Genomics (Ebersberg, Germany). For western blotting, the following primary antibodies were used: mouse antitubulin (ab7291; 1:4000; Abcam, Cambridge, UK); rabbit anti–hexa-histidine tag (6xHis, ab9108; 1:4000; Abcam); and sheep anti–green fluorescent protein (produced in house). Secondary antibodies (800CW goat anti-mouse, 680RD goat anti-mouse, 800CW donkey anti-rabbit, and 800CW donkey anti-goat) and 680LT streptavidin were purchased from LI-COR (Cambridge, UK) and were all used at 1:10,000. Acetyl–norleucine–substance P (Ac-Nle-SP) and probe 1 were synthesized as described here.
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3

Western Blotting of Mitochondrial Complexes

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Cells were harvested in RIPA buffer followed by lysis by shaking the samples for 30 min at 950 rpm and 4 °C for 30 min. This was followed by centrifugation at 16,000g and 4 °C for 20 min to remove cell debris. Supernatants/lysates were kept at −80 °C until use. Then 10–20 μg of protein were separated on mini-PROTEAN TGX pre-stained gels (Bio-Rad) followed by activation of pre-stained Bio-Rad MP imager. The proteins were blotted onto Trans-Blot Turbo Transfer Packs (Bio-Rad), using Bio-Rad semidry blotter, and total protein for loading control was determined from the pre-stains. Membranes were blocked with 10% BSA or 5% skim milk (for mitochondrial complexes I–V experiments) in TRIS-buffered saline (TBS) unless otherwise stated and hybridized with antibodies for MICU2/EFHA1 (Abcam, ab101465), β-tubulin (Abcam, ab6046), α-tubulin (Abcam, ab7291), and mitochondrial complexes I–V (Abcam, ab110413).
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4

Protein Extraction and Western Blot Analysis

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RIPA lysis buffer (P0013B, Beyotime, Shanghai, China) with protease inhibitor (P0100, Solarbio life sciences, Beijing, China) was added to rat myocardial tissue or H9C2 cells to extract protein according to the manufacture’s protocol. The protein concentration was detected using a BCA Protein Assay Kit (P0012, Beyotime, Shanghai, China). Protein samples, which were mixed with loading buffer and heated at 100°C for 8 min, were separated by 12% SDS-PAGE gel electrophoresis and transferred to a polyvinylidene fluoride membrane (PVDF) pre-activated with methanol. The membrane was then blocked with 5% bovine serum albumin (BSA) for 1 h and immersed in the primary antibody solution overnight at 4°C. The primary antibodies were anti-NRF2, anti-HO-1 (E3F4S, CST, United States), anti-PKC (ab23511, Abcam, United Kingdom), anti-PKC (phosphor T497, ab59411, Abcam, United Kingdom), anti-α-tubulin (ab7291, Abcam, United Kingdom), and anti-H3 (17168-1-AP, Proteintech, Wuhan, China). The membranes were incubated with secondary antibodies (ZB-2301 or ZB-2305, ZSGB-BIO, Beijing, China) and the protein signals were detected using enhanced chemiluminescence (ECL) detection system. Images were analyzed using Image J software (National Institutes of Health, United States).
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5

EV-D68 Virus Infection Western Blot

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Western blot assay was performed
in RD cells. Briefly, RD cells seeded in six-well plates with 8.0
× 104 per well. After 24 h, the cells were inoculated
with EV-D68 virus at an MOI of 0.01 in the presence of gradient-diluted
compounds or DMSO for 1.5 h. After 12 hpi, cells were harvested and
lysed by 140 μL of RIPA lysis buffer. For Western blot analysis,
equal amounts of protein samples were separated on SDS-PAGE (10% polyacrylamide)
and then were transferred onto PVDF membrane (Roche, Indianapolis,
IN). Then the membrane was blockaded with 5% skimmed milk and incubated
with EV-D68 primary antibodies (GeneTex, GTX132313) and tublin primary
antibodies (abcam, ab7291). Then the membrane was incubated with the
corresponding HRP-conjugated secondary antibody (abcam, ab6721, and
ab6789). The proteins were detected with the ECL luminescence reagent
(ThermoFisher Scientific, Waltham, MA).
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6

Exosome-mediated Neuroprotection in Oxidative Stress

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Exosomes in ERCMs obtained from AMMSCs were labeled with red CM-DiI membrane dye (C7000; Invitrogen) and prepared at 4 × 1010 particles/mL [45 (link),49 (link),50 (link)].
pRGCs were seeded on 8-well chamber slides (NUNC C7182; Thermo Fisher Scientific, Waltham, MA, USA) at 1 × 105/mL. After 24 h, cells were damaged with 150 µM H2O2, and then incubated with labeled exosomes (50 μL/mL) for 4 h at 37 °C in a CO2 (5%) incubator. The cells were fixed with 4% paraformaldehyde for 20 min at room temperature. Fixed cells were treated with 0.1% Triton X-100 (Thermo Fisher Scientific) at room temperature. Five min later, they were washed in PBS, and blocked with 1% bovine serum albumin (BSA) for 1 h. The cells were immunostained with anti-α-tubulin antibody (1:1000, ab7291; Abcam, Cambridge, UK) for 2 h at 37 °C followed by goat anti-mouse IgG Alexa FluorTM 488 (1:500, Invitrogen) for 1 h at room temperature. The cell nuclei were stained with DAPI (Thermo Fisher Scientific) and examined under a microscope (BX51; Olympus, Tokyo, Japan) [45 (link),49 (link)].
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7

Protein Expression Analysis in Muscle

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Western blotting was performed on whole-muscle homogenate as previously described (21 (link)) using the following commercially available antibodies: α-tubulin (Ab7291; Abcam), ANT1 (MSA02; MitoSciences), ANT2 (AP1057; Millipore), 4HNE (HNE11-S; Alpha Diagnostic International), OXPHOS (MS604; MitoSciences), COXIV (Invitrogen), CAT (AB1877; Abcam), and SOD2 (AB11889; Abcam), and for protein carbonylation, the OxyBlot Protein Oxidation Detection Kit (S7150; Millipore) was used. Ponceau staining was used to confirm equal loading for antibodies that required the entire membrane (e.g., 4HNE and protein carbonylation). In addition, Western blotting was performed on recovered permeabilized fibers following respiration protocols as previously described (30 (link)). All samples for a given protein were detected on the same membrane using chemiluminescence and the FluorChem HD imaging system (Alpha Innotech, Santa Clara, CA).
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8

Profibrotic Factors Regulation of Fibrosis

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Human EGF and bFGF were from Thermo Fisher Scientific (NY, USA). Human TGFβ1 and TNF-α were from R&D systems, Inc. (MN, USA). Human TGFβ2 and TGFβ3 were from Prospec-Tany TechnoGene Ltd. (East Brunswick, NJ, USA). Thrombin, PD98059, SB202190, SP600125 were purchased from Sigma-Aldrich Chemical Co. (St Louis, MO, USA). Human recombinant VEGF was purchased from Prospect Biotech (Rehovot, Israel). Estrogen and progesterone were purchased from Cayman Chemical Co. (Ann Arbor, Michigan, USA). Recombinant human CTGF was obtained from Thermo Fisher Scientific eBioscience (Waltham, MA, USA). The antibodies (Abs) raised against vimentin (sc-6260), HSP47 (sc-8352) and phospho-Smad2/3 (sc-11769) were from Santa Cruz Biotechnology Inc. (Dallas, TX, USA). The Ab for total Smad2/3 (#3102) was purchased from Cell Signaling Technology, Inc. (Danvers, Massachusetts, USA). The Ab for α-SMA (GTX100034) was purchased from GeneTex (Hsinchu City, Taiwan). The Abs for collagen (ab34710), CTGF (ab6992) and α-tubulin (ab7291) were purchased from Abcam (Cambridge, MA). TGFβ isoforms were dissolved in 4 mM HCl/0.1% BSA (vehicle).
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9

Quantifying Intracellular Protein Delivery

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To determine the delivered protein in cells and check the leakage of the in-cell NMR samples, each cell sample was centrifuged at 300 g for 3 min immediately after the experiment. Then the supernatants and pellets were resuspended in Laemmli buffer to a final volume of 500 μL, and boiled for 10 min. These samples were diluted by 10 times, and loaded to a 15% SDS-PAGE gel. The primary antibodies used were listed as follows: Tau/k19 (abcam, ab64193, 1:1000), pk19 (abcam, ab75603, 1:1000) and tubulin (abcam, ab7291, 1:1000). Delivered k19 in HEK-293T cells was ~25 μM measured by ImageJ (Available online: https://imagej.net/Welcome) [54 (link)].
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10

Protein-Protein Binding Assay

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Glutathione Sepharose 4B beads (17-0756-01, GE Healthcare) were incubated with 10 μg GST or 10 μg GST-ABS6329–387 in PEM buffer for 1 h at 4 °C. GST- or GST-ABS6329–387-bound beads were washed with the PEM buffer for three times, incubated with 10 μg tubulin for 1 h, washed again with the PEM buffer for three times, and eluted with the elution buffer (50 mM Tris-HCl pH8.0, 10 mM reduced glutathione). All buffers used in pull-down assays were supplemented with 1 mM dithiothreitol and 1 × protease inhibitor cocktail (04693132001, Roche). Input and pull-down fractions were immunoblotted with anti-GST (ab19256, Abcam) and anti-tubulin (ab7291, Abcam) antibodies.
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