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6 protocols using β tubulin

1

Piezo1 Protein Expression in Myoblasts and Myotubes

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Total protein lysates were obtained from EDL- and SOL-derived myoblasts and myotubes. After exposure to RIPA buffer (Thermo Fisher Scientific, Yokohama, Japan). Primary antibodies (Piezo1, Proteintech, 15939-1-AP) and β-tubulin (Wako, 10G10) diluted 1:100 and 1:5000 respectively in 5% skim milk, were incubated either for 90 min (β-tubulin) or at 4 °C overnight (Piezo1). Samples were then incubated with HRP-conjugated secondary antibodies (Cell signalling, anti-rabbit, 7074P2, and anti-mouse, 7076S) in 5% skimmed milk at 1:5000 dilution for 1 h at room temperature. Samples were visualised by chemiluminescence with a digital luminescent image analyser LAS-4000 (GE Healthcare, Tokyo, Japan).
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2

Mitochondrial Protein Expression Analysis

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The following antibodies were used: mtIF2 (1:200, Santa Cruz Biotechnology, Dalla, TX, USA, sc‐365477); mtIF3 (1:2000, Origene, Rockville, MD, USA, TA800421); mtEFTu (1:5000, Abcam, Cambridge, UK, ab173300); mtEFTs (1:10,000, Abcam, ab173528); mtEFG1(1:3000, Abcam, ab173529); mtRF1L (1:1000, Proteintech, Rosemont, IL, 16694‐1‐AP); mtRRF1 (1:1000, Proteintech, 12357‐2‐AP); mtEFG2 (1:1000, Proteintech, 16941‐1‐AP); TACO1 (1:3000, Proteintech, 21147‐1‐AP); insulin receptor substrate 1 (IRS‐1, 1:3000, Cell Signaling Technology, Danvers, MA, USA, #3194); hormone sensitive lipase (HSL, 1:3000, Cell Signaling Technology, #18381); glyceraldehyde 3‐phosphate dehydrogenase (GAPDH, 1:10000, Wako, Osaka, Japan, 016‐25523); β‐tubulin (1:10,000, Wako, 014‐25041).
We used the Total OXPHOS Rodent WB Antibody Cocktail (1:3000, Abcam, ab110413) to detect the proteins involved in mitochondrial oxidative phosphorylation (OXPHOS). This cocktail contains five monoclonal antibodies: mitochondrial NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 (NDUFB8, ab110242); mitochondrial succinate dehydrogenase [ubiquinone] iron‐sulfur subunit (SDHB, ab14714); mitochondrial cytochrome b‐c1 complex subunit 2 (UQCRC2, ab14745); mitochondrial encoded cytochrome c oxidase I (MTCO1, ab14705); mitochondrial ATP synthase subunit alpha (ATP5A, ab14748).
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3

Western Blotting Protocol for GPER1 Detection

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Antibodies specific to GPER1 (ab39742; Abcam, Cambridge, MA, USA), β-actin (sc-47778; Santa Cruz Biotechnology, Dallas, TX, USA), α-tubulin (017-25031; FUJIFILM Wako Pure Chemical Corporation), and β-tubulin (014-25044; FUJIFILM Wako Pure Chemical Corporation) were used. Whole-cell extracts were prepared, and Western blot analysis was performed as previously described [32 (link)]. The protein concentrations of whole-cell extracts were determined using the RC DCTM Protein Assay (Bio-Rad, Hercules, CA, USA). The polyvinylidene difluoride membrane was stained with Ponceau S solution (Beacle Inc., Kyoto, Japan). Pink-stained blots were scanned, and the images were converted to grayscale for publication. Band intensities were quantified using the ImageJ 1.46r software “https://imagej.nih.gov/ij/ (accessed on 21 September 2022)”. The values obtained for the GPER1 band were normalized to the intensity of the β-actin band (internal control).
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4

Antibody panel for RNA-binding proteins

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The following antibodies were used in this study: hnRNPF/H (sc-32310, RRID:AB_2248257), Splicing factor, proline- and glutamine-rich (SFPQ) (sc-374502, RRID:AB_10989589), non-POU domain-containing octamer-binding protein (NONO) (sc-166702, RRID:AB_2152178), hnRNPQ (sc-56703, RRID:AB_2200715), hnRNPA2/B1 (sc-374053, RRID:AB_10947257), and glutathione S-transferase (GST) (sc-138, RRID:AB_627677) from Santa Cruz Biotechnology (Dallas, TX); hnRNPM (A500–011A, RRID:AB_11125542) from Bethyl Laboratories (Montgomery, TX); horseradish peroxidase (HRP)-conjugated FLAG (A8592, RRID:AB_439702) from Sigma-Aldrich (St. Louis, MO); HA (11867423001, RRID:AB_390918) and HRP-conjugated HA (12013819001, RRID:AB_390917) from Roche Diagnostics (Basel, Swiss); monoclonal TDP-43 (89789, RRID:AB_2800143) and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (2118, RRID:AB_561053) from Cell Signaling Technology (Danvers, MA); β-Tubulin (014–25041, RRID:AB_2650453) from FUJIFILM Wako Pure Chemical Corporation (Osaka, Japan); polyclonal TDP-43 (12892–1-AP, RRID:AB_2200505) and polyclonal Matrin3 (MATR3) (12202–2-AP, RRID:AB_2281752) from Proteintech Group (Rosemont, IL); HRP-conjugated goat anti-rabbit IgG (H + L) secondary antibody (170–6515, RRID:AB_11125142) and HRP-conjugated goat anti-mouse IgG (H + L) secondary antibody (170–6516, RRID:AB_11125547) from Bio-Rad Laboratories (Hercules, CA).
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5

Immunoblotting Analysis of Lactyllysine

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The cells were washed with phosphate-buffered saline (–) and lysed with 0.0625 M Tris-HCl buffer (pH 6.8) containing 2% sodium dodecyl sulfate (SDS) and 10% glycerol. DNA was sheared with MYJECTOR 29G × 1/2 (TERUMO, Tokyo, Japan). Protein concentration was determined using a BCA protein assay. After reduction and heating, cellular proteins were subjected to immunoblotting with an antibody against lactyllysine (#PTM-1401, PTM Biolabs Inc., Chicago, Illinois). For subcellular fractionation, the cells were disrupted in 20 mM HEPES buffer (pH 7.4) containing 0.25 M sucrose, 1.5 mM MgCl2, 2 mM KCl, 0.5% Triton X100, and proteinase inhibitor cocktail (Nacalai Tesque, Inc., Kyoto). The lysate was centrifuged at 2000 × g and 4°C for 10 min. The supernatant was designated as the cytoplasmic fraction. Insoluble materials were resuspended in the same buffer and centrifuged under identical conditions. The resulting pellets were designated as nuclear fractions. Successful subcellular fractionation was confirmed via immunoblotting with antibodies against β-tubulin (cytoplasm) (#014-25041, Fuji film/Wako, Tokyo, Japan) and histone H3 (nucleus) (#819411, BioLegend, San Diego, California, USA).
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6

Protein Expression Analysis in Lentivirus-Infected Cells

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Cell culture medium and lysate from lentivirus-infected HB2 cells was subjected to 10% TGX FastCast gel (Bio-Rad Laboratories, Hercules, CA, USA) electrophoresis and transferred onto a nylon membrane. The membrane was blocked using TBS T (20 mmol/L of Tris HCl, pH 7.5, 137 mM of NaCl, and 0.1% Tween 20) containing 5% nonfat dry milk and was then probed with an anti DYKDDDDK (Flag) tag (WAKO), PGC1-α (Santa Cruz Biotechnology, Santa Cruz, CA, USA), UCP1 (Abclonal, Tokyo, Japan), or β-tubulin (WAKO) antibody. After washing with TBS T, the bound antibody was detected using an ECL system (Amersham, Buckinghamshire, UK).
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