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8 protocols using femto ecl substrate

1

Quantitative Immunoblot Analysis of GluA2

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Immunoblot analysis was performed as described previously (Gonzalez-Lozano et al., 2021 (link)) on 5 μg of synaptosomal protein from each experimental group. After electrophoresis, gels were scanned using a Gel Doc EZ imager (Bio-Rad) and electro-transferred onto a PVDF membrane overnight at 40 V. After blocking in 5% milk, membranes were incubated with a primary antibody against GluA2 (1:1,000, Cat nr. 75-002, Neuromab) overnight at 4°C and with a matching HRP-conjugated secondary antibody for 2 h at room temperature. The membranes were then scanned with Femto ECL Substrate (Thermo Fisher Scientific, Waltham, MA, USA) on an Odyssey Fc system (LI-COR Bioscience, Lincoln, NA, USA) and quantified using Image Studio software (version 2.0.38). Input differences were corrected using total protein amounts loaded on the gel (Gonzalez-Lozano et al., 2021 (link)).
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2

Western Blot Analysis of Phosphorylated CTD

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Purified phosphorylated CTD was mixed in 1X XT buffer (Bio-Rad) and run on 3–8% Criterion™ XT Tris-acetate Precast Gels (Bio-Rad) at 100 V until the dye front reached the end of the gel. Protein was then wet transferred to a 0.45 μm PVDF membrane (Millipore, IPVH00010) in ice-cold transfer buffer (25 mM Tris, 192 mM glycine, 10% methanol) at 250 mA for 2 hours at 4°C. After transfer, the membrane was blocked with 5% non-fat milk in TBS for 1 hour at room temperature, with shaking. The membrane was then incubated with a 1:5,000 dilution of anti-GFP (Abcam #ab290) antibodies in 5% non-fat milk in TBST overnight at 4°C, with shaking. The membrane was washed three times with TBST for 10 min at room temperature with shaking. The membrane was incubated with 1:10,000 secondary antibodies (GE health) for 1 hr at RT and washed three times in TBST for 5 mins. Membranes were developed with Femto ECL substrate (Thermo Scientific, 34095) and imaged using a CCD camera.
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3

Kinase Expression Analysis in Cellular Lysates

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Tissue samples and PBMCs were lysed using 1 mmol/L phenylmethylsulfonyl fluoride (PMSF) and protease/phosphatase inhibitor cocktail (Cell Signaling Technology). Lysate was centrifuged at 6000 × g for 10 minutes at 4°C and supernatant was collected for protein determination using a BCA protein assay kit (ThermoFisher). A 50 µg protein sample was resolved by SDS gel electrophoresis and transferred to a nitrocellulose membrane. Membranes were probed using primary antibodies for adenylate kinase 2 (AK2), creatine kinase muscle (CKM), pyruvate kinase liver and red blood cell (PKLR), pyruvate kinase muscle (PKM) (all kinase antibodies from Fisher Scientific), GAPDH (Cell Signaling) or β‐actin (Cell Signaling). Visualization was performed using SuperSignal West Dura or Femto ECL Substrate (ThermoFisher) and a BioRad Gel Doc XR (BioRad).
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4

Western Blot Analysis of Astrocyte Proteins

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Astrocytes (95,000 cells/well, 24 well-plate) were lysed 48 h after treatment with 5× Laemmli buffer. Samples were incubated at 90 °C for 5 min, and proteins were separated on SDS-polyacrylamide gels. After electrophoresis, gels were transferred on to a PVDF membrane overnight at 40 V. Membranes were blocked with 5% non-fat milk (Sigma-Aldrich, St. Louis, MO, USA), followed by primary antibody incubation over night at 4 °C. Next, HRP-conjugated secondary antibodies were added (Agilent Dako, Santa Clara, CA, USA) to the membranes and kept for 1 h at RT. Finally, membranes were scanned with Femto ECL Substrate (Thermo Fisher Scientific, Waltham, MA, USA) using the Odyssey Fc system (LI-COR Bioscience, Lincoln, NE, USA). Images were quantified with Image Studio software (version 2.0.38). The following primary antibodies were used: rabbit anti-GFAP (1:1000; Agilent Dako, Santa Clara, CA, USA), mouse anti-Vimentin (1:200, Santa Cruz, Heidelberg, Germany), and mouse anti-actin (1:10,000, Sigma-Aldrich, St. Louis, MO, USA). Total protein levels for GFAP and Vimentin were normalized to actin.
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5

Analyzing Tap-Tom5 Interactions in Yeast

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Yeast cultures were grown in YP+2% galactose or YP+2% dextrose to express or suppress TAP–Tom5, respectively. Log phase cultures (30 OD600 units) were collected by centrifugation and resuspended in 400 µl of lysis buffer (250 mM NaCl, 50 mM Tris-HCl pH 7.4, 50 mM NaF, 5 mM EDTA, 1 mM DTT, 1 mM AEBSF, and 0.1% NP-40). Cells were disrupted with glass beads for 5 min at 4°C. The resulting lysate was centrifuged at 16,100×g for 5 min, and a sample of the supernatant was collected. The supernatant was then incubated under rotation with 20 µl of prewashed GFP–Trap_A bead slurry (Chromotek) for 1 h at 4°C. The supernatant was removed and the beads were washed with lysis buffer (3×1 ml, then 3×500 µl with 5-min incubations). Beads were resuspended in 100 µl of sample buffer (50 mM Tris-HCl pH 6.8, 10% glycerol, 2% SDS, 4% 2-mercaptoethanol, and 0.02% bromophenol blue) and eluted by heating at 65°C for 20 min. The eluted protein was subjected to SDS-PAGE (10% polyacrylamide) and immunoblotted with anti-TAP (1∶5,000 dilution, Pierce, CAB1001) or anti-GFP (1∶5,000 dilution, Roche, 11814460001) antibodies. Goat anti-rabbit IgG-HRP (1∶5,000 dilution, Bio-Rad, 172-1019) and goat anti-mouse IgG-HRP (1∶5,000 dilution, Bio-Rad, 172-1011) were used as secondary antibodies. Blots were imaged with either Supersignal West Pico or Femto ECL substrate (Thermo Scientific).
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6

Western Blot Analysis of Synaptic Proteins

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Synaptosome samples were mixed with 5× Laemmli buffer and incubated at 90 °C for 5 min. Proteins were separated on SDS-polyacyrlamide gels containing 2,2,2-trichloroethanol for total protein amount visualization. After electrophoresis, gels were scanned using a Gel Doc EZ imager (Bio-Rad) and electro-transferred onto a PVDF membrane overnight at 40 V. Membranes were blocked with 5% non-fat milk (Sigma-Aldrich, St. Louis, MO, USA), incubated with primary antibody at 4 °C for 1 h and then with matching HRP-conjugated secondary antibodies at 4 °C for 1 h (Agilent Dako, Santa Clara, CA, USA). After washing, the membranes were scanned with Femto ECL Substrate (Thermo Fisher Scientific, Waltham, MA, USA) using the Odyssey Fc system (LI-COR Bioscience, Lincoln, NA, USA). Images were quantified using Image Studio software (version 2.0.38). Differences in loading were corrected using the quantification of the total protein amount and immunoblot signals were normalized to the controls. The following primary antibodies were used: anti-ME3 (Abcam, Cambridge, UK; ab172972), anti-mGluR5 (GenScript, Piscataway, NJ, USA; A01493), anti-Rat mGluR1α (BD Biosciences, San Jose, CA, USA; 556331) and anti-PSD-95 (NeuroMab, Davis, CA, USA; 75-028).
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7

Western Blot Analysis of Phosphorylated CTD

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Purified phosphorylated CTD was mixed in 1X XT buffer (Bio-Rad) and run on 3–8% Criterion™ XT Tris-acetate Precast Gels (Bio-Rad) at 100 V until the dye front reached the end of the gel. Protein was then wet transferred to a 0.45 μm PVDF membrane (Millipore, IPVH00010) in ice-cold transfer buffer (25 mM Tris, 192 mM glycine, 10% methanol) at 250 mA for 2 hours at 4°C. After transfer, the membrane was blocked with 5% non-fat milk in TBS for 1 hour at room temperature, with shaking. The membrane was then incubated with a 1:5,000 dilution of anti-GFP (Abcam #ab290) antibodies in 5% non-fat milk in TBST overnight at 4°C, with shaking. The membrane was washed three times with TBST for 10 min at room temperature with shaking. The membrane was incubated with 1:10,000 secondary antibodies (GE health) for 1 hr at RT and washed three times in TBST for 5 mins. Membranes were developed with Femto ECL substrate (Thermo Scientific, 34095) and imaged using a CCD camera.
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8

Western Blot Analysis of Histone Deacetylases and Chromatin Regulators

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Whole-cell lysates of 1 × 10 6 -1.5 × 10 6 cells in RIPA buffer containing protease inhibitors were sonicated and 30-50 μg of each protein extract was resolved on 4-12% NuPAGE gels (Invitrogen). Blocking and incubation with primary and secondary antibodies were performed with 5% skim milk in phosphate-buffered saline. Rabbit polyclonal/monoclonal antibodies: anti-HDAC7 (ab12174), anti-HDAC3 (ab1791), anti-HDAC1 (ab7028), anti-H3K27ac (ab4729), and anti-c-MYC (ab32072) were obtained from Abcam, Inc. Rabbit polyclonal anti-H3ac (06-599) antibody was obtained from Millipore and anti-CD44 Pan Specific (BBA10) antibody from R&D Systems. Rabbit polyclonal/monoclonal antibodies: anti-EZH2 (#5246), anti-p27 Kip1 (#3686), and anti-GAPDH (#5174) were obtained from Cell Signaling Technology. Rabbit polyclonal anti-VDR (sc-1008), anti-p300 (sc-584), and mouse monoclonal anti-ACTB (sc-69879) antibodies were obtained from Santa Cruz Biotech. Horseradish peroxidase-conjugated secondary antibodies were obtained from Amersham Biosciences. The protein bands were visualized with SuperSignal West Dura or Femto ECL substrate (ThermoScientific). All experiments were repeated a minimum of three times. Autoradiographic signals were quantified by densitometric analysis using ImageJ from National Institute of Health.
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