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7 protocols using gapdh 6c5

1

Western Blot Analysis of Protein Targets

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About 30 μg proteins were loaded into 10% SDS/PAGE gel and then transferred onto a PVDF membrane. After incubated with the primary antibody in a 4°C condition for overnight and secondary antibody at room temperature for 1–2 h, the membrane was visualized with ECL system. The SLTRK4 (ab67315), PCDH7 (ab139274) and GAPDH (6C5) antibodies were purchased from Abcam company. UGT2A3 (PA5-48900) antibody was purchased from Thermo Fisher Scientific company.
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2

Antibody Generation and Utilization

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Affinity-purified rabbit antibodies against myosin VI, TAX1BP1 and optineurin were generated as previously described (Buss et al., 1998 (link); Morriswood et al., 2007 (link); Sahlender et al., 2005 (link)). Commercial antibodies against the following proteins were used: Cx43 [C6219; 1:200 immunofluorescence (IF), 1:2000 western blotting (WB)] and actin (A2066; 1:5000 WB) polyclonal antibodies (Sigma), Cx43 (05-763; 1:200 IF) monoclonal antibody (Millipore), GAPDH (6C5; 1:1000 WB) and clathrin (X22; 1:100 IF) monoclonal antibodies (Abcam), Dab2 (H-110; 1:100 IF) and GIPC1 (N-19; 1:100 IF) polyclonal antibodies (Santa Cruz Biotechnology) and pan-cadherin (4068; 1:1000 WB) polyclonal antibody (Cell Signaling). Phalloidin–Alexa-Fluor-647, Calcein AM, WGA–647 and Hoechst 33342 were purchased from ThermoFisher. Bafilomycin A1, brefeldin A and biotin were purchased from Sigma-Aldrich. JF646-HaloTag ligand was a kind gift from Joel Slaughter and Luke Lavis (Janelia Farm, HHMI, Ashburn, VA) (Grimm et al., 2015 (link)).
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3

Western Blot Analysis of Immune Signaling Proteins

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Cells were lysed with ice-cold radioimmunoprecipitation assay (RIPA) buffer (5 mm EDTA, 150 mm NaCl, 10 nm Tris-HCl, pH 7.2, 0.1% SDS, 0.1% Triton X-100, and 1% sodium deoxycholate) containing protease mixture inhibitors P8340, P5726, and P0044 (Sigma). Protein concentration was determined by bicinchoninic acid assay (BCA) (Thermo Scientific) according to the manufacturer's protocol, using BSA as standards. Protein samples were denatured and resolved on SDS-PAGE gels using a Bio-Rad PowerPac HC and transferred onto PVDF membranes (Millipore). Membranes were probed overnight at 4 °C (1:1000) for the following primary antibodies to PD-L1 (E1L3N), SOCS1 (A156), STAT1 (9172), P-STAT1 Tyr-701 (D4A7), STAT3 (9132), and P-STAT3 Tyr-705 (D3A7) all from Cell Signaling, and for 1 h at room temperature for GAPDH (6C5) and β-actin (ab6276), both from Abcam. Membranes were further incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies and visualized with ECL (GE Healthcare). Band intensity was quantified using ImageJ version 1.50e (NIH, Bethesda, MD).
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4

Protein Expression Analysis of Extracellular Matrix

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Cells were lysed and protein was extracted using RIPA buffer (Invitrogen). In addition, the BCA protein assay kit (Beyotime Bio, Shanghai, China) was used to detect the concentration of protein. Equal amounts of protein (30 μg) samples were separated using 10% SDS-PAGE gels and then transferred to PVDF membranes (Millipore, Billerica, MA, USA). After blocking with 5% skim milk, the membranes and the following primary antibodies were incubated overnight at 4°C: anti-HGF (EPR12230, 1:1000, Abcam, Cambridge, MA, USA), anti-MMP-3 (EP1186Y, 1:1000, Abcam), anti-MMP-13 (1: 2000; Abcam), anti-Aggrecan (6-B-4, 1:1000, Abcam), anti-Collagen II (EPR12268, 1:1000, Abcam), anti-c-MET (EPR19067, 1:1000, Abcam), anti-p-c-MET (EP2367Y, 1:1000, Abcam), and GAPDH (6C5, 1:2000, Abcam). GAPDH protein was used as the inner control. After washing, the membranes were incubated with the HRP-conjugated secondary antibody at 1:2000 dilution for 1 h at room temperature. The resulting bands were detected with an ECL detection system (Millipore).
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5

Generation and Characterization of RasV12 and IRF1-/- MEFs

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NIH3T3 cells were obtained from the American Type Culture Collection (Manassas, VA, USA). RasV12 transformed NIH3T3 cells were generated as previously described [6 (link)]. IRF1deficient and wild type MEFs were established from Day 14 embryos of C57BL/6-Irf1tm1Mak 47 and C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME, USA), respectively. The animal care protocol (13-10-KH) was approved by the Institutional Animal Care Committee, in accordance with Canadian Council on Animal Care guidelines. All the animals were euthanized in a CO2 chamber before MEF isolation. All cell lines used in this study were maintained in high glucose Dulbecco's modified Eagle's medium (DMEM) (Invitrogen) with 10% fetal bovine serum (FBS) (GE Healthcare Life Sciences, Mississauga, ON, Canada). U0126 was purchased from Cell Signaling Technology (Danvers, MA). Antibodies to phospho-ERK-1/2 was purchased from Calbiochem, GAPDH (6C5) from Abcam (Toronto, ON, Canada), mouse IRF1 (M-20) and total ERK (sc-94) from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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6

Western Blot Analysis of Protein Expression

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Whole cell lysates were prepared directly in 2× sample buffer (100 mM Tris pH 6.8, 4% SDS, 20% glycerol). Equal amounts of protein lysates were electrophoresed on a 4-12% gradient SDS-polyacrylamide gel (Thermo Fisher Scientific, Grand Island, NY) and transferred to Immobilon-FL membrane (Millipore Sigma, Burlington, MA). Blots were probed with antibodies: Cytokeratin 1 (PA5-26699) (Thermo Fisher Scientific, Grand Island, NY); p53 (OP03) at 1:1000 (Millipore Sigma, Burlington, MA); Involucrin (SY5) at 1:1000; total JNK(D-2) at 1:500, Actin (I-19) at 1:1000, (Santa Cruz Biotechnology, Santa Cruz, CA); P-JNK/SAPK (81E11) at 1:1000, total SEK1/MKK4 (9153) at 1:1000, total MKK7 (4127S) at 1:1000, (Cell Signaling Technology, Danvers, MA); GAPDH (6C5) at 1:100,000 (Abcam, Cambridge, MA); total ERK (W15133B) at 1:1000, (BioLegend, San Diego, CA). The rabbit polyclonal anti-NFX1-123 antibody was used 1:1000 and generously provided by Dr. Ann Roman.
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7

Antibody Validation for Protein Detection

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Rabbit polyclonal CLDN7 (Cat#34-9100) was purchased from Zymed Laboratories Inc (CA, USA). Mouse monoclonal GAPDH (6C5) were obtained from Abcam (Cambridge, UK). Rabbit polyclonal APLP2 (Cat#128603) and mouse monoclonal beta-actin (AC15) antibodies were obtained from Abcam. Mouse monoclonal antibodies directed against LeX A were obtained from Dualsystems Biotech. Peroxidase-linked donkey antirabbit immunoglobulin and sheep antimouse IgG horseradish antibodies were obtained from Amersham Biosciences (GE Healthcare, NJ, USA). Alexa fluor antibodies were purchased from Molecular Probes (Thermo Fisher).
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