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15 protocols using af5003

1

Apoptosis and Autophagy Assay Protocol

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25HC was purchased from Sigma-Aldrich. Caspase-1 activity assay kit was purchased from Beyotime Institute of Biotechnology. Lipofectamine 3000 was purchased from Invitrogen. Annexin V-FITC and PI apoptosis detection kits were purchased from Keygen Biotech Company (Nanjing, China). Antibodies used in the present study were as follows: ALV-J envelope protein JE9-specific mouse monoclonal antibody (provided by Professor Qin Aijian of Yangzhou University), rabbit anti-LC3II antibody (NB100-2220SS, Novus Biologicals), rabbit anti-ATG5 antibody (12994, Cellsignal), mouse monoclonal anti-flag antibody (AP007M, Bioworld), rabbit anti- SQSTM1/p62 antibody (P0067, Sigma-Aldrich), and anti-myc antibody (A02060, Abbkine), rabbit anti-β-actin antibody (AF5003, Beyotime), goat anti-rabbit IgG (H+L) antibody (A21020, Abbkine), Goat anti-mouse IgG/HRP antibody (A25112, Abbkine).
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2

Immunoblotting Analysis of Mitochondrial and Antioxidant Proteins

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BCPAP cells or C643 cells were harvested and lysed with RIPA buffer (Millipore). Immunoblotting was performed in a standard fashion. The following antibodies were used: β-actin (1 : 1000; cat #AF5003; Beyotime, China), NDUFB3 (1 : 500; cat #SC-393351; Santa Cruz, CA), MT-ND1 (1 : 1000, cat #ab181848; Abcam), MT-ND2 (1 : 1000, cat #PA5-37185; Invitrogen), MT-ND3 (1 : 1000, cat #ab192306; Abcam), MT-ND4 (1 : 1000, cat #ab219822; Abcam), MT-ND4L (1 : 1000, cat #PA5-103953; Invitrogen), MT-ND5 (1 : 1000, cat #ab230509; Abcam), MT-ND6 (1 : 1000, cat #PA5-109993; Invitrogen), GPX1 (1 : 1000, cat #ab22604; Abcam), MnSOD (1 : 1000, cat #ab68155; Abcam), CuMnSOD (1 : 1000, cat #ab13498; Abcam), PRDX1 (1 : 1000, cat #NBP1-82558; Novus), PRDX3 (1 : 1000, cat #NBP2-67043; Novus), PRDX6 (1 : 1000, cat #H00009588-M01; Novus), and α-tubulin (1 : 1000; cat# AF0001; Beyotime, China).
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3

Extraction and Analysis of Glycolytic Proteins

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Metaphysis mesenchymal progenitors were extracted and cultured as described above. RIPA (Beyotime (Shanghai, China), P0013B) lysis buffer containing a 10% protease and phosphatase inhibitor cocktail was used to isolate total protein from Gli1+ MMPs. We separated the protein samples by SDS-PAGE and transferred them into PVDF (Millipore (Burlington, MA, USA), ISEQ00010) membranes. PVDF membranes containing proteins were blocked with 5% BSA for 1 h before incubating with primary antibody for HK2 (Cell Signaling Technology (Danvers, MA, USA), C64G5, 1:1000), LDHA (proteintech (Rosemont, IL, USA), 19987-1-AP, 1:1000), PDK1 (ENZO life science (Farmingdale, NY, USA), ADI-KAP-PK112, 1:1000), Glut1 (Abcam, ab115730, 1:1000) and anti-β-actin (Beyotime, AF5003, 1:1000) for about 16 h at 4 °C. After washing three times with PBST for 5 min, the PVDF membranes were incubated with goat anti-rabbit IgG H&L (HRP) (Abcam, ab66721, 1:5000) for one hour at room temperature and visualized using the Ori Supersensitive ECL Kit (Oriscience (Chengdu, China), PD203).
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4

Western Blot Analysis of Osteoblast Proteins

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Primary mouse calvarial osteoblasts and bone samples from the right femurs were lysed with RIPA lysis buffer (Beyotime, China) supplemented with protease inhibitor (Beyotime, China). The protein concentration was quantified with a BCA protein assay kit (Solarbio, China). Western blot was then performed as described previously [20 (link)]. Briefly, equal amounts of proteins from each sample were separated on a 10% SDS-PAGE gel and then transferred to PVDF membranes (Millipore, USA). The membranes were blocked with 5% nonfat milk for 1 h at room temperature and then incubated with primary antibodies against Runx2 (1:2000, abcam, ab236639), osteocalcin (OCN) (1:300, Beyotime, AF6300), HIF-1α (1:500, abcam, ab179483), β-catenin (1:500, abcam, ab68183) and β-actin (1:1000, Beyotime, AF5003) overnight at 4 °C. Then, the membranes were incubated with the appropriate secondary antibody (1:5000, Beyotime, A0208). The protein bands were visualized using Novex® Chemiluminescent HRP Substrate (Invitrogen, USA) and an enhanced chemiluminescence detection system (Pierce Biotechnology, USA). The band intensity was quantified with ImageJ software.
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5

Perihematomal Protein Analysis by Western Blot

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The Western blot was conducted as previously described.7 (link) Briefly, protein samples were obtained from the perihematomal area and BV2 cells using RIPA lysis buffer. Then, protein lysate was centrifuged for 20 min at 12,000 g at 4°C. After centrifuging, the supernatant protein solution was collected. After loading an equal amount of protein onto the gel, the electrophoresis procedure was initiated. The proteins were then transferred to PVDF membranes and blocked with a solution containing 5% bovine serum albumin (BSA) for 1 h at room temperature. After blocking, membranes were incubated with primary antibodies at 4°C overnight. The following primary antibodies were used: Dectin-1 (1:1000; ab140039, Abcam), NLRP3 (1:1000; ab263899, Abcam), ASC (1:2000; sc-33958, Santa Cruz Biotechnology), phospho-SYK (1:1000; AF3315, Affinity Biosciences), IL-18 (1:1000; 60070-1-Ig, Proteintech), GSDMD-N (1:1000; AF4012, Affinity Biosciences), caspase-1 (1:1000; 22915-1-AP, Proteintech), β-actin (1:1000; AF5003, Beyotime Biotechnology), and IL-1β (1:1000; 26048-1-AP, Proteintech). After washing three times with TBST, the membranes were incubated with secondary antibody at room temperature for 1 h and then washed a further three times. Finally, a Bio-Rad Molecular Imager was used to detect protein signals, which were quantified by Image J.
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6

Western Blot Analysis of Protein Interactions

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Whole-cell lysate and the Co-IP supernatant were mixed with 5× SDS-PAGE Plus sample buffer (GenStar, Beijing, China) and then incubated in a boiling water bath before separation by SDS-PAGE and subsequent transfer to PVDF membrane (Millipore, Bedford, MA). The membrane was blocked with 5% skim milk (Solarbio, Beijing, China) for 3 h then incubated with primary antibody overnight at 4°C. The membrane was washed thrice for 10 min each time using Tris-buffered saline and 0.1% Tween-20 (Solarbio, Beijing, China) and incubated with the appropriate secondary antibody. The primary antibodies used for Western blot were β-catenin rabbit polyclonal antibody (1:2,000) (ab6302, Abcam, Cambridge, UK), Myc-tag rabbit monoclonal antibody (1:5,000) (AE070, ABclonal), and HA-tag rabbit monoclonal antibody (1:1,000) (C29F4, Cell Signaling). β-actin rabbit monoclonal antibody (1:2,000) (AF5003, Beyotime) was used as a loading control. The secondary antibody was goat anti-rabbit IgG (1:5,000) (A0208, Beyotime). The blot signal was visualized using ECL reagent (Thermo Fisher Scientific, Carlsbad, CA). The protein expression level was quantified by the band density using Quantity One 4.6.3 software (Bio-Rad Laboratories, Hercules, CA) and normalized by β-actin.
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7

Western Blot Analysis of Cell Proteins

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Cellular protein samples were extracted using RIPA lysis buffer. After quantification with the BCA Protein Assay Kit (Beyotime, China), the concentration of each sample was adjusted. Samples were mixed with SDS-PAGE protein loading buffer and stored at −20°C. The mixed samples were electrophoresed with 120V for 1h and transferred to a 0.45-um poly vinylidene fluoride membrane. Then, the membrane was blocked and incubated with primary antibody for 12h (4°C), followed by secondary antibody incubation for 1h and detection (ChemiDoc MP; Bio-Rad, USA). The antibodies used in this study were β-actin rabbit monoclonal antibody (AF5003, Beyotime, China), CDK1 rabbit polyclonal antibody (AF0111, Beyotime, China), Phospho-CDK1 (pCDK1, Tyr15) rabbit polyclonal antibody (AF5761, Beyotime, China), and HRP-labeled goat anti-rabbit IgG (H+L) (A0208, Beyotime, China).
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8

Western Blot Analysis of Cellular Proteins

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The cells were lysed with RIPA lysis buffer (P0013B, Beyotime) on ice for 30 min. The supernatants of cells were harvested after centrifugation at 12,000 g for 10 min at 4°C. A BCA protein assay kit (P0012S, Beyotime) was used to determine the total protein concentration. Protein extracts were mixed with loading buffer and boiled at 95°C for 10 min. The boiled samples were loaded onto SDS-polyacrylamide gels followed by electrophoresis and transferred onto polyvinylidene difluoride membranes. The membranes were blocked with TBS-tween containing 5% skim milk, inculcated with either RUNX2 (1:1,000 dilution, S12556, Cell Signaling Technology), BMP2 (1:1,000 dilution, AF0075, Beyotime), HMOX-1 (1:1,000 dilution, AF1333, Beyotime), BID (1:1,000 dilution, AF6306, Beyotime), IL-6 (1:1,000 dilution, AF7236, Beyotime), HIF-1α (1:1,000 dilution, CSB-PA002906, CUSABIO), PRKAA2 (1:2,000 dilution, CSB-PA805325LAO1HU, CUSABIO), β-actin (1:5,000 dilution, AF5003, Beyotime), or GAPDH (1:10,000 dilution, S2118, Cell Signaling Technology) antibodies overnight at 4°C. The membranes were washed and inculcated with HRP-labeled secondary antibody (1:5,000 dilution, ab205718, Abcam). Detection was done using clarity western ECL (WBKLS0100, Millipore). The images were acquired through the e-Blot Touch Imager and semiquantitative analyses were performed by the FIJI software.
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9

SARS-CoV-2 S1 Protein Binding Assay

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A549 cells purchased from the Cell Bank of the Chinese Academy of Sciences (CAS, Shanghai, China) were seeded into a 6-well plate (1 × 106 cells/well) and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Thermo Fisher Scientific, Shanghai, China) containing 10 % fetal bovine serum (FBS, Gibco). SARS-CoV-2 S1 (20 μg/mL, 40591-V08H, Sino Biological) preincubated with LD-11, ED-10, or GK-7 (1, 10, and 50 μg/mL) for 15 min was added to the cells, followed by coincubation at 37 °C for 1 h. The cells were then washed three times with sterile PBS to remove dissociative SARS-CoV-2 S1 and lysed with RIPA lysis and extraction buffer (89900, Thermo Fisher Scientific). The amount of SARS-CoV-2 S1 attached to the cells was detected using an anti-spike rabbit polyclonal primary antibody (40591-T62, Sino Biological, 1:1000) and a goat anti-rabbit secondary antibody (A0208, Beyotime, Shanghai, China). As a reference, the amount of β-actin was detected using a rabbit monoclonal antibody (AF5003, Beyotime). The experiment was repeated three times on different days.
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10

Western Blot Analysis of Mitochondrial Proteins

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Western blot was carried out essentially as described30 (link) with slight modifications. Total protein was extracted using a whole protein extraction kit (Solarbio, Beijing, China), and protein concentrations were measured using a BCA protein assay kit (Solarbio, Beijing, China). Next, total proteins were separated by SDS/PAGE electrophoresis and then transferred to a PVDF membrane (EpiZyme, Shanghai, China) at 25 °C for 1 h. Overnight incubation with the primary antibody at 4 °C was performed, and then goat anti-rabbit IgG (Beyotime, Shanghai, China) was added at 25 °C for 1 h. Finally, the proteins were detected using a developing solution (Thermo Fisher Scientific, USA). The following primary antibodies were used: CST1 (1:1000; ab307416, Abcam, British), MEK1/2 (1:1000; #9122, CST, USA), p-MEK1/2 (Ser217/221) (1:1000; #9121, CST, USA), p44/42 MAPK (Erk1/2) (1:1000; #9102, CST, USA), p-p44/42 MAPK (Erk1/2) (1:1000; #9101, CST, USA), GRIM19 (1:1000; A18071, Abclonal, China), SDHA (1:1000; A16204, Abclonal, China), UQCRC2 (1:1000; A4184, Abclonal, China), COX IV (1:1000; A6564, Abclonal, China), ATP5A1 (1:1000; A11217, Abclonal, China), VDAC1 (1:1000; A19707, Abclonal, China), MMP2 (1:1000; #4022, CST, USA), and β-actin (1:1000; AF5003, Beyotime, Shanghai, China). All experiments were repeated three times.
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