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14 protocols using gapdh ap0063

1

Erlotinib, 5-Azacytidine, and miR-9 Modulation

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Erlotinib (qE-4007) was purchased from LC Laboratories, and dissolved in DMSO at 20 mmol/L. 5-Azacytidine (A2385) was purchased from Sigma-Aldrich, and dissolved in PBS at 20 mmol/L. Stock solutions were at −20 °C and diluted just before use. Lipofectamine 2000 transfection reagent was purchased from Life Technologies Co. Invitrogen (11668-019). Antibodies FoxO1 (BS3573), actin (AP0064), and GAPDH (AP0063) were purchased from Bioworld Technology Inc. NFκB p105/p50 antibody (1559-1) was purchased from Epitomics, Inc. The synthetic miR-9 mimic, miR-9 inhibitor, and their relative control were purchased from Dharmacon.
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2

Western Blot Analysis of Cell Signaling

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Western blot analysis was performed as described previously (10 (link)). Primary antibodies α-SMA (A2547; mouse) and vimentin (V6630; mouse) (1:1000; Sigma-Aldrich; Merck KGaA), ICAM-1 (sc-1511; goat; 1:1,000), fibronectin (sc-6953; goat; 1:500), and Smad7 (sc-11392; rabbit; 1:1,000) (Santa Cruz Biotechnology, Inc., Dallas, TX, USA), type I collagen (1310-01; goat; 1:1,000; SouthernBiotech), phospho-Smad2 (3101; rabbit), phospho-Smad3 (9520; rabbit), acetyl-histone H3 (14932; rabbit), and histone H3 (9715; rabbit) (1:1,000; Cell Signaling Technology Inc., Danvers, MA, USA), and Smad2/3 (07-408; rabbit; 1:1,000; EMD Millipore, Billerica, MA, USA) were used. GAPDH (AP0063; rabbit; 1:2,000; Bioworld Technology, Inc., St. Louis Park, MN, USA) was used as an internal control. All signals were analyzed by densitometric scanning (LAS-3000; FujiFilm, Tokyo, Japan).
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3

Antibody Sourcing for EMT Markers

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Antibodies against EFNA4 (19685-1-AP), E-cadherin (60335-1-Ig), N-cadherin (66219-1-Ig), vimentin (10366-1-AP), EPHA2 (66736-1-Ig), and GSK3β (22104-1-AP) were purchased from Proteintech (Wuhan, China). Antibodies against β-catenin (#8480), AKT (#4691), phospho-AKT (Ser473; #4060), phospho-GSK3β (Ser9; #9323), and EPHA2 (#6997) were obtained from Cell Signaling Technology (Beverly, MA, USA). Antibodies against Ki67 (ab16667), PIK3R2 (ab180967), and CTCF (ab128873) were obtained from Abcam (Cambridge, MA, USA). The antibody against glyceraldehyde 3-phosphate dehydrogenase (GAPDH; AP0063) was purchased from Bioworld Technology (Bloomington, MN, USA). Human EFNA4 antibody (MAB3692) was purchased from Bio-Techne (Minneapolis, MN, USA). Phospho-EPHA2 (Ser897; AP1082) and phospho-EPHA2 (Tyr772; AP0817) were purchased from ABclonal Technology (Wuhan, China). Monoclonal anti-FLAG M2 antibody (1804) was obtained from Merck KGaA (Darmstadt, Germany).
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4

Western Blot Analysis of HTR-8/SVneo Cells

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The HTR-8/SVneo cells transfected with overexpressing plasmid groups were lysed for protein extraction using RIPA supplemented with phenylmethylsulfonyl fluoride (PMSF) (both from Beyotime Biotech). The Bradford assay (Beyotime Biotech) was used to determine the protein concentration of each sample. Samples containing 50–100 µg of extracted protein were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The separated proteins were transferred to 0.22 µm nitrocellulose membranes and were incubated with primary antibodies against GABRP (ab26055; Abcam); caspase-3 (19677-1-AP; ProteinTech Group, Wuhan, China); cleaved caspase-3 (Asp175; Cell Signaling Technology, Inc., Danvers, MA, USA); Bcl-2 (AP13823c), Bad (AP1314c) and Bax (AP18517a) (all from Abgent, Inc., San Diego, CA, USA); and GAPDH (AP0063; Bioworld Technology, Inc., St. Louis Park, MN, USA) at 1:1,000 dilution. The secondary antibody was goat anti-rabbit IgG (1:1,000; Zhongshan Goldenbridge). All experiments were repeated at least three times.
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5

Mitochondrial Acetylome Analysis in Liver

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Hepatocytes or liver tissue were lysed with ice-cold RIPA buffer and the protein extraction were immunoblotted to analysis the protein expression. The protein lysates were separated by SDS-PAGE and transferred onto polyvinylidene fluoride membranes (Millipore Co, Ltd.). Immunoblotting was performed according to standard procedures with the following primary antibodies: G-6-Pase (sc-15840, 1:500) and SIRT3 (sc-365175, 1:500) antibodies were from Santa Cruz Biotechnology, Inc. (Santa, CA, USA), antibodies for PEPCK (ab70358, 1:1000), PC (ab128952, 1:1000), p-PDH (S293) (ab177461, 1:1000) were from Abcam (Cambridge, MA, USA), antibodies of MPC1 (14462, 1:1000), PDH (2784, 1:1000) and Acetylated-Lysine (9441, 1:1000) were obtained from Cell Signaling Technology (Beverly, MA, USA), VDAC1 (CY5416, 1:1000) antibody was from Abways Technology, Inc. and antibodies of GAPDH (AP0063, 1:3000), Goat Anti-Rabbit IgG (H + L) HRP (BS13278, 1:10000) and Goat Anti-Mouse IgG (H + L) HRP (BS12478, 1:10000) were from Bioworld Technology (St. Paul, MN, USA). To determine the mitochondrial acetylated-lysine in the liver, mitochondrial protein was prepared with Tissue Mitochondria Isolation Kit (Beyotime Institute of Biotechnology, Shanghai, China) as manufacturer's instructions.
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6

Cardiac Protein Expression Analysis

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Total protein was obtained from the ventricular myocardial tissues using tissue homogenates, centrifugation and heat denaturation. The protein lysates were electrophoresed and separated by 6–12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto PVDF membranes (Millipore Immobion-P; BioSharp, Anhui, China). The membranes were blocked with 5% skim milk at room temperature for 1 h, and then incubated overnight at 4°C with primary antibodies, including rabbit anti-Bcl-2 (BA0412; 1:500), rabbit anti-Bax (BA0315-2; 1:500), rabbit anti-Calr (BM1798; 1:500), rabbit anti-GRP78 (BA2042; 1:500) (all from Boster Biotechnology, Inc., Wuhan, China), and rabbit anti-glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (AP0063; 1:5,000; BioWorld, Inc., Jiangsu, China). The membranes were then incubated with IRDye800-conjugated secondary antibodies (1:20,000; Rockland, Inc., Gilbertsville, PE, USA) at room temperature for 1 h. The Odyssey double color infrared laser imaging system (LI-COR; Lincoln, NE, USA) was used to detect the antigen-antibody complexes in a western blotting detection system (Bio-Rad). The results were expressed as density values normalized to GAPDH.
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7

Detecting Inflammasome Activation Markers

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LPMCs culture supernatant (serum free) were precipitated with methanol and chloroform for secreted proteins, and the cell lysates were collected by direct lysis by 1x Laemmli loading buffer. Samples were boiled to denature at 100 °C for 10 min before the SDS-PAGE gel electrophoresis for protein separation. After electrophoresis, the protein was wet-transferred to a 0.45 μm nitrocellulose membrane (Millipore), and then blotted for indicated proteins using the antibodies as following: mouse caspase-1 p10 (sc-514, dilution 1:400), mouse IL-1β (sc-7884, dilution 1:400), and ASC (sc-22514, dilution 1:400) were from Santa Cruz, NLRP3 (Cryo2, dilution 1:1000) was from Adipogen, and GAPDH (ap0063, dilution 1:10000) was from Bioworld. The uncropped blot images can be found in Supplementary Fig. 8.
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8

Browne Adipose Tissue Protein Analysis

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Protein from brown adipocytes or brown adipose tissue was extracted using lysing buffer. Protein concentration was determined using BCA Protein Assay kit (Beyotime Institute of Biotechnology, Nanjing, China). Proteins (30 μg) were separated by SDS-PAGE, transferred to PVDF nitrocellulose membrane (Millipore, Boston, MA, USA), blocked with 5% fat-free milk for 2 h at room temperature and then incubated with primary antibodies in 5% milk overnight at 4°C. Sirt1 (ab110304), Sirt2 (ab191383), CHOP (ab179823), GRP78 (ab108615), ATF4 (ab184909), ERDJ4 (ab118282), Bax (ab32503), Apaf-1 (ab32372), UCP1 (ab2384) and PRDM16 (ab106410) antibodies were all purchased from Abcam (Cambridge, UK). Active-Caspase 3 (bs7004), active-Caspase 9 (bs7070), Bcl-2 (bs1511) and GAPDH (ap0063) antibodies were purchased from Bioworld (Nanjing, China). Smad3 (9523S) and IRE1 (3294S) antibodies were purchased from Cell Signaling Technology (CST, Boston, MA, USA). Rabbit HRP-conjugated secondary antibody (Boaoshen, Beijing, China) was added and incubated at room temperature for 2 h. Proteins were visualized using chemiluminescent peroxidase substrate (Millipore, Boston, MA, USA), and then the blots were quantified using ChemiDoc XRS system (Bio-Rad, Hercules, CA, USA).
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9

Muscle Protein Analysis by Western Blot

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For protein content analysis, skeletal (quadriceps femoris) and cardiac (left ventricle) muscle samples were homogenized and analyzed by Western blotting. The following antibodies were used: BNIP3 (ab109362, rabbit, 1 : 1000), p-AMPK (ab131357, rabbit, 1 : 500) from Abcam (USA); PGC-1α (sc-13067, rabbit, 1 : 200) from Santa Cruz (USA); CS (16131-1-AP, rabbit, 1 : 1000), LC 3 I/II (14600-1-AP, rabbit, 1 : 500), AMPK (10929-2-AP, rabbit, 1 : 500), DRP1 (12957-1-AP, rabbit, 1 : 500), MFN1 (13798-1-AP, rabbit, 1 : 500), and p62 (18420-1-AP, rabbit, 1 : 1000) from Proteintech (USA); and GAPDH (AP0063, rabbit, 1 : 5000) from Bioworld (USA). Membranes were analyzed and quantified using the Quantity One Imaging System (BIO-RAS, USA). Protein expression was normalized to that of GAPDH.
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10

Investigating Apigenin's Anti-inflammatory Effects

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Apigenin (98% in purity) was obtained from Aladdin (Shanghai, China). GAPDH (AP0063) was purchased from Bioworld (Nanjing, China). IL-1 beta (26048-1-AP), IL-6 (66146-1-lg), MMP3 (17873-1-AP), and MMP13 (18165-1-AP) were purchased from Proteintech (Wuhan, China). JNK (ET1601-28), P-JNK (ET1609-42), ERK (ET1601-29), P-ERK (ET1610-13), P38 (ET1602-26), P-P38 (ER2001-52), TRPM7 (ER61334), p-mTOR (HA600094), and mTOR (ET1608-5) were purchased from HUABIO (Hangzhou China). Bax (#40635) and Bcl-2 (#40639) were purchased from SAB (Nanjing, China). Cleaved-caspase3 (TA7022S) was purchased from Abmart (Shanghai, China).
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