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9 protocols using cleaved parp c parp

1

Western Blot Analysis of Apoptosis Markers

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For Western blotting analysis, cells were lysed as described previously [19 (link)]. Primary antibody, KIFC1 (H00003833-M01, Abnova, Taipei, Taiwan), Bcl-2 (sc-7382, Santa Cruz Biotechnology, Santa Cruz, CA, USA), Bax (sc-7480, Santa Cruz Biotechnology, Santa Cruz, CA, USA), cleaved PARP (c-PARP) (#5625, Cell Signaling Technology, Inc., Danvers, MA, USA), cleaved caspase-3 (c-caspase-3) (#9661, Cell Signaling Technology, Inc., Danvers, MA, USA) were used. β-Actin (Sigma-Aldrich, St. Louis, MO, USA) was used as a loading control.
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2

Antibody Validation for ER Stress Response

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Antibodies against Lipocalin 2 (LCN2) (#44058), cleaved PARP (cPARP) (#5625), CHOP/GADD153 (#2895), PDI (#3501) and PERK (#3192) were purchased from Cell Signaling Technology. Mouse monoclonal antibodies against BiP/GRP78 (#610978) were from BD Biosciences. Anti-FLAG (#014–22383) monoclonal antibody, holo-transferrin (holo-Tf), Brefeldin A, and ferritic chloride (FeCl3) were from Fujifilm WAKO Pure Chemical Corporation. As an internal control of E. coli, E. coli RNA polymerase alpha (RNAPα) monoclonal antibody (#WP003) was obtained from BioLegend. Anti-GAPDH antibody was from GeneTex. Anti-SubAB and Stx2 antibodies were prepared as described previously70 (link). 2,2′-Dipyridyl (DPI) and Deferoxamine mesylate salt (DF) were from Sigma Aldrich; and recombinant human LCN2 (1757-LC-050) was from R&D systems. N-Glycosidase F (P0704S) was purchased from New England BioLabs.
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3

Docetaxel Resistance in Lung Cancer Cell Lines

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Human LAD cell lines SPC-A1 and H1299 were purchased from the Tumor Cell Bank of Chinese Academy of Medical Science (Shanghai, China) and cultured in RPMI 1640 medium containing 10% fetal bovine serum and ampicillin and streptomycin at 37°C in a humidified atmosphere of 95% air and 5% CO2. Docetaxel-resistant SPC-A1 and H1299 cell lines (SPC-A1/DTX and H1299/DTX) were established and preserved in 50 μg/L final concentration of docetaxel in our laboratory. Antibodies against GAPDH, LC3, p62, caspase3, activated (cleaved) caspase3 (c-caspase3), PARP, cleaved PARP (c-PARP), Atg5, HMGB1, mTOR, phosphorylated mTOR (p-mTOR), Akt, p-Akt, S6RP, p-S6RP, MEK, ERK1/2, p-ERK1/2, and H2A were obtained from Cell Signaling Technology. Bafilomycin A1, 3-methyladenine (3-MA), ethyl pyruvate (EP) and PD098059 were purchased from Sigma Aldrich (St. Louis, MO).
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4

Protein Expression Analysis of Cancer Cells

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After various treatments as indicated, cancer cells were harvested, and the total protein was lysed in radio immunoprecipitation assay (RIPA) lysis buffer (Beyotime, Shanghai, China) and then quantified by a BCA kit (Epizyme, Shanghai, China). Equal amounts of proteins were resolved on 10%-12.5% SDS-PAGE gels, followed by transferring the proteins to an Immobilon PVDF Membrane (Merck Millipore Ltd, Tullagreen, Ireland). PVDF membranes with proteins were blocked with 5% skim milk for 1 hour, incubated with primary antibodies overnight at 4°C, and then conjugated with secondary antibodies (Cell Signaling Technology, Danvers, MA, USA) at room temperature for 1 hour. Signals were visualized by ECL reagent (Epizyme, Shanghai, China) and photographed by Tanon 5200 visualizer (Tanon, Shanghai, China).
The primary antibodies used are as follows: p27, p21, Cyclin D1, PARP, cleaved PARP (c-PARP), cleaved caspase 3, cleaved caspase 9, cleaved caspase 7, cleaved caspase 8, Noxa, Bak, Bax, Bik, Bim, Bad, Puma, Bcl2, Bcl-xl, Mcl-1, XIAP, BID, TRAIL, DR4, DR5, CHOP, ATF4, eIF2α, and p-eIF2α were from Cell Signaling Technology (USA). Cyclin E, CDK2, CDK4, CDK6, Fas, DR3, c-Myc, and p53 were from Santa Cruz Biotechnology (USA). TNFR1 and TNFR2 were from Proteintech (USA). β-Actin was from HuaBio (China).
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5

Cisplatin-Induced Apoptosis Signaling

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Cisplatin (DDP, Cat.#H20010743) injection was purchased from Jiangsu Hausen Pharmaceutical Co., Ltd (Jiangsu, China). Dulbecco's modified Eagle's medium (DMEM, Cat.#11965092), fetal bovine serum (FBS, Cat.#10270106), penicillin/streptomycin (Cat.#10378016), and phosphate-buffered saline (PBS, Cat.#10010023) were supplied by Gibco (NY, USA). Primary antibodies against Beclin1 (Cat.#11306-1-AP), p62 (Cat.#66184-1-Ig), Cytochrome c (cyto. C, Cat.#66264-1-Ig), and DAPK1 (Cat.#25136-1-AP) were purchased from Proteintech (Wuhan, China). Primary antibodies against Phospho-AMPKα (p-AMPKα, Cat.#50081S), Phospho-mTOR (p-mTOR, Cat.#5536T), Atg7 (Cat.#8558T), LC3A/B (Cat.#12741S), Cleaved Caspase-9 (c-Casp 9, Cat.#20750S), Cleaved Caspase-3 (c-Casp 3, Cat.#9661T), Cleaved PARP (c-PARP, Cat.#5625T), Phospho-SAPK/JNK (p-JNK, Cat.#9255S), Phospho-p53 (p-p53, Cat.#9284T), Bax (Cat.#2772T), and GAPDH (Cat.#5174T) and rabbit (Cat.#7074P2) or mouse (Cat.#7076P2) secondary antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA).
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6

Western Blot Analysis of Protein Targets

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Cells were harvested and lysed in ice-cold RIPA lysis buffer with added protease and phosphatase inhibitor (Cell Signaling Technology, Danvers, MA USA). Equal amounts of protein were resolved and separated on an SDS/PAGE gel (BioRad TrisGlycine 4–20% gel), transferred onto PVDF membranes, and subjected to immunoblot analyses. The membranes were blocked with 5% nonfat dry milk in Tris-buffered saline, pH 7.4, containing 0.05% Tween 20, and were incubated with primary and secondary antibodies according to the manufacturer’s instructions. Blotting was performed using antibodies targeting PLK1 (Abcam, Cambridge, UK; Cat. #: 17056), DNA methyltransferase 1 (DNMT1) (BD Biosciences, San Jose, CA USA; Cat. #: 612618), Bcl-xL (Cell Signaling; Cat. #: 2764), Cleaved PARP (c-PARP) (Cell Signaling; Cat. #: 9541), p53 (DO-1) (Santa Cruz, Cat. #126), p-p53 (Ser15) (Cell Signaling; Cat. #: 9284), STAT3 (BD Biosci, Cat. #: 610189), p-STAT3 (Tyr705) (abcam; Cat. #: 76315), Cleaved Caspase-7 (c-Caspase-7) (Cell Signaling; Cat. #: 9491), Cleaved Caspase-3 (c-Caspase-3) (Cell Signaling; Cat. #: 9541), and Vinculin (Cell Signaling; Cat. # 4650). Dilutions used for Cleaved Caspase-3 and Cleaved Caspase-7 were 1:250, and for other antibodies were according to the company’s recommendations.
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7

Apoptosis Quantification by Flow Cytometry

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About 1 × 106 cells were plated 6-well plates. After 48-hour of treatment, cells were then fixed and permeabilized using the Click-iT EdU Plus flow cytometry assay kit (Thermo Scientific) according to the manufacturer's instructions. Briefly, cells were pulse labeled with 10 μM EdU for 1.5 hours prior to performing he Click-iT reaction. The cells were then fixed and permeabilized, before stained with cleaved Caspase-3 (cC3) (Cell Signaling) and cleaved PARP (cPARP) (Cell Signaling) antibodies for one hour then stained with appropriate secondary antibody for 30 minutes. Finally, cells were incubated in DAPI (1 μg/ml). Cells were then analyzed by flow cytometry (MoFlo Astrios cell sorter with Summit acquisition software, Beckman Coulter). Data analysis was completed with Kaluza software (Beckman Coulter). All data are presented as a percentage mean ± SEM.
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8

Apoptosis Signaling Pathway Assay

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Primary antibodies to the following proteins were used: cleaved PARP (c-PARP), cleaved caspase 8 (c-caspase 8), cleaved caspase 9 (c-caspase 9), ATF4, CHOP, Noxa, DR3, Bax, Bad, Bid, Bim, p53, p21, p-histone 3 (p-H3), p-H2AX, p-cdc2 (Cell Signaling Technology, Danvers, MA, United States); DR5 and FoxO3a (Abcam, Cambridge, MA, United States); TNFR1, TNFR2 and β-actin (HuaBio, China).
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9

Signaling Pathway Analysis Protocol

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Antibodies against AKT, phosphorylated AKT at S473, ERK1/2, phosphorylated ERK1/2 (T202/Y204), mTOR, phosphorylated mTOR (S2481), p70S6K, phosphorylated p70S6K (T421/S424), cleaved caspase-3 (C-Cas3), cleaved caspase-9 (C-Cas9), and cleaved PARP (C-PARP) were purchased from Cell Signaling Technology (Boston, MA, USA). Antibodies against GAPDH and Tubulin were obtained from Huaan Biotechnology Co., Ltd. (Hangzhou, China). Z-VAD-fmk was obtained from Selleck Chemicals (Houston, TX, USA). Muse™ Cell Cycle Kit and Muse® Annexin V & Dead Cell Kit were purchased from Millipore (Billerica, MA, USA). Other reagents were purchased from Beyotime Biotechnology, Shanghai, China.
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