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23 protocols using anti puma

1

Western Blot Assays with Antibodies and Plasmids

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The following antibodies were used in western blot assays: anti-β-actin (A15), anti-Flag M2 and anti-Flag M2 agarose resin (Sigma), anti-HA (3F10), anti-HA agarose resin (Roche Applied Science), anti-p53 (DO-1, which detects the N-terminal epitope comprising amino acids 11–25), anti-p53 (full-length), anti-CBP(Cell Signaling Technology), anti-p21, anti-PUMA, anti-MDM2 (Santa Cruz), anti-Ac-K101-p53, anti-Ac-K164-p53, anti-Ac-p53 C-terminal (made in-house), anti-pan-acetylation-Lysine (Ac-K) and anti-pan β-hydroxybutyrylation-Lysine (BHB-K) (PTM BioLabs; Hangzhou, China).
Plasmids Flag-p53, Flag-p300, CBP-HA and CBP-HA mutants were from Dr. Gu’s lab4 (link),8 (link).
siRNA targeting CBP and p300 (1#: 5′-GAGGUCGUUUACAUAAATT-3′; 2#: 5′-UUUAUGUAAACGCGACCUCTT-3′) and a negative control (5′-UUCUCCGAACGUGUCACGUTT-3′) were synthesized by GenePharma (China).
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2

Immunoblotting Antibody Protocol

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Immunoblotting was performed as described [74 (link), 75 (link)]. The antibodies used were anti-Flag (Sigma-Aldrich), polyclonal anti-YOD1 (Proteintech, Rosemont, IL), monoclonal and polyclonal anti-p53 (Cell Signaling Technology, Beverly, MA and Santa Cruz Biotechnology respectively), anti-Myc, anti-PUMA, anti-BAX, and anti-MDM2 antibodies (Santa Cruz Biotechnology), anti-K48 ubiquitin and β-actin (Cell Signaling Technology), anti-HA (Abcam), and horseradish peroxidase-conjugated secondary antibodies (Cell Signaling Technology).
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3

Apoptosis Pathway Antibody Panel

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Antibodies used include anti-Bid (Luo et al.12 (link)), anti-Bim (Santa Cruz, Biotechnology, Inc, Dallas, TX, USA, Sc-11425, Calbiochem, San Diego, CA, USA, #202000), anti-Puma (Santa Cruz, Sc-28226, Pro-Sci, Inc, Poway, CA, USA, 3041), anti-Bad (Santa Cruz, Sc-8044), anti-Noxa (Santa Cruz, Sc-56169 Novus Biologicals, Littleton, CO, USA, IMG-349A), anti-Bax (Santa Cruz, Sc-493), anti-Bak (Santa Cruz, Sc-832, Cell Signaling Technology, Danvers, MA, USA, #3814), anti-Bcl-2 (Santa Cruz, Sc-509), anti-Bcl-xL (Santa Cruz, Sc-8392), anti-Mcl-1 (Santa Cruz, Sc-819), anti-β-actin (Sigma-Aldrich, St. Louis, MO, USA, A5441), anti-PARP (Cell Signaling Technologies, #9524), anti-GFP (Santa Cruz, Sc-459), and anti-p53 (Santa Cruz, Sc-393). z-VAD(OMe)-FMK was purchased from MP Biomedicals (Santa Ana, CA, USA). Thapsigargin was purchased from Adipogen. Corp (San Diego, CA, USA) ABT-737 was purchased from Cayman Chemical (Ann Arbor, MI, USA). Human recombinant TRAIL was made as previously described.61 (link)
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4

Western Blot Analysis of Apoptosis Signaling

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Proteins were extracted by RIPA buffer, separated by SDS-PAGE, and analyzed by Western
blotting. Primary antibodies (obtained from Cell Signaling, Danvers, MA, unless otherwise
noted) included anti-caspase-3, anti-caspase-8 (Enzo Life Sciences, Farmingdale, NY),
anti-p53, anti-p21, anti-phospho-p38, anti-p38, anti-phospho-ERK, anti-ERK,
anti-phospho-AKT, anti-AKT, anti-BIM, anti-Puma, and anti-Bcl2 (Santa Cruz Biotechnology,
Dallas, TX). Anti-actin and anti-laminin antibodies (Sigma-Aldrich, St Louis, MO) were
used as controls. Secondary antibodies were labeled with horseradish peroxidase
(Pierce/Thermo-Fisher Scientific, Waltham, MA). Antigen-antibody complexes were revealed
by enhanced chemiluminescence by following the manufacturer’s instructions (Millipore,
Billerica, MA). Western blotting films were scanned, and band signal intensities were
determined using ImageJ software (National Institutes of Health, Bethesda, MD).
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5

Characterizing Hematopoietic Stem Cells

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Bone marrow cells were collected and stained with antibodies against c-kit and Sca-1. FACS analysis was gated on Lin- cells and the cells positive for c-kit and Sca-1 were counted. For Western blot analysis, bone marrow cells were collected and the whole cell lysates were prepared with RIPA buffer. The proteins were separated by SDS-PAGE before transferred onto the membrane and probed with the indicated antibodies: anti-mouse p53 (CM5, Novocastra), anti-p21 (Santa Cruz, SX118), anti-PUMA (Santa Cruz, H-136). Levels of β-actin (Sigma) were used as total protein control.
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6

Analyzing Apoptosis Markers in Mouse Tissues

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The whole cell extracts were prepared from mouse tissues using RIPA buffer. The whole cell extracts of spleen or thymus from an untreated wild type mouse and an irradiated (6 Gy) wild type mouse were used as controls. The proteins were then resolved by SDS-PAGE, transferred onto the membrane, and probed using the following antibodies: anti-mouse p53 (CM5, Novocastra), anti-PUMA (Santa Cruz, H-136), anti-cleaved Caspase 3 (Cell Signaling 9661), anti-p21 (Santa Cruz Biotechnology, SX118). Levels of Vinculin were used as total protein control.
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7

Oxidative Stress and Apoptosis Pathway Analysis

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MTT, dimethyl sulfoxide (DMSO), PI, DAPI and DCFH-DA were purchased from Sigma (St Louis, MO). RIPA buffer and JC-1 staining kit were purchased from Beyotime Biotechnology, China. The following antibodies were used: anti-PUMA, anti-p53, anti-Chk1, anti-Chk2, anti-p-Chk1(Ser345), anti-p-Chk2 (Thr68), anti-ATM, anti-p-ATM (Ser1981), anti-PARP, anti-GAPDH and anti-β-actin (Santa Cruz Technology, Santa Cruz, CA, USA); Anti-NOX1, anti-NOX4, anti-DUOX1 and anti-SOD1, anti-Keap1, anti-Nrf2, anti-HO-1, anti-DNA-PKcs, anti-p-DNA-PKcs (Thr 2609), anti-Caspase-3 and anti-Caspase-9 (Cell Signaling Technology, Danvers, MA, USA); Anti-γ H2AX (Ser139), anti-H2AX and anti-JNK, anti-p-JNK, anti-BCL-XL, anti-MCL-1 and anti-BCL-2 (Abcam). Rhodamine (TRITC) AffiniPure Goat anti-Rabbit IgG was from Santa Cruz Biotechnology; KU-60019, VE-821 and NU7026 were obtained from Selleck (USA). SP600125 were obtained from Calbiochem (La Jolla, CA, USA). Z-VAD-fmk was purchased from R&D Systems (Minneapolis, MN). These inhibitors were dissolved in DMSO and diluted to appropriate concentrations with cell culture media. Mitotracker and MitoSOX red mitochondrial superoxide indicator was purchased from Molecular Probe (USA).
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8

Apoptotic Pathway Analysis in Synovial Tissue

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Processed paraffin-embedded synovial sections were stained with anti-GFP (Santa Cruz), anti-PUMA (Santa Cruz), anti-p73 (Santa Cruz), anti-iASPP (Santa Cruz), anti-cadherin-11 (Cell Signaling) or isotype control IgG (Santa Cruz), followed by secondary antibodies and substrate chromogen with expression intensities quantitated by the HistoQuest software (Tissue Gnostics). Apoptotic cells in cryostat synovial sections were detected by the TUNEL assay (Promega). For immunofluorescent analyses, pre-treated paraffin-embedded synovial sections were incubated with anti-p73 (Santa Cruz), anti-iASPP (Santa Cruz), or isotype control IgG (Santa Cruz), followed by FITC- and Texas red-conjugated secondary antibodies (BD Biosciences), respectively, and observed by the fluorescence microscopy. Apoptotic and fluorescence-positive cells were counted by averaging their numbers in 3 randomly selected fields at the ×400 magnification, as previously described [18 (link)]. Purified SFs were subjected to anti-p73 (Santa Cruz) and anti-iASPP (Santa Cruz), followed by Alexa Fluor 488- and Alexa Fluor 594-conjugated secondary antibodies (Life Technologies), respectively, and observed by the confocal microscopy.
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9

Immunoblotting Assay for Protein Analysis

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Following antibodies were used: anti-FBXO31 (F4431), anti-FLAG (F1840), anti-phosphoserine (P5747), anti-phosphothreonine (P6623) and anti-tubulin (T5168) from Sigma. Anti-FBXL20 (TA306520) and anti-DDK (TA50011) from Origene. Anti-myc (#11667149001) from Roche. Anti-His (sc-8036), anti-cleaved PARP-1(sc-56196), anti-HA (sc-7392), anti-BIM (sc-374358), anti-GFP (sc-9996), anti-p53 (sc-126) anti-GSKa/b (sc-7291) from Santacruz. Anti-PUMA (#4976), BAX (#2772), anti-AKT1 (#9272), anti-pAKT473 (#4058), anti-cleaved Caspase-9 (#9501), anti-K48-ubiquitin (#8081), anti-GST(#2624), anti-BCL2 (#4223) from Cell Signaling technology.
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10

Comprehensive Western Blot Analysis

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Cell extracts were prepared in RIPA (radioimmunoprecipitation assay) buffer supplemented with Complete protease inhibitor cocktail (Roche). Equal amounts of cell extracts were resolved on acrylamide: bis-acrylamide gels and electroblotted onto PVDF membrane (Immobilon-P, Millipore) and probed with appropriate primary and HRP-conjugated secondary antibodies (Jackson ImmunoResearch). When necessary, membranes were stripped using Restore Western Blot Stripping Buffer (Thermo) and reprobed with anti-PUMA, anti-GAPDH, anti-S100A4, anti-MMP-2/9, anti-bcl-2, anti-bax and cleaved-caspase-3 (Santa Cruz, Shanghai, China). Unless otherwise specified, western blots were representative of n = 3.
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