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19 protocols using suberoylanilide hydroxamic acid

1

Comparative Analysis of Melanoma Cell Line Responses to Diverse Treatments

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Human melanoma cell lines A375 (CLS Cat# 300110/p852_A-375, RRID:CVCL_0132) and C8161 (RRID:CVCL_6813; kindly provided by Prof. D. Constam, EPFL, Lausanne, Switzerland) were grown in DMEM supplemented with 10% FBS. Pooled human healthy primary melanocytes (ATCC) and primary melanocytes from individual donors (kindly provided by Prof. D. Fisher (Massachusetts General Hospital, Cutaneous Biology Research Center, Boston, USA) were grown in Melanocyte Growth Medium M2 supplemented with SupplementMix Melanocyte Growth Medium (PromoCell). All cultures were maintained at 37 °C in a 5% CO2 humidified atmosphere, with medium renewal every 2 or 3 days.
A375 cells were treated during 24 h with PLX4032 (100 nM; Axon Medchem), U0126 (5 μM; New England Biolabs), suberoylanilide hydroxamic acid (5 μM), colchicine (100 nM), camptothecin (1 μM), dichloroacetate (50 mM) and sodium oxamate (10 mM) all from Sigma-Aldrich. The effect of each drug was normalized to its corresponding control: the vehicle for PLX4032, U0126, suberoylanilide hydroxamic acid and camptothecin was DMSO, used alone in control cells at a maximal concentration of 0.1% (vol/vol); an equimolar sodium chloride solution was used as a control for colchicine, dichloroacetic acid and sodium oxamate treatments.
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2

Epigenetic Regulation of Calcium Sensing

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DMEM, FBS, hepes, l-glutamine, penicillin and streptomycin were obtained from Life Technologies (Vienna, Austria). 5-aza-2′-deoxycytidine (DAC), Trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), Tween-20, Triton-X, and proteinase K were purchased from Sigma Aldrich (Vienna, Austria). The bisguanidine polyamine analog that inhibits LSD1 (LSD1i) was obtained from Merck Millipore (Darmstadt, Germany). NPS-2143 was obtained from Tocris (Bristol, UK). NPS-R568 was a kind gift from Dr. Arthur Christopoulos. POWER SYBR GREEN Mastermix, PureLink Quick Gel Extraction Kit, PureLink Quick Plasmid Miniprep Kit, and Topo TA Cloning Kit were purchased from Life Technologies. EpiTect Bisulfite Kit and HotStarTaq DNA Polymerase were from Qiagen (Hilden, Germany). Total human RNA was obtained from Clontech (Saint-Germain-en-Laye, France). Polyclonal anti-H3K4me2 and anti-H3K9ac antibodies were obtained from Diagenode (Liège, Belgium). Polyclonal anti-CaSR antibody was from AnaSpec (Seraing, Belgium), monoclonal anti-CaSR and anti-IgG antibodies were purchased from Abcam (Cambridge, UK). Dylight 549 anti-IgG antibody was obtained from Vector Laboratories (Peterborough, UK), DAPI was from Roche (Vienna, Austria), goat serum was obtained from Jackson ImmunoResearch (Suffolk, UK), and Fluoromount-G was purchased from Southern Biotech (Alabama, USA).
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3

Doxorubicin and Epigenetic Modulators Protocol

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Doxorubicin, neocarzinostatin, trichostatin A, suberoylanilide hydroxamic acid (SAHA), chloroquine and bafilomycin were obtained from Sigma-Aldrich (St. Louis, MO). Antibodies recognizing dyskerin and GAPDH were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). All other antibodies, including secondary antibodies, were obtained from Cell Signaling Technology (Danvers, MA).
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4

Modulation of S. aureus RN4220 Virulence

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S. aureus RN4220 was kindly provided by Prof. Bok Luel Lee (Pusan National University, Busan, Korea). Luria-Bertani (LB) broth was purchased from LPS Solution (Daejeon, Korea). Dulbecco's modified Eagle's medium (DMEM) and fetal bovine serum (FBS) were purchased from Welgene (Gyeongsan, Korea) and Gibco (Burlington, ON, Canada), respectively. Recombinant murine M-CSF was obtained from CreaGene (Seongnam, Korea). Sodium acetate, sodium propionate, sodium butyrate, trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), mepenzolate bromide (MPN), pertussis toxin (PTX), Triton X-114, octyl β-D-glucopyranoside, and thiazolyl blue tetrazolium bromide were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA). Anti-iNOS rabbit polyclonal IgG antibody was obtained from Upstate Biotechnology (Lake Placid, NY, USA). Anti-acetyl-histone H3 (Lys9) polyclonal antibody was purchased from Millipore (Billerica, MA, USA). Anti-STAT1 and -phosphorylated STAT1 (P-STAT1) rabbit polyclonal antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA). Anti-β-actin mouse monoclonal antibody was purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). All other reagents were purchased from Sigma-Aldrich Inc. unless indicated otherwise.
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5

HIV Latency Reactivation Agents

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ACH-2 and J1.1 cells were obtained from the NIH HIV-1 Reagent Program (Germantown, MD, USA) and maintained in RPMI 1640 supplemented with 10% fetal calf serum, penicillin, streptomycin and L-glutamine (all from ThermoFisher Scientific, Waltham, MA USA) at 37 °C and 5% CO2. Phorbol 12-myristate 13-acetate (PMA), Prostratin, Valproic Acid (VPA), Trichostatin A (TSA), JQ1, and Suberoylanilide hydroxamic acid (SAHA) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Panobinostat was from BioVision (Milpitas, CA, USA). EPZ-6438 and AZD5582 were obtained from Selleck Chem (Houston, TX, USA). BIX-01294 and 5-azacytidine were from StemCell Technologies (Vancouver, BC, Canada). Hexamethylene bisacetamide (HMBA) was obtained from Abcam (Boston, MA, USA). All inhibitors were solubilized in DMSO, except for HMBA, which was resuspended in sterile water.
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6

Multimodal Regulation of Cell Pathways

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Gossypol (GOS), valproic acid sodium salt (VPA), Tween 80, suberoylanilide hydroxamic acid (SAHA), tubacin, 3-methyladenine (3-MA), propidium iodide (PI), dimethyl sulfoxide (DMSO), Hoechst 33342, and MG132 were purchased from Sigma-Aldrich (St. Louis, MO, USA). GOS was dissolved in dimethyl sulfoxide (DMSO). The final concentration of DMSO never exceeded 0.2%, which had no cytotoxicity in this study (data not shown). WST-1 assay kit was obtained from Roche (Penzberg, Germany). RNase A, Dulbecco's modified Eagle's medium (DMEM), RPMI-1640, fetal bovine serum (FBS), penicillin and streptomycin were purchased from Invitrogen (Carlsbad, CA, USA). Polyvinylidene difluoride (PVDF) membranes (Hybond-P) were purchased from GE Healthcare Life Sciences (Piscataway, NJ, USA). The antibodies against cyclin A2 (#4656), Bcl-2 (#2870), Bax (#2772), Bim (#2933), PARP(#9532), cleaved caspase-3 (#9664), cleaved caspase-8 (#9496), cleaved caspase-9 (#7237), phospho(p)-Akt (Thr308: #2965), Akt (#2920), FOXO3a (#2497), p-FOXO3a (Ser253: #9466), acetyl-histone H3 (Lys9: #9649), acetyl-histone H4 (Lys16: #8804), histone H3 (#9717), LC3B (#3868), and β-tubulin (#2128) were obtained from Cell Signaling Technology (Danvers, MA, USA). The antibody against survivin (sc-10811) was from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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7

Preparation of HDAC Inhibitor Compounds

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Suberoylanilide hydroxamic acid (SAHA; Sigma Aldrich, USA) and chloroquine (chloroquine diphosphate salt; Sigma Aldrich, USA) were prepared as 10 mM stock solutions in 100% DMSO. Belinostat (PXD101), romidepsin (FK228) and panobinostat (LBH589) were purchased from Selleck Chemicals and prepared as 20 mM stock solutions in 100% DMSO. Pentamidine, diminazene aceturate and puromycin were all purchased from Sigma Aldrich and 0.16, 9.7 and 9.2 mM stock solutions prepared in 100% DMSO.
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8

Investigating Anticancer Potency of HDAC Inhibitors

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Vincristine and suberoylanilide hydroxamic acid (SAHA) were purchased from Sigma Chemical Co. (St. Louis, MO, USA), and tubastatin A (HDAC6 inhibitor) was synthesized from Dr. Jing-Ping Liou (Taipei Medical University, Taiwan). The above drugs were dissolved in DMSO (dimethylsulfoxide) and then preserved at −20 °C. Rhodamine 123, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium, propidium iodide, anti-β-tubulin, FITC-conjugated anti-mouse IgG, and all of the other chemical reagents used in this study were purchased from Sigma Chemical (St. Louis, MO, USA) and of analytical grade. Primary antibodies against Cdc2 (pY15), aurora B, caspase 8, caspase 9, HDAC1, HDAC2, HDAC3, HDAC4, and Bid were all purchased from Cell Signaling Technology (Beverly, MA); cyclin B, Cdc25C, Cdc2, PARP, Mcl-1, Bcl-2, Bcl-xl, and secondary antibodies were purchased from Santa Cruz (Santa Cruz, CA, USA); MPM2 (pSer/Thr) and H3 (pS10) were purchased from Upstate Biotechnology (Lake Placid, NY, USA); PLK (pT210), caspase 6, and caspase 7 were purchased from BD Biosciences (San Jose, CA, USA); caspase 3 was purchased from Imgenex (San Diego, CA, USA); acetyl-histone 3 was purchase from Millipore (Billerica, MA, USA); and an internal control, GAPDH, was purchased from Novus Biologicals (Littleton, CO, USA). Vectashield® mounting medium with DAPI was purchased from Burlingame, CA, USA.
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9

HDAC8 Inhibition Assay Protocol

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All reagents, including the inhibitors suberoylanilide hydroxamic acid (SAHA) and M344, were purchased from Sigma-Aldrich. The Fluor de Lys HDAC8 assay substrate RHKacKac-AMC (Kac = acetyllysine, AMC = aminomethylcoumarin) was purchased from Enzo Life Sciences.
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10

Synthesis and Characterization of MO-OH-Nap

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MO-OH-Nap was synthesized as previously described [2 (link), 10 (link)]. Stock solutions of MO-OH-Nap were prepared in DMSO (10 mM) and stored at −20°C. Suberoylanilide hydroxamic acid (SAHA), bortezomib, DFO, FC, AFS and zinc chloride were purchased from Sigma-Aldrich (St Louis, MO, USA).
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