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17 protocols using a 485

1

Generation of Acetylated Nucleosome Arrays

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To generate acetylated nucleosome arrays for microinjection, recombinant p300 histone acetyl transferase domain was generated (VBCF Protein technologies Facility) using plasmid pET duet+p300HAT according to a purification strategy described previously13 (link). To induce histone acetylation of nucleosome arrays, arrays with 8% Alexa Fluor 488 or Alexa Fluor 594 label density at a concentration of 3.85 μM were incubated with 6.12 μM p300-HAT (enzyme stock 61.2 μM in gel-filtration buffer (20 mM Tris·HCl, pH 8.0, 150 mM NaCl, 10% (w/v) glycerol, 1 mM DTT)) in the presence of 750 μM Acetyl-CoA (Sigma-Aldrich, A2056) in gel-filtration buffer at room temperature for 2 h with occasional agitation. The acetylation was next stopped by the addition of A-485 (Tocris, 6387) to a final concentration of 9 μM and the reaction mixture was stored in the dark. To 10 μl of quenched acetylation reaction, 10 μl dilution buffer containing 5 μM A-485 (Tocris, 6387) was added and the reaction was allowed to equilibrate at room temperature for 10 min. Next, 1 volume of phase-separation buffer containing 5 μM A-485 (Tocris, 6387) was added and the mixture was incubated for 10 min at room temperature before transferring the suspension to a well of a passivated 384-well microscopy plate.
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2

Acetylated Nucleosome Arrays for Microinjection

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To generate acetylated nucleosome arrays for microinjection, recombinant p300 histone acetyl transferase domain was generated (VBCF Protein technologies Facility) using plasmid pETduet+p300HAT according to a purification strategy described previously13 (link). To induce histone acetylation of nucleosome arrays, arrays with 8% Alexa Fluor 488 or Alexa Fluor 594 label density at a concentration of 3.85 µM were incubated with 6.12 µM p300-HAT (enzyme stock 61.2 µM in gel-filtration buffer (20 mM Tris·HCl, pH 8.0, 150 mM NaCl, 10% (w/v) glycerol, 1 mM DTT)) in the presence of 750 µM Acetyl-CoA (Sigma-Aldrich, A2056) in gel-filtration buffer at room temperature for 2 h with occasional agitation. The acetylation was next stopped by the addition of A-485 (Tocris, 6387) to a final concentration of 9 µM and the reaction mixture was stored in the dark. To 10 µl of quenched acetylation reaction, 10 µl dilution buffer containing 5 µM A-485 (Tocris, 6387) was added and the reaction was allowed to equilibrate at room temperature for 10 min. Next, 1 volume of phase-separation buffer containing 5 µM A-485 (Tocris, 6387) was added and the mixture was incubated for 10 min at room temperature before transferring the suspension to a well of a passivated 384-well microscopy plate.
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3

IFNγ and A485 Treatment Protocol

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Cells were treated with IFNγ (Prospec Bio #CYT-358) at the concentrations stated in the text; if not stated, then the concentration is 10 ng/ml, which corresponds to 100 U/ml. For A485 treatment, cells were treated with 10 μM of A485 (Tocris #6387) for 2 h before addition of IFNγ.
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4

Transcriptomic Profiling of Hindbrain Neurons

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Ex vivo cultured E12.5 hindbrain neurons were treated with 2 μM trichostatin A (TSA) (MBJ. JM-1606-1) at the culture Day 1 and incubated for 16 hours. As for the KCl treatment, cultured hindbrain neurons were treated with a cocktail of neuronal activity blockers (TDN cocktail = 1 μM tetrodotoxin (TTX)(TOCRIS, 1069) + 100 μM D-AP5 (Sigma, A8054) + 20 μM NBQX (TOCRIS, 0373) at Day 1 for an over-night incubation, and 55 mM KCl containing medium was treated at Day 2 in the presence or absence of 35 μM GSK-J4 (Sigma, SML0701), 50 μM A-485 (TOCRIS, 6387) or 10 μM Flavopiridol (Sigma, F3055) after a rinse. As for Drg11tdTomato/+ cultured hindbrain neuorns, tdTomato+ neurons were sorted immediately after the KCl treatment. Processing of these cells was adapted for further analyses (mRNA-seq, ATAC-seq and ChIP-seq, see below and Supplementary Methods).
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5

Manipulating HepG2 and MEF Cells

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HepG2 cells were obtained from ATCC. Cells were validated to be free of mycoplasma contamination and maintained in DMEM medium containing 4.5 g glucose per liter and 10% FBS. Immortalized Crebbpfl/fl; Ep300fl/fl mouse embryonic fibroblasts (MEFs) stably expressing Cre-ERT2 were kindly provided by Dr. P. K. Brindle36 (link). The floxed CBP and p300 alleles were deleted as previously described37 (link). Briefly, Crebbpfl/fl; Ep300fl/fl MEFs were treated with 2 μM 4-hyroxy-tamoxifen (Cat. H7904, Sigma), media were changed and fresh 4-OHT added every 12 h for 2 days. Cells were cultured for an additional 1 day to allow for complete depletion of CBP and p300 protein. For transfection, plasmids expressing human full-length WT-p300 (Cat. 89094, addgene), and the p300 acetyltransferase activity-defective mutant (Cat. 89095, addgene)86 (link), were purchased from addgene and transfected with the Lipofectamine 3000 Reagent (Cat. L3000015, ThermoFisher). CBP/p300 acetyltransferase inhibitors A-485 (Cat. 6387, TOCRIS) and bromodomain inhibitor PF-CBP1 (Cat. S8180, Selleck Chemicals) were dissolved in DMSO and treated with final concentrations as described in the Figure legends. For the treatment of worms with CBP/p300 inhibitors, A-485 or PF-CBP1 was added into the NGM agar medium with final concentrations as indicated just before pouring the plates.
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6

Characterization of Myeloid Cell Lines

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MOLM-13 (DMSZ # ACC554), F36-P (DMSZ # ACC543) and SKK-1 have been obtained from DSMZ as a collaboration with Hans Drexler and have been characterized in detail36 (link). SKK-1 cells are available from the original authors37 (link). MDS-L cells were kindly provided by Tohyama and colleagues61 (link).
Cells were maintained in RPMI 1640 (Gibco, Thermo Scientific, Waltham, MA) supplemented with 10% of fetal bovine serum (FBS), 1% penicillin–streptomycin and 1% l-Gutamine (Gibco) at 37 °C in 5% CO2. HEK293T (ATCC #CRL-11268) and HS-5 (ATCC #CRL-11882) were obtained from American Type Culture Collection and cultured in Dulbecco’s modified Eagle’s media (Gibco) supplemented with 10% FBS, 1% penicillin–streptomycin and 1% l-Glutamine (Gibco) at 37 °C in 5% CO2. Cells were authenticated and passaged for <6 months. CD34+ cells were isolated from mononuclear cells of healthy donors (see Supplementary Data 2 for donor characteristics) and cultured in suspension as described62 (link). For combinatorial treatments, cells were treated with AZA (Sigma-Aldrich, St. Louis, MO), decitabine (Sigma-Aldrich), C646 (Sigma-Aldrich), A-485 (Tocris, Bristol, UK), iCBP-112 (Tocris), CCS1477 (CellCentric, Ltd, Cambridge, UK), JQ-1 (Sigma-Aldrich), DMSO (Sigma-Aldrich) or CHX (Sigma-Aldrich) at the indicated amounts.
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7

Transient Inhibition of CBP/p300 and HDACs in Embryos

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To transiently inhibit CBP/p300, embryos were cultured in KSOM containing 10 μM A‐485 (Tocris) between 4 and 20 hpi. For transient inhibition of HDACs, embryos were cultured in KSOM containing 50 nM TSA (Sigma) between 0–20 or 8–28 hpi. Embryos were washed at least six times when they were transferred between different culture conditions.
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8

Microinjection of Acetylated Nucleosome Arrays

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For the microinjection of dodecameric nucleosome arrays, arrays were acetylated in vitro prior to injection. Nucleosome arrays with a concentration of 5.5 μM, labeled with Alexa Fluor 488 or Alexa Fluor 594 were incubated with 2.3 μM recombinant p300 histone-acetyl transferase domain in the presence of 0.8 mM acetyl coenzyme A. Control reactions were conducted using only buffer without enzyme and coenzyme A added to the same amount of nucleosome arrays. After 2 hours at room temperature the reaction was quenched by addition of A-485 (100 μM in 10 % DMSO, Tocris) to 10 μM final concentration. Nucleosome arrays were wither injected directly or acetylated and nonacetylated arrays with differential fluor labels were mixed 1:1 for microinjection. The microinjection was performed using an Eppendorf InjectMan® 4 controller with FemtoJet® 4i, mounted on a Zeiss LSM780. For nuclear injections of nucleosome arrays commercial Femtotips™ Microinjection capillaries were used. Injection parameters were 150 hPa, 0.7 to 1 s, 20 hPa for delivery of medium to high volumes into nuclei.
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9

Targeted Inhibition of Cell Signaling

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Where indicated, the following chemicals were added to the media as indicated in the text: doxycycline hyclate (Sigma-Aldrich), SCH772984 (Selleck Chemicals, Houston, TX, USA), MK-2206 (Selleck Chemicals), RO4929097 (Selleck Chemicals), SB-747651A (Tocris Bioscience, Bristol, UK), A-485 (Tocris Bioscience), trichostatin A (Selleck Chemicals), C646 (Selleck Chemicals), ERGi-USU (Tocris Bioscience), and osimertinib (Selleck Chemicals).
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10

Inhibition of Cellular Pathways

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NDGA (Sigma), C646 (Sigma), A485 (Tocris), and Bafilomycin A1 (Adipogen) were dissolved in dimethyl sulfoxide (DMSO) (Sigma-Aldrich), Chloroquine (Biovision) was dissolved in water. Phosphate-buffered saline (PBS) was purchased from Corning. Tris-buffered saline with Tween (TBST) buffer (150 mM NaCl, 0.01% (v/v) Tween-20, 50 mM Tris-HCl buffer, pH 7.6) was used for immunoblotting. Blocking buffer and primary antibody incubation solution was 5% (w/v) BSA (Sigma), pH 7.0, in TBST. Secondary antibody incubation buffer was 5% (w/v) blocking reagent (Sigma) in TBST.
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