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sonication buffer  (Thermo Fisher)


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    Structured Review

    Thermo Fisher sonication buffer
    Sonication Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/sonication+buffer/Triton+X-100/bio_rxiv__64898__2026__04__30__721885-222-8-27
    Average 99 stars, based on 1 article reviews
    sonication buffer - by Bioz Stars, 2026-10
    99/100 stars

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    Related Articles

    Sonication:

    Article Title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
    Article Snippet: After proximity ligation, the chromatin was collected by centrifugation (12000x g, 5 min), resuspended in 200 μl 1x NEBuffer 1 (NEB #B7001S) and 200 U NEB Exonuclease III (NEB #M0206S), and incubated for 15 min at 37 °C to remove biotin from unligated ends. .. After ExoIII digestion, chromatin was resuspended in the sonication buffer (0.1% IGEPAL CA-630, 50 mM NaCl, 10 mM Tris–HCl, pH 7.5, 5 mM MgCl 2 , 2 mM EDTA, 0.5% SDS (Invitrogen #15553-035)), 1x protease inhibitor) and sonicated for 10 cycles (sonication cycle: 30 s ON, 30 s OFF) using Bioruptor Plus (Diagenode). ..

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Article Title: Germ granule compartments coordinate specialized small RNA production
    Article Snippet: .. Briefly, the animals were sonicated in sonication buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl 2 , and 0.5% NP-40); the eluates were incubated with TRIzol reagent (Invitrogen) prior to isopropanol precipitation. .. The RNA solution was subjected to DNase I digestion (Thermo Fisher) and re-extracted with TRIzol prior to isopropanol precipitation.

    Article Title: Nuclear mTOR-Polycomb synergism at developmental gene promoters prone to activation
    Article Snippet: Cells were then washed 2 times in ice-cold PBS before incubation at 4 °C in swelling buffer (25 mM HEPES, pH 7.9, 1.5 mM MgCl 2 , 10 mM KCl, 0.1% Igepal 630, 1x protease and phosphatase inhibitor cocktail (Thermo Fisher, 78443), 1 mM PMSF, 1 mM NaVO 3 , 5 mM NaF) for 10 min. To collect the nuclei, cells were scraped on ice, passed through a 18G needle for 5 times and spun at 3000 x g for 5 minutes at 4°C. .. Nuclei pellets were resuspended in 1 ml of sonication buffer (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate (Thermo Fisher Scientific, 89904), 0.1% SDS, 1 mM PMSF, 1 mM NaVO3, 5 mM NaF) and incubated on ice for 10 min. .. Resulting chromatin was sheared to an average size of 500-1000 bp using an E220 Evolution Covaris sonicator for 6 cycles (1 minute per cycle).

    Article Title: The T1150A cancer mutant of the protein lysine dimethyltransferase NSD2 can introduce H3K36 trimethylation.
    Article Snippet: .. In brief, the cell pellets were thawed on ice and resuspended in sonication buffer (50 mM Tris/HCl pH 7.5, 150 mM NaCl, 1 mM DTT, 5% glycerol) supplemented with protease inhibitor cocktail containing AEBSF-HCL (1 mM, Biosynth), pepstatin (10 μM, Roth), aprotinin (0.4 μM, Applichem), E−64 (15.14 μM, Applichem), leupeptin (22.3 μM Alfa Aesar), and bestatin (50 μM, Alfa Aesar), and the cells were disrupted by sonication. .. The lysed cells were centrifuged at 40,000 rcf for 90 min at 4 C. The supernatant was loaded onto a column containing sonication buffer pre-equilibrated glutathione-Sepharose 4B beads resin (GE Healthcare).

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons.
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Article Title: E2F1 K117 methylation by SETD6 disrupts BRD4–E2F1 binding and modulates E2F1 chromatin binding and gene regulation in prostate cancer cells
    Article Snippet: .. Cell pellets were resuspended in sonication buffer [50 mM Tris/HCl, pH 7.5, 150 mM NaCl, 1 mM Dithiothreitol (DTT), and 5% (w/v) glycerol] supplemented with protease inhibitor cocktail containing AEBSF–HCL (1 mM; Biosynth), Pepstatin (10 μM; Roth), Aprotinin (0.4 μM; Applichem), E‐64 (15.14 μM; Applichem), Leupeptin (22.3 μM; Alfa Aesar), and Bestatin (50 μM; Alfa Aesar) and lysed by sonication (14 cycles of 30 s at 30% power; Bandelin Sonopuls) at 4°C. ..

    Article Title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
    Article Snippet: After proximity ligation, the chromatin was collected by centrifugation (12000x g, 5 min), resuspended in 200 μl 1x NEBuffer 1 (NEB #B7001S) and 200 U NEB Exonuclease III (NEB #M0206S), and incubated for 15 min at 37°C to remove biotin from unligated ends. .. After ExoIII digestion, chromatin was resuspended in the sonication buffer (0.1% IGEPAL CA-630, 50 mM NaCl, 10 mM Tris–HCl, pH 7.5, 5mM MgCl 2 , 2mM EDTA, 0.5% SDS (Invitrogen #15553-035)), 1x protease inhibitor) and sonicated for 10 cycles (sonication cycle: 30 sec ON, 30 sec OFF) using Bioruptor Plus (Diagenode). ..

    Protease Inhibitor:

    Article Title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
    Article Snippet: After proximity ligation, the chromatin was collected by centrifugation (12000x g, 5 min), resuspended in 200 μl 1x NEBuffer 1 (NEB #B7001S) and 200 U NEB Exonuclease III (NEB #M0206S), and incubated for 15 min at 37 °C to remove biotin from unligated ends. .. After ExoIII digestion, chromatin was resuspended in the sonication buffer (0.1% IGEPAL CA-630, 50 mM NaCl, 10 mM Tris–HCl, pH 7.5, 5 mM MgCl 2 , 2 mM EDTA, 0.5% SDS (Invitrogen #15553-035)), 1x protease inhibitor) and sonicated for 10 cycles (sonication cycle: 30 s ON, 30 s OFF) using Bioruptor Plus (Diagenode). ..

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Article Title: The T1150A cancer mutant of the protein lysine dimethyltransferase NSD2 can introduce H3K36 trimethylation.
    Article Snippet: .. In brief, the cell pellets were thawed on ice and resuspended in sonication buffer (50 mM Tris/HCl pH 7.5, 150 mM NaCl, 1 mM DTT, 5% glycerol) supplemented with protease inhibitor cocktail containing AEBSF-HCL (1 mM, Biosynth), pepstatin (10 μM, Roth), aprotinin (0.4 μM, Applichem), E−64 (15.14 μM, Applichem), leupeptin (22.3 μM Alfa Aesar), and bestatin (50 μM, Alfa Aesar), and the cells were disrupted by sonication. .. The lysed cells were centrifuged at 40,000 rcf for 90 min at 4 C. The supernatant was loaded onto a column containing sonication buffer pre-equilibrated glutathione-Sepharose 4B beads resin (GE Healthcare).

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons.
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Article Title: E2F1 K117 methylation by SETD6 disrupts BRD4–E2F1 binding and modulates E2F1 chromatin binding and gene regulation in prostate cancer cells
    Article Snippet: .. Cell pellets were resuspended in sonication buffer [50 mM Tris/HCl, pH 7.5, 150 mM NaCl, 1 mM Dithiothreitol (DTT), and 5% (w/v) glycerol] supplemented with protease inhibitor cocktail containing AEBSF–HCL (1 mM; Biosynth), Pepstatin (10 μM; Roth), Aprotinin (0.4 μM; Applichem), E‐64 (15.14 μM; Applichem), Leupeptin (22.3 μM; Alfa Aesar), and Bestatin (50 μM; Alfa Aesar) and lysed by sonication (14 cycles of 30 s at 30% power; Bandelin Sonopuls) at 4°C. ..

    Article Title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP
    Article Snippet: After proximity ligation, the chromatin was collected by centrifugation (12000x g, 5 min), resuspended in 200 μl 1x NEBuffer 1 (NEB #B7001S) and 200 U NEB Exonuclease III (NEB #M0206S), and incubated for 15 min at 37°C to remove biotin from unligated ends. .. After ExoIII digestion, chromatin was resuspended in the sonication buffer (0.1% IGEPAL CA-630, 50 mM NaCl, 10 mM Tris–HCl, pH 7.5, 5mM MgCl 2 , 2mM EDTA, 0.5% SDS (Invitrogen #15553-035)), 1x protease inhibitor) and sonicated for 10 cycles (sonication cycle: 30 sec ON, 30 sec OFF) using Bioruptor Plus (Diagenode). ..

    Expressing:

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Article Title: Botulinum neurotoxin X lacks potency in mice and in human neurons.
    Article Snippet: Whole cell lysate was evaluated for expression via SDS-PAGE Coomassie staining or western blot with 1° polyclonal α-A1 or α-X antibody or monoclonal α-His antibody (BioLegend 906102). .. Expression culture was pelleted at 6,000 × g for 8 minutes, resuspended in 50 mL sonication buffer [50 mM Tris, 50 mM NaCl, 20 mM imidazole, 5% glycerol, and protease inhibitor cocktail tablet (Pierce), pH 5.5], sonicated and loaded on to an equilibrated 2–3-mL Ni-IMAC column, washed to background with the same buffer, and eluted with 250 mM imidazole. ..

    Incubation:

    Article Title: Germ granule compartments coordinate specialized small RNA production
    Article Snippet: .. Briefly, the animals were sonicated in sonication buffer (20 mM Tris-HCl [pH 7.5], 200 mM NaCl, 2.5 mM MgCl 2 , and 0.5% NP-40); the eluates were incubated with TRIzol reagent (Invitrogen) prior to isopropanol precipitation. .. The RNA solution was subjected to DNase I digestion (Thermo Fisher) and re-extracted with TRIzol prior to isopropanol precipitation.

    Article Title: Nuclear mTOR-Polycomb synergism at developmental gene promoters prone to activation
    Article Snippet: Cells were then washed 2 times in ice-cold PBS before incubation at 4 °C in swelling buffer (25 mM HEPES, pH 7.9, 1.5 mM MgCl 2 , 10 mM KCl, 0.1% Igepal 630, 1x protease and phosphatase inhibitor cocktail (Thermo Fisher, 78443), 1 mM PMSF, 1 mM NaVO 3 , 5 mM NaF) for 10 min. To collect the nuclei, cells were scraped on ice, passed through a 18G needle for 5 times and spun at 3000 x g for 5 minutes at 4°C. .. Nuclei pellets were resuspended in 1 ml of sonication buffer (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate (Thermo Fisher Scientific, 89904), 0.1% SDS, 1 mM PMSF, 1 mM NaVO3, 5 mM NaF) and incubated on ice for 10 min. .. Resulting chromatin was sheared to an average size of 500-1000 bp using an E220 Evolution Covaris sonicator for 6 cycles (1 minute per cycle).



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