s2 ultrasonicator  (Covaris)


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  • 99
    Name:
    S220 Focused ultrasonicator
    Description:
    High performance Ultrasonicator for samples of mass 1000mg and or volume 10ml Single sample preparation system serial process Includes computer and SonoLab software
    Catalog Number:
    500217
    Product Aliases:
    S220, Ultrasonicator
    Price:
    None
    Size:
    8 W x 21 D x 13 H
    Category:
    Instrument
    Score:
    85
    Quantity:
    1
    Buy from Supplier


    Structured Review

    Covaris s2 ultrasonicator
    S220 Focused ultrasonicator
    High performance Ultrasonicator for samples of mass 1000mg and or volume 10ml Single sample preparation system serial process Includes computer and SonoLab software
    https://www.bioz.com/result/s2 ultrasonicator/product/Covaris
    Average 99 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    s2 ultrasonicator - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Methylation Sequencing:

    Article Title: Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium
    Article Snippet: Paragraph title: Whole Genome Bisulfite Sequencing ... Briefly, sample DNA spiked with λ phage genome DNA was fragmented into 200–300 bp with ultra-sonication (Covaris S220 System, Thermo Fisher Scientific, United States).

    Article Title: Mapping of histone-binding sites in histone replacement-completed spermatozoa
    Article Snippet: Paragraph title: Targeted bisulfite sequencing (TGBS) ... Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent).

    Amplification:

    Article Title: TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency
    Article Snippet: Cells were centrifuged and cell pellets lysed in 350 μL of RLT buffer, and total RNA was extracted using an RNeasy micro kit (Qiagen) or RNeasy mini kit (Qiagen). cDNA was amplified using Ovation RNA-Seq System V2 (Nugen) according to the manufacturer's instructions. .. Amplified cDNA was then sheared to ∼200 bp length by a Covaris S220 Focused ultrasonicator. .. RNA-seq libraries were constructed by using Ovation Rapid Library Systems (Nugen, 0319-32 for index 1–8 and 0320-32 for index 9–16) and quantified by a KAPA library quantification kit (Illumina).

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range. .. Bisulphite conversion was carried out with the EpiTect Kit (QIAGEN), performing two consecutive rounds of conversion for a total of 10 h of incubation.

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting. .. 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting.

    Article Title: Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
    Article Snippet: Each pool was then sheared to a 350 pb average size using a Covaris S220 sonicator (KBiosciences), and size-selected on agarose gel to keep DNA fragments within the size range 300–700 pb. .. Each library was then submitted to end-repair, A-tailing and ligation to P2 adapter before PCR amplification for 18 cycles.

    Construct:

    Article Title: Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium
    Article Snippet: Briefly, sample DNA spiked with λ phage genome DNA was fragmented into 200–300 bp with ultra-sonication (Covaris S220 System, Thermo Fisher Scientific, United States). .. The bisulfite conversion was conducted according to the protocol provided by the kit. λ phage genome DNA was included to help assess the methylation rate (bisulfite conversion rate).

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Size and quantity of DNA fragments were determined on 2200 TapeStation Instrument (Agilent Technologies, USA). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. Library preparation was performed by SeqCap EZ System (Roche NimbleGen, USA) with probes for PAX9 , MSX1 , AXIN2 , EDA , EDAR , and WNT10A genes according to manufacturer’s recommendations.

    Real-time Polymerase Chain Reaction:

    Article Title: Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways
    Article Snippet: The procedure was based on the Magna ChIP protocol (Millipore, 17-10085) and Chromatrap Premium ChIP qPCR (Chromatrap, 500115). .. After 10 min on ice, lysed cells were diluted 2-fold in ChIP dilution buffer and disrupted with the S220 Focused Ultrasonicator (Covaris) to yield genomic DNA fragments of 300 bp.

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range. .. Converted DNA was amplified according to the following PCR programme: denaturation at 98°C for 2 min, 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s and final extension at 72°C for 5 min. All libraries obtained after bisulphite treatment were sequenced by an Illumina HiSeq2000 system (Illumina, San Diego, CA, USA) using 100 bp single-end reads.

    Article Title: DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer
    Article Snippet: Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam). .. Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam).

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL).

    Incubation:

    Article Title: Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways
    Article Snippet: After 10 min on ice, lysed cells were diluted 2-fold in ChIP dilution buffer and disrupted with the S220 Focused Ultrasonicator (Covaris) to yield genomic DNA fragments of 300 bp. .. Immunocomplexes were pulled down with 20 μL of magnetic protein A beads as described in the Magna ChIP protocol.

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: ChIP assays for GFI1B, RUNX1, H3K27ac, LSD1 and CoREST were performed as described previously [ ]. .. Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range. .. Library preparation was performed using the Illumina TruSeq DNA Sample Prep according to the manufacturer’s instruction.

    Article Title: DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer
    Article Snippet: ChIP analysis was performed using Magna ChIP A/G chromatin immunoprecipitation kit (Merck Millipore, MA, USA) as per manufacturer’s protocol on cells isolated from NT and TT by ED. .. Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam). .. Isotype-matched control antibodies were used as negative controls.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: The quality of DNA was evaluated with Nano drop for purity, Qubit for dsDNA concentration and QPCR for estimation of amplifiable DNA content. .. 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting. .. The fragmented DNA was end-repaired and ligated to Illumina adaptor oligonucleotides with Kapa Hyper Prep Kit (KAPA Biosystems, Wilmington, MA; Cat.KK8504).

    Article Title: Antitumor activity of sorafenib plus CDK4/6 inhibitor in pancreatic patient derived cell with KRAS mutation
    Article Snippet: Formalin-fixed paraffin embedded (FFPE) samples containing > 40% tumor cellularity were dissected under microscopy from 4-μm-thick unstained sections (10 to 20 slides) or from fresh frozen tissues by comparison with a hematoxylin and eosin-stained slide. .. Briefly, DNA was extracted using standard procedures (Qiagen, Hilden, Germany) and extracted genomic DNA was sheared to 150-200 bp using Covaris S220 (Covaris, Woburn, MA, USA), and targeted genes were captured using a custom panel capture library (Agilent Technologies, Santa Clara, CA, USA) covering 2.5 Mb of exonic regions for the Illumina Paired-End Sequencing Library kit.

    Article Title: Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
    Article Snippet: For Nanopore sequencing, 1.5 µg of DNA (5.49 µL of 273 ng/uL DNA) was used to prepare a 1D sequencing library (SQK-LSK108) according to the manufacturer’s instructions, including the FFPE repair step. .. For Illumina sequencing, ∼600-bp fragments were generated from 500 ng of DNA using a Covaris S220 sonicator.

    Modification:

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: DNA was extracted from 200 μL whole blood by using automatic instrument ZEPHYRUS Magneto with modified protocol as specified for BodyFluid DNA/RNA isolation kit (Elisabeth Pharmacon, Czech Republic). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL).

    Hybridization:

    Article Title: The impact of endogenous content, replicates and pooling on genome capture from faecal samples, et al. The impact of endogenous content, replicates and pooling on genome capture from faecal samples
    Article Snippet: Paragraph title: Library preparation, hybridization and capture ... Genomic DNA was fragmented by shearing using a Covaris S2 focused ultrasonicator with the following settings for 200‐bp fragments: intensity 5, duty cycle 10%, cycles per burst 200, treatment time 120 s, temperature 7°C and water level 12.

    Flow Cytometry:

    Article Title: Mapping of histone-binding sites in histone replacement-completed spermatozoa
    Article Snippet: Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). .. Single-read sequencing (100 cycles) was performed on Illumina HiSeq 2500 using HiSeq SR Rapid Cluster Kit v2 (Illumina) and HiSeq Rapid SBS Kit v2 (Illumina).

    Article Title: Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
    Article Snippet: The 75-µl library was then immediately loaded onto a R9.5 flow cell prepared according to the manufacturer’s instructions and run for approximately 24 hr. .. For Illumina sequencing, ∼600-bp fragments were generated from 500 ng of DNA using a Covaris S220 sonicator.

    Ligation:

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting. .. The fragmented DNA was end-repaired and ligated to Illumina adaptor oligonucleotides with Kapa Hyper Prep Kit (KAPA Biosystems, Wilmington, MA; Cat.KK8504).

    Digital PCR:

    Article Title: Antitumor activity of sorafenib plus CDK4/6 inhibitor in pancreatic patient derived cell with KRAS mutation
    Article Snippet: Briefly, DNA was extracted using standard procedures (Qiagen, Hilden, Germany) and extracted genomic DNA was sheared to 150-200 bp using Covaris S220 (Covaris, Woburn, MA, USA), and targeted genes were captured using a custom panel capture library (Agilent Technologies, Santa Clara, CA, USA) covering 2.5 Mb of exonic regions for the Illumina Paired-End Sequencing Library kit. .. We aligned the sequencing reads to the human reference genome (GRCh37/hg19), excluded duplicated reads, and extracted uniquely mapped and properly paired reads with an insert size.

    Generated:

    Article Title: Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
    Article Snippet: Reads collected during the mux phase of sequencing were not included. .. For Illumina sequencing, ∼600-bp fragments were generated from 500 ng of DNA using a Covaris S220 sonicator. .. Fragments of 500–700 bp were selected using a Pippin and libraries were prepared using a KAPA High Throughput Library Preparation kit and Bioo Scientific NEXTflex DNA Barcodes.

    other:

    Article Title: Role of Some Natural Antioxidants in the Modulation of Some Proteins Expressions against Sodium Fluoride-Induced Renal Injury
    Article Snippet: DNA samples were fragmented by ultrasound using Covaris S220 (Covaris, Woburn, MA, USA) [ ].

    DNA Sequencing:

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: Paragraph title: Preparation of DNA sequencing libraries ... The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Sequencing:

    Article Title: TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency
    Article Snippet: Amplified cDNA was then sheared to ∼200 bp length by a Covaris S220 Focused ultrasonicator. .. RNA-seq libraries were constructed by using Ovation Rapid Library Systems (Nugen, 0319-32 for index 1–8 and 0320-32 for index 9–16) and quantified by a KAPA library quantification kit (Illumina).

    Article Title: NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus
    Article Snippet: Lysates from 2 × 150 mm dishes were sonicated in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, ph 8) using the Covaris S220 (35 min, 147 Watts, 200 cycle/burst, duty factor of 5) and tubes containing an AFA fiber (Covaris, Woburn, MA). .. NRF2 was immunoprecipitated from the lysate using rabbit anti-NRF2 antibodies (Diagenode, Denville, NJ, C15410242-100; Santa Cruz, SC-722).

    Article Title: The impact of endogenous content, replicates and pooling on genome capture from faecal samples, et al. The impact of endogenous content, replicates and pooling on genome capture from faecal samples
    Article Snippet: Genomic DNA was fragmented by shearing using a Covaris S2 focused ultrasonicator with the following settings for 200‐bp fragments: intensity 5, duty cycle 10%, cycles per burst 200, treatment time 120 s, temperature 7°C and water level 12. .. Genomic DNA was fragmented by shearing using a Covaris S2 focused ultrasonicator with the following settings for 200‐bp fragments: intensity 5, duty cycle 10%, cycles per burst 200, treatment time 120 s, temperature 7°C and water level 12.

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: Paragraph title: 2.2 Construction and sequencing of whole genome bisulphite libraries ... The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range.

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: Paragraph title: Illumina sequencing library preparation and sequencing on Hiseq2500 ... 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting.

    Article Title: Genome–wide binding of transcription factor ZEB1 in triple‐negative breast cancer cells. Genome–wide binding of transcription factor ZEB1 in triple‐negative breast cancer cells
    Article Snippet: Paragraph title: DNA library preparation and sequencing protocols ... Input and ChIP DNA was sheared with a Covaris S2 sonicator (Covaris, Inc., Woburn, MA).

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Size and quantity of DNA fragments were determined on 2200 TapeStation Instrument (Agilent Technologies, USA). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. Library preparation was performed by SeqCap EZ System (Roche NimbleGen, USA) with probes for PAX9 , MSX1 , AXIN2 , EDA , EDAR , and WNT10A genes according to manufacturer’s recommendations.

    Article Title: Mapping of histone-binding sites in histone replacement-completed spermatozoa
    Article Snippet: Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). .. The enriched DNA was subjected to PBAT, followed by 5 cycles of PCR enrichment with Kapa Library Amplification Kit (Illumina).

    Article Title: Antitumor activity of sorafenib plus CDK4/6 inhibitor in pancreatic patient derived cell with KRAS mutation
    Article Snippet: Formalin-fixed paraffin embedded (FFPE) samples containing > 40% tumor cellularity were dissected under microscopy from 4-μm-thick unstained sections (10 to 20 slides) or from fresh frozen tissues by comparison with a hematoxylin and eosin-stained slide. .. Briefly, DNA was extracted using standard procedures (Qiagen, Hilden, Germany) and extracted genomic DNA was sheared to 150-200 bp using Covaris S220 (Covaris, Woburn, MA, USA), and targeted genes were captured using a custom panel capture library (Agilent Technologies, Santa Clara, CA, USA) covering 2.5 Mb of exonic regions for the Illumina Paired-End Sequencing Library kit. .. We performed DNA sequencing of 100 or 101-bp paired-end reads using the Illumina HiSeq 2,500 sequencer (Illumina, San Diego, CA, USA).

    Article Title: Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
    Article Snippet: Reads collected during the mux phase of sequencing were not included. .. For Illumina sequencing, ∼600-bp fragments were generated from 500 ng of DNA using a Covaris S220 sonicator. .. Fragments of 500–700 bp were selected using a Pippin and libraries were prepared using a KAPA High Throughput Library Preparation kit and Bioo Scientific NEXTflex DNA Barcodes.

    Sonication:

    Article Title: NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus
    Article Snippet: ChIP-PCR was performed as described previously ( ). .. Lysates from 2 × 150 mm dishes were sonicated in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, ph 8) using the Covaris S220 (35 min, 147 Watts, 200 cycle/burst, duty factor of 5) and tubes containing an AFA fiber (Covaris, Woburn, MA). .. NRF2 was immunoprecipitated from the lysate using rabbit anti-NRF2 antibodies (Diagenode, Denville, NJ, C15410242-100; Santa Cruz, SC-722).

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: ChIP assays for GFI1B, RUNX1, H3K27ac, LSD1 and CoREST were performed as described previously [ ]. .. Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: An aliquot (200 ng) of viral DNA was sheared by sonication and used as input for the library preparation protocol as described in the manufacturer's instructions. .. The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Article Title: “Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
    Article Snippet: One library (SSMethylSeq_A_opt) made using 3 µg of DNA according to the company’s specifications using manual version B, 2013, (SureSelectXT cat # 5190-4836, Agilent Technologies, Santa Clara CA). .. DNA (3 µg) was sonicated using a Covaris S220 sonicator (Covaris, Woburn, MA) to obtain products of 150–200 bp. .. DNA was then end-repaired, A-tailed and ligated with methylated adapters to create a pre-capture DNA library.

    Article Title: DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer
    Article Snippet: ChIP analysis was performed using Magna ChIP A/G chromatin immunoprecipitation kit (Merck Millipore, MA, USA) as per manufacturer’s protocol on cells isolated from NT and TT by ED. .. Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam). .. Isotype-matched control antibodies were used as negative controls.

    RNA Sequencing Assay:

    Article Title: TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency
    Article Snippet: Paragraph title: RNA-Seq ... Amplified cDNA was then sheared to ∼200 bp length by a Covaris S220 Focused ultrasonicator.

    Methylation:

    Article Title: Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium
    Article Snippet: Briefly, sample DNA spiked with λ phage genome DNA was fragmented into 200–300 bp with ultra-sonication (Covaris S220 System, Thermo Fisher Scientific, United States). .. Barcodes were ligated to the DNA fragments, and then bisulfite converted with EZ DNA Methylation Gold Kit (Zymo Research, United States).

    Isolation:

    Article Title: The impact of endogenous content, replicates and pooling on genome capture from faecal samples, et al. The impact of endogenous content, replicates and pooling on genome capture from faecal samples
    Article Snippet: 2.3 Compared to what would be expected from DNA isolated from a fresh tissue source, all samples presented degradation. .. Genomic DNA was fragmented by shearing using a Covaris S2 focused ultrasonicator with the following settings for 200‐bp fragments: intensity 5, duty cycle 10%, cycles per burst 200, treatment time 120 s, temperature 7°C and water level 12.

    Article Title: DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer
    Article Snippet: ChIP analysis was performed using Magna ChIP A/G chromatin immunoprecipitation kit (Merck Millipore, MA, USA) as per manufacturer’s protocol on cells isolated from NT and TT by ED. .. Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam).

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: DNA was extracted from 200 μL whole blood by using automatic instrument ZEPHYRUS Magneto with modified protocol as specified for BodyFluid DNA/RNA isolation kit (Elisabeth Pharmacon, Czech Republic). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL).

    Labeling:

    Article Title: Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
    Article Snippet: Briefly, 1 μg of genomic DNA from each individual was digested with the restriction enzyme Sbf I-HF (New England Biolabs), and then ligated to a P1 adapter labeled with a unique barcode. .. Each pool was then sheared to a 350 pb average size using a Covaris S220 sonicator (KBiosciences), and size-selected on agarose gel to keep DNA fragments within the size range 300–700 pb.

    Purification:

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: DNA bands were excised and purified using a QIAquick gel extraction kit (Qiagen). .. The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Article Title: “Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
    Article Snippet: DNA (3 µg) was sonicated using a Covaris S220 sonicator (Covaris, Woburn, MA) to obtain products of 150–200 bp. .. DNA was then end-repaired, A-tailed and ligated with methylated adapters to create a pre-capture DNA library.

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: For additional purification after extraction, gDNA was treated with the Genomic DNA Clean & Concentrator Kit (Zymo Research, Irvine, CA). .. The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range.

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting. .. 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting.

    Polymerase Chain Reaction:

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

    Article Title: “Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
    Article Snippet: DNA (3 µg) was sonicated using a Covaris S220 sonicator (Covaris, Woburn, MA) to obtain products of 150–200 bp. .. DNA (3 µg) was sonicated using a Covaris S220 sonicator (Covaris, Woburn, MA) to obtain products of 150–200 bp.

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range. .. Bisulphite conversion was carried out with the EpiTect Kit (QIAGEN), performing two consecutive rounds of conversion for a total of 10 h of incubation.

    Article Title: Parallel (Randomized) Phase II Evaluation of Tivantinib (ARQ197) and Tivantinib in Combination with Erlotinib in Papillary Renal Cell Carcinoma: SWOG S1107
    Article Snippet: 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting. .. 250 ng of QC passed FFPE genomic DNA was fragmented by using Covaris S220 (Covaris, Woburn, MA) with the 200bp peak setting.

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Size and quantity of DNA fragments were determined on 2200 TapeStation Instrument (Agilent Technologies, USA). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. Library preparation was performed by SeqCap EZ System (Roche NimbleGen, USA) with probes for PAX9 , MSX1 , AXIN2 , EDA , EDAR , and WNT10A genes according to manufacturer’s recommendations.

    Article Title: Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
    Article Snippet: Each pool was then sheared to a 350 pb average size using a Covaris S220 sonicator (KBiosciences), and size-selected on agarose gel to keep DNA fragments within the size range 300–700 pb. .. Each library was then submitted to end-repair, A-tailing and ligation to P2 adapter before PCR amplification for 18 cycles.

    Microscopy:

    Article Title: Antitumor activity of sorafenib plus CDK4/6 inhibitor in pancreatic patient derived cell with KRAS mutation
    Article Snippet: Formalin-fixed paraffin embedded (FFPE) samples containing > 40% tumor cellularity were dissected under microscopy from 4-μm-thick unstained sections (10 to 20 slides) or from fresh frozen tissues by comparison with a hematoxylin and eosin-stained slide. .. Briefly, DNA was extracted using standard procedures (Qiagen, Hilden, Germany) and extracted genomic DNA was sheared to 150-200 bp using Covaris S220 (Covaris, Woburn, MA, USA), and targeted genes were captured using a custom panel capture library (Agilent Technologies, Santa Clara, CA, USA) covering 2.5 Mb of exonic regions for the Illumina Paired-End Sequencing Library kit.

    Gel Extraction:

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: DNA bands were excised and purified using a QIAquick gel extraction kit (Qiagen). .. The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Chromatin Immunoprecipitation:

    Article Title: NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP)-PCR assays ... Lysates from 2 × 150 mm dishes were sonicated in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, ph 8) using the Covaris S220 (35 min, 147 Watts, 200 cycle/burst, duty factor of 5) and tubes containing an AFA fiber (Covaris, Woburn, MA).

    Article Title: Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways
    Article Snippet: Cells (2 × 106 ) were cross-linked in 1% formaldehyde for 10 min at room temperature, harvested by scraping, centrifuged, and resuspended in SDS lysis buffer. .. After 10 min on ice, lysed cells were diluted 2-fold in ChIP dilution buffer and disrupted with the S220 Focused Ultrasonicator (Covaris) to yield genomic DNA fragments of 300 bp. .. Immunocomplexes were pulled down with 20 μL of magnetic protein A beads as described in the Magna ChIP protocol.

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) ... Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA).

    Article Title: Genome–wide binding of transcription factor ZEB1 in triple‐negative breast cancer cells. Genome–wide binding of transcription factor ZEB1 in triple‐negative breast cancer cells
    Article Snippet: ChIP DNA quality was analyzed with a Bioanalyzer. .. Input and ChIP DNA was sheared with a Covaris S2 sonicator (Covaris, Inc., Woburn, MA). .. DNA libraries were constructed using the AB Library Builder System (Life Technologies, Carlsbad, CA), followed by amplification and wildfire conversion according to the manufacturer's protocols.

    Article Title: DNA methylation and repressive histones in the promoters of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, PD-L1, and galectin-9 genes in human colorectal cancer
    Article Snippet: ChIP analysis was performed using Magna ChIP A/G chromatin immunoprecipitation kit (Merck Millipore, MA, USA) as per manufacturer’s protocol on cells isolated from NT and TT by ED. .. Briefly, nuclear lysate was prepared as per manufacturer’s protocol and sonicated using Covaris S2 system (Covaris, MA, USA) to make small DNA fragments (100–200 base pairs) and then incubated with ChIP grade anti-Histone H3 rabbit mAb (Active Motif, CA, USA), anti-Histone H3 (tri methyl K9) rabbit mAb (Abcam Cambridge, UK), and anti-Histone H3 (tri methyl K27) rabbit mAb (Abcam). .. Isotype-matched control antibodies were used as negative controls.

    Software:

    Article Title: Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing
    Article Snippet: Basecalling was completed using ONT Albacore Sequencing Pipeline Software version 2.0.2. .. For Illumina sequencing, ∼600-bp fragments were generated from 500 ng of DNA using a Covaris S220 sonicator.

    Selection:

    Article Title: Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
    Article Snippet: Each pool was then sheared to a 350 pb average size using a Covaris S220 sonicator (KBiosciences), and size-selected on agarose gel to keep DNA fragments within the size range 300–700 pb. .. Each library was then submitted to end-repair, A-tailing and ligation to P2 adapter before PCR amplification for 18 cycles.

    Agarose Gel Electrophoresis:

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: A MinElute reaction clean‐up kit (Qiagen) was used to purify the DNA between steps, and DNA fragments of approximately 500 bp were selected by agarose gel electrophoresis. .. The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Article Title: Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata
    Article Snippet: Seven pools of 32 individuals were made by mixing individual DNA in equimolar proportions. .. Each pool was then sheared to a 350 pb average size using a Covaris S220 sonicator (KBiosciences), and size-selected on agarose gel to keep DNA fragments within the size range 300–700 pb. .. Each library was then submitted to end-repair, A-tailing and ligation to P2 adapter before PCR amplification for 18 cycles.

    Ethanol Precipitation:

    Article Title: Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways
    Article Snippet: After 10 min on ice, lysed cells were diluted 2-fold in ChIP dilution buffer and disrupted with the S220 Focused Ultrasonicator (Covaris) to yield genomic DNA fragments of 300 bp. .. The DNA was recovered by 2 hr digestion with proteinase K at 65°C, followed by a 10-min incubation at 95°C.

    Next-Generation Sequencing:

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. The library was sequenced on a MiSeq V2 2x151 bp sequencing run according to manufacturer recommendations for 14 pM libraries.

    DNA Methylation Assay:

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: Global DNA methylation levels were estimated by performing sodium bisulphite treatment, based on the chemical conversion of unmethylated cytosines, followed by high-throughput sequencing (BS-seq). .. The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range.

    Concentration Assay:

    Article Title: Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks, et al. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks
    Article Snippet: The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer. .. The Genome Analysis Centre (now the Earlham Institute; UK) prepared viral DNA libraries using a Covaris S2 sonicator and an Illumina TruSeq DNA library preparation kit as described by the manufacturer.

    Article Title: Next generation sequencing reveals a novel nonsense mutation in MSX1 gene related to oligodontia
    Article Snippet: Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL). .. Paired end sequencing libraries were constructed from 150 ng of fragmented DNA in 50 μL PCR water using the Covaris S220 Sonicator (Covaris, USA) to a size 200 bp (treatment time 180 s, volume 130 μL).

    Article Title: Mapping of histone-binding sites in histone replacement-completed spermatozoa
    Article Snippet: Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). .. Single-read sequencing (100 cycles) was performed on Illumina HiSeq 2500 using HiSeq SR Rapid Cluster Kit v2 (Illumina) and HiSeq Rapid SBS Kit v2 (Illumina).

    High Throughput Screening Assay:

    Article Title: Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
    Article Snippet: Global DNA methylation levels were estimated by performing sodium bisulphite treatment, based on the chemical conversion of unmethylated cytosines, followed by high-throughput sequencing (BS-seq). .. The concentrations were quantified using a Qubit 2.0 fluorometer (Life Technology, Carlsbad, CA) and total gDNA was fragmented with a Covaris S-2 ultrasonicator to obtain fragments spanning from 150 to 300 bp size range.

    Lysis:

    Article Title: NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus
    Article Snippet: ChIP-PCR was performed as described previously ( ). .. Lysates from 2 × 150 mm dishes were sonicated in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, ph 8) using the Covaris S220 (35 min, 147 Watts, 200 cycle/burst, duty factor of 5) and tubes containing an AFA fiber (Covaris, Woburn, MA). .. NRF2 was immunoprecipitated from the lysate using rabbit anti-NRF2 antibodies (Diagenode, Denville, NJ, C15410242-100; Santa Cruz, SC-722).

    Article Title: Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage-and Histone Methylation-Dependent Pathways
    Article Snippet: Cells (2 × 106 ) were cross-linked in 1% formaldehyde for 10 min at room temperature, harvested by scraping, centrifuged, and resuspended in SDS lysis buffer. .. After 10 min on ice, lysed cells were diluted 2-fold in ChIP dilution buffer and disrupted with the S220 Focused Ultrasonicator (Covaris) to yield genomic DNA fragments of 300 bp.

    Article Title: Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells
    Article Snippet: ChIP assays for GFI1B, RUNX1, H3K27ac, LSD1 and CoREST were performed as described previously [ ]. .. Briefly, after crosslinking with 0.5% or 1% paraformaldehyde for 10 min and quenching with 100 mM glycine for 10 min, cells were lysed and incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100) on ice for 10 min. After two washes, the pellets were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0) and sonicated using S220 ultrasonicators (Covaris, Woburn, MA, USA). .. The sonicated samples were incubated overnight at 4° C with 2 or 4 μg of an indicated antibody and precipitated with 20 μL of Dynabeads Protein A or protein G. After extensive wash, the precipitated magnetic beads were treated with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% SDS).

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    S2 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Covaris s2 ultrasonicator
    S2 Ultrasonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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