acoustic shearing instrument  (Covaris)


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    Structured Review

    Covaris acoustic shearing instrument
    Acoustic Shearing Instrument, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/acoustic shearing instrument/product/Covaris
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    acoustic shearing instrument - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Sequencing was accomplished using M13F and M13R primers, as well as φ52237-sequence guided primer walking of fragment clones and PCR amplicons using an ABI 3130xL Genetic Analyzer (Applied Biosystems, Carlsbad, CA) at the Colorado State University Proteomics and Metabolomics Facility. φX216 Illumina sequencing libraries were prepared using the TruSeq DNA Sample Preparation Kit v2, (Illumina, San Diego, CA), following the manufacturer's instructions. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Amplification:

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: The sequence of AnchorX is 5′-GTCGACGGCGCGCCGGATCCATA-3′ and the sequence of AnchorY is 5′-ATATCTCGAGGGCGCGCCGGATCC-3′. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. The fragmented cDNAs were end-repaired, a single A base was added to the 3′ end, and then ligated with illumina PE adaptors.

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. After adaptor ligation using standard Illumina adaptor ligation protocol, ligated fragments were separated by 2% agarose gel and DNA fragments of around 400 bp were selected and purified using Qiagen Gel extraction kit.

    Article Title: Non-random DNA fragmentation in next-generation sequencing
    Article Snippet: Heavy amplification in single-cell sequencing induces bias, which can lead to uneven coverage . .. Hence we report and analyze bias produced by three DNA shearing methods, sonication, nebulization and Covaris, and demonstrate that the instances of bias in different fragmentation methods highly correlate with each other and are common for all of the hydrodynamic DNA shearing methods.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: Amplified cDNA (~5ng cDNA) was used to construct Illumina sequencing libraries using either Illumina’s “Ultra Low Input mRNA-Seq Guide” (the “PE” protocol) or a modification of Epicentre’s Nextera DNA sample preparation protocol (the “Tn5” protocol). .. With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument. .. The resulting fragments were end-repaired, followed by the addition of a single A base, ligation to Illumina PE adaptors, and then amplification with 12–18 cycles of PCR (depending on starting amounts of RNA, see for detailed instructions of all libraries generated).

    Article Title: A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples
    Article Snippet: Paragraph title: Illumina Amplicon Library Preparation ... Fifty nanograms were sheared to 400 bp using Covaris™ DNA Shearing (Woburn, MA, USA) and concentrated using 1∶1× volume Ampure XP Beads.

    High Throughput Screening Assay:

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: Paragraph title: High-throughput DNA sequencing analysis ... Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Article Title: Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania
    Article Snippet: Paragraph title: High-Throughput Small RNA, SL RNA, dsRNA, and DNA Sequencing ... Chromatin immunoprecipitation sequencing (ChIP-seq) libraries were prepared with the Illumina sample preparation kit and modified in the use of Covaris DNA Shearing (Covaris, MA, USA).

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation. .. Ligation products were purified on an agarose gel and the DNA fragments enriched via PCR.

    Construct:

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: The sequence of AnchorX is 5′-GTCGACGGCGCGCCGGATCCATA-3′ and the sequence of AnchorY is 5′-ATATCTCGAGGGCGCGCCGGATCC-3′. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. The fragmented cDNAs were end-repaired, a single A base was added to the 3′ end, and then ligated with illumina PE adaptors.

    Article Title: Mutation assay using single-molecule real-time (SMRTTM) sequencing technology
    Article Snippet: The rest of the mixture was poured onto a minimum agar plate in 2 mL of 0.6 % soft agar and incubated for two days at 37 °C, following which the revertant colonies were counted. .. The genomic DNA samples (5 μg each) were sheared to 50-1000 bp (average 280 bp) fragments by using a Covaris Shearing Device, and used to construct a PacBio DNA library using a SMRTbell Template Prep Kit 1.0 following the manufacturer’s guidelines ( http://www.pacb.com/samplenet/PC_250bp_Amplicon_Library_Preparation_and_Sequencing.pdf ). .. Each sample was sequenced on the PacBio RS platform on a single SMRT Cell with C2-P4 chemistry.

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Genomic DNA libraries were constructed according to the standard Illumina protocol. .. Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: Amplified cDNA (~5ng cDNA) was used to construct Illumina sequencing libraries using either Illumina’s “Ultra Low Input mRNA-Seq Guide” (the “PE” protocol) or a modification of Epicentre’s Nextera DNA sample preparation protocol (the “Tn5” protocol). .. With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Random and φ52237-sequence guided φX216 genome fragment clones were constructed by restriction digest of purified φX216 genomic DNA with Eco RI, Eco RI + Hin dIII or Age I and ligation with Eco RI, Eco RI + Hin dIII or Sma I digested pUC19 DNA [ ], respectively, followed by transformation of E . coli DH5α or GBE180 [ ] using standard transformation protocols [ ] and recovery of white colonies on LB plates containing 100 μg/mL ampicillin and 50 μg/mL 5’-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal). φ52237-sequence-guided PCR amplicons were designed to close gaps and confirm fragment clone borders. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Incubation:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154). .. Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154).

    Stripping Membranes:

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument. .. With the Tn5 protocol, the amplified cDNA was “tagmentated” at 55°C for 5 min in 20μl reaction with 0.25μl of transposase and 4μl of 5x HMW Nextera reaction buffer.

    Modification:

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: All cell culture and nucleic acid extractions were performed at ATCC following their standard protocol. .. 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec. .. The resulting libraries were sequenced on a HiSeq2500 in rapid mode with read length 101 × 101.

    Article Title: Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania
    Article Snippet: Genomic DNA was sheared into fragments of 100–1,200 bp (Nebulizer, Illumina) and was made into a DNA sequencing (DNA-seq) library by using the Genomic DNA Sample Preparation Kit (Illumina, San Diego, USA). .. Chromatin immunoprecipitation sequencing (ChIP-seq) libraries were prepared with the Illumina sample preparation kit and modified in the use of Covaris DNA Shearing (Covaris, MA, USA). .. Small RNA was purified by using 15% polyacrylamide/urea/TBE gel electrophoresis and ligated to 5′ and 3′ small RNA adapters, reverse transcribed, and prepared for sequencing.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: Amplified cDNA (~5ng cDNA) was used to construct Illumina sequencing libraries using either Illumina’s “Ultra Low Input mRNA-Seq Guide” (the “PE” protocol) or a modification of Epicentre’s Nextera DNA sample preparation protocol (the “Tn5” protocol). .. With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument.

    Western Blot:

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: Genomic DNA was extracted from the liver using a Wako DNA Extractor WB Kit (Wako, Osaka, Japan). .. Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Transformation Assay:

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Random and φ52237-sequence guided φX216 genome fragment clones were constructed by restriction digest of purified φX216 genomic DNA with Eco RI, Eco RI + Hin dIII or Age I and ligation with Eco RI, Eco RI + Hin dIII or Sma I digested pUC19 DNA [ ], respectively, followed by transformation of E . coli DH5α or GBE180 [ ] using standard transformation protocols [ ] and recovery of white colonies on LB plates containing 100 μg/mL ampicillin and 50 μg/mL 5’-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal). φ52237-sequence-guided PCR amplicons were designed to close gaps and confirm fragment clone borders. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Flow Cytometry:

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: All cell culture and nucleic acid extractions were performed at ATCC following their standard protocol. .. 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec. .. The resulting libraries were sequenced on a HiSeq2500 in rapid mode with read length 101 × 101.

    Gas Chromatography:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: To minimize potential biases between individual donors, ChIP was performed on two independent biological replicates each consisting of 3–5 GC B cell isolations. .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Ligation:

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Sequencing was accomplished using M13F and M13R primers, as well as φ52237-sequence guided primer walking of fragment clones and PCR amplicons using an ABI 3130xL Genetic Analyzer (Applied Biosystems, Carlsbad, CA) at the Colorado State University Proteomics and Metabolomics Facility. φX216 Illumina sequencing libraries were prepared using the TruSeq DNA Sample Preparation Kit v2, (Illumina, San Diego, CA), following the manufacturer's instructions. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation. .. Ligation products were purified on an agarose gel and the DNA fragments enriched via PCR.

    Methylation:

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: Paragraph title: 2.10 Methylated DNA capture by affinity purification (MeCAP) and quantitation ... Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core.

    Generated:

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    DNA Sequencing:

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: Paragraph title: High-throughput DNA sequencing analysis ... Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Article Title: Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania
    Article Snippet: Paragraph title: High-Throughput Small RNA, SL RNA, dsRNA, and DNA Sequencing ... Chromatin immunoprecipitation sequencing (ChIP-seq) libraries were prepared with the Illumina sample preparation kit and modified in the use of Covaris DNA Shearing (Covaris, MA, USA).

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: Paragraph title: DNA sequencing and mutation determination ... Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions.

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: miRNA targets were identified using Target scan ( ) and the top 100 with highest scores for probability of conserved targeting and context score were subjected to further functional analysis using DAVID ( ) and ConceptGen programs ( ). .. Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core. .. Approximately 400 ng of sonicated DNA was subjected to MeCAP using the Active Motif MethylCollector™ Ultra Kit according to the manufacturer’s instructions.

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154). .. Complexes were isolated using 50 μL of Dynabeads (Invitrogen, 10004D) previously blocked with 1 mg/mL BSA.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: Paragraph title: Whole-genome DNA sequencing ... Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell.

    Polymerase Chain Reaction:

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols.

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: All cell culture and nucleic acid extractions were performed at ATCC following their standard protocol. .. 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec. .. The resulting libraries were sequenced on a HiSeq2500 in rapid mode with read length 101 × 101.

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. After adaptor ligation using standard Illumina adaptor ligation protocol, ligated fragments were separated by 2% agarose gel and DNA fragments of around 400 bp were selected and purified using Qiagen Gel extraction kit.

    Article Title: Enhanced whole exome sequencing by higher DNA insert lengths
    Article Snippet: For exploring the effect of different genomic DNA insert lengths on the uniformity of coverage in whole exome sequencing (WES), we varied the DNA shearing by acoustic fragmentation (Covaris). .. Exome enrichment was conducted with Agilent SureSelectXT All Exon v5+UTR/v5 and sequencing produced 18–54 million reads per sample (see Table ).

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core. .. Approximately 400 ng of sonicated DNA was subjected to MeCAP using the Active Motif MethylCollector™ Ultra Kit according to the manufacturer’s instructions.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument. .. 35μl of PB was added to the tagmentation reaction mix to strip the transposase off the DNA, and the tagmentated DNA was purified with 88μl of SPRI XP beads (sample to beads ratio of 1:1.6).

    Article Title: A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples
    Article Snippet: Fifty nanograms were sheared to 400 bp using Covaris™ DNA Shearing (Woburn, MA, USA) and concentrated using 1∶1× volume Ampure XP Beads. .. Fifty nanograms were sheared to 400 bp using Covaris™ DNA Shearing (Woburn, MA, USA) and concentrated using 1∶1× volume Ampure XP Beads.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Sequencing was accomplished using M13F and M13R primers, as well as φ52237-sequence guided primer walking of fragment clones and PCR amplicons using an ABI 3130xL Genetic Analyzer (Applied Biosystems, Carlsbad, CA) at the Colorado State University Proteomics and Metabolomics Facility. φX216 Illumina sequencing libraries were prepared using the TruSeq DNA Sample Preparation Kit v2, (Illumina, San Diego, CA), following the manufacturer's instructions. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Sonication:

    Article Title: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism
    Article Snippet: Genomic DNA from TCBQ or Control DMSO treated MRC-5 cells was purified by using Wizard genomic DNA purification kit (Promega) according to the manufacturer’s instructions. .. Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions. .. Sonicated DNA was then purified with phenol/chloroform/isoamyl alcohol (25:24:1) precipitation.

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: The sequence of AnchorX is 5′-GTCGACGGCGCGCCGGATCCATA-3′ and the sequence of AnchorY is 5′-ATATCTCGAGGGCGCGCCGGATCC-3′. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. The fragmented cDNAs were end-repaired, a single A base was added to the 3′ end, and then ligated with illumina PE adaptors.

    Article Title: Non-random DNA fragmentation in next-generation sequencing
    Article Snippet: For the first time we venture to show that the bias in NGS reads strongly correlates with the bias produced by sonication of pure restriction DNA fragments, which was shown to be sequence-specific . .. Hence we report and analyze bias produced by three DNA shearing methods, sonication, nebulization and Covaris, and demonstrate that the instances of bias in different fragmentation methods highly correlate with each other and are common for all of the hydrodynamic DNA shearing methods. .. In 2006 we discovered that double-strand breaks resulting from sonication at 22 and 44 kHz of double-stranded DNA fragments with the known nucleotide sequences occurring preferentially in 5′-CpG-3′ dinucleotides .

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: miRNA targets were identified using Target scan ( ) and the top 100 with highest scores for probability of conserved targeting and context score were subjected to further functional analysis using DAVID ( ) and ConceptGen programs ( ). .. Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core. .. Approximately 400 ng of sonicated DNA was subjected to MeCAP using the Active Motif MethylCollector™ Ultra Kit according to the manufacturer’s instructions.

    Affinity Purification:

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: Paragraph title: 2.10 Methylated DNA capture by affinity purification (MeCAP) and quantitation ... Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core.

    Binding Assay:

    Article Title: Epstein-Barr Virus-Encoded Latent Membrane Protein 1 Upregulates Glucose Transporter 1 Transcription via the mTORC1/NF-κB Signaling Pathways
    Article Snippet: Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations. .. The immunoprecipitated DNA was purified and analyzed by qRT-PCR.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    ChIP-sequencing:

    Article Title: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism
    Article Snippet: Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions. .. Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions.

    Article Title: Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania
    Article Snippet: Genomic DNA was sheared into fragments of 100–1,200 bp (Nebulizer, Illumina) and was made into a DNA sequencing (DNA-seq) library by using the Genomic DNA Sample Preparation Kit (Illumina, San Diego, USA). .. Chromatin immunoprecipitation sequencing (ChIP-seq) libraries were prepared with the Illumina sample preparation kit and modified in the use of Covaris DNA Shearing (Covaris, MA, USA). .. Small RNA was purified by using 15% polyacrylamide/urea/TBE gel electrophoresis and ligated to 5′ and 3′ small RNA adapters, reverse transcribed, and prepared for sequencing.

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: Paragraph title: ChIP-seq ... Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154).

    Sensitive Assay:

    Article Title: A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples
    Article Snippet: Amplicons were quantified and quality assessed using Quant-IT Qubit dsDNA High Sensitivity Assay (Invitrogen) and 1% E-gel (Invitrogen) respectively. .. Fifty nanograms were sheared to 400 bp using Covaris™ DNA Shearing (Woburn, MA, USA) and concentrated using 1∶1× volume Ampure XP Beads.

    Magnetic Beads:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Sheard chromatin was incubated overnight with 4µg of anti-CREBBP (A-22 rabbit polyclonal, Santa Cruz Biotechnology), anti-H3K27Ac (Active Motif), anti-H3K4me3 (Abcam), or 2µg of anti-H3K4me1 (Abcam).

    Mutagenesis:

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: Paragraph title: DNA sequencing and mutation determination ... Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions.

    Isolation:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: To minimize potential biases between individual donors, ChIP was performed on two independent biological replicates each consisting of 3–5 GC B cell isolations. .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200–500bp.

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: Demultiplexing and FastQ file generation were done using bcl2fastq version 2.17.1.14. .. Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154). .. Chromatin was sheared in 1-mL millitubes (Covaris, 520135) using a Covaris S200 (5% duty cycle, intensity of 4, 200 cycles per burst, for 8 min) to obtain chromatin fragments 100–700 base pairs in length.

    Size-exclusion Chromatography:

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: All cell culture and nucleic acid extractions were performed at ATCC following their standard protocol. .. 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec. .. The resulting libraries were sequenced on a HiSeq2500 in rapid mode with read length 101 × 101.

    Purification:

    Article Title: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism
    Article Snippet: Genomic DNA from TCBQ or Control DMSO treated MRC-5 cells was purified by using Wizard genomic DNA purification kit (Promega) according to the manufacturer’s instructions. .. Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions.

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Article Title: Epstein-Barr Virus-Encoded Latent Membrane Protein 1 Upregulates Glucose Transporter 1 Transcription via the mTORC1/NF-κB Signaling Pathways
    Article Snippet: Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations. .. Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations.

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Purified GC B cells were cross-linked with 1% formaldehyde for 10 min at RT, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen. .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: The genomes of the ancestor R0 and the evolved cell population R7 were resequenced using a next-generation sequencer (Junior, Roche). .. Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions. .. Whole-genome shotgun sequencing by the 454 GS Junior platform (Roche) was performed according to the manufacturer’s instructions.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument. .. With the Tn5 protocol, the amplified cDNA was “tagmentated” at 55°C for 5 min in 20μl reaction with 0.25μl of transposase and 4μl of 5x HMW Nextera reaction buffer.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Random and φ52237-sequence guided φX216 genome fragment clones were constructed by restriction digest of purified φX216 genomic DNA with Eco RI, Eco RI + Hin dIII or Age I and ligation with Eco RI, Eco RI + Hin dIII or Sma I digested pUC19 DNA [ ], respectively, followed by transformation of E . coli DH5α or GBE180 [ ] using standard transformation protocols [ ] and recovery of white colonies on LB plates containing 100 μg/mL ampicillin and 50 μg/mL 5’-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal). φ52237-sequence-guided PCR amplicons were designed to close gaps and confirm fragment clone borders. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Sequencing:

    Article Title: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism
    Article Snippet: Paragraph title: 5hmC pull-down, deep sequencing and data analysis ... Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions.

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: The sequence of AnchorX is 5′-GTCGACGGCGCGCCGGATCCATA-3′ and the sequence of AnchorY is 5′-ATATCTCGAGGGCGCGCCGGATCC-3′. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. The fragmented cDNAs were end-repaired, a single A base was added to the 3′ end, and then ligated with illumina PE adaptors.

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: One ENU-treated family and one control family were employed in the high-throughput sequencing analyses (Fig. ), where each family comprised six mice, i.e., parents (male and female) and offspring (two males and two females). .. Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: Paragraph title: Library preparation and sequencing ... 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec.

    Article Title: Mutation assay using single-molecule real-time (SMRTTM) sequencing technology
    Article Snippet: Paragraph title: Preparation of SMRTbellTM templates and sequencing ... The genomic DNA samples (5 μg each) were sheared to 50-1000 bp (average 280 bp) fragments by using a Covaris Shearing Device, and used to construct a PacBio DNA library using a SMRTbell Template Prep Kit 1.0 following the manufacturer’s guidelines ( http://www.pacb.com/samplenet/PC_250bp_Amplicon_Library_Preparation_and_Sequencing.pdf ).

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Paragraph title: DNA preparation and sequencing ... Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation and sequencing (ChIP) ... Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Article Title: Non-random DNA fragmentation in next-generation sequencing
    Article Snippet: For the first time we venture to show that the bias in NGS reads strongly correlates with the bias produced by sonication of pure restriction DNA fragments, which was shown to be sequence-specific . .. Hence we report and analyze bias produced by three DNA shearing methods, sonication, nebulization and Covaris, and demonstrate that the instances of bias in different fragmentation methods highly correlate with each other and are common for all of the hydrodynamic DNA shearing methods.

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions. .. Whole-genome shotgun sequencing by the 454 GS Junior platform (Roche) was performed according to the manufacturer’s instructions.

    Article Title: Enhanced whole exome sequencing by higher DNA insert lengths
    Article Snippet: Altogether, we would like to provide a short technical note on the effect of DNA insert length on the evenness of coverage for paired-end sequenced reads. .. For exploring the effect of different genomic DNA insert lengths on the uniformity of coverage in whole exome sequencing (WES), we varied the DNA shearing by acoustic fragmentation (Covaris). .. Two DNA inserts groups of six samples each were yielded with approximately 130 and 170 bp length (Fig. + ).

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: Paragraph title: Construction and sequencing of Smart-Seq sequencing libraries ... With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument.

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Paragraph title: Sequencing and annotation ... Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Article Title: A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
    Article Snippet: Peter Vos for assistance in the marker-trait analysis. .. We like to thank Dr. Alexander Hoischen for access to the Covaris DNA shearing apparatus at Radboud University, and Pieter van der Vlies of University Medical Centre Groningen for sequencing the DNA libraries. ..

    Quantitative RT-PCR:

    Article Title: Epstein-Barr Virus-Encoded Latent Membrane Protein 1 Upregulates Glucose Transporter 1 Transcription via the mTORC1/NF-κB Signaling Pathways
    Article Snippet: Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations. .. Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations.

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core. .. DNA fragments from the methylation-enriched fraction were purified using QIAquick PCR Purification Kits (Qiagen).

    Gel Extraction:

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Concentration Assay:

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. Size selected DNA fragments were then amplified using standard Illumina PCR amplification protocol with 12 PCR cycles.

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Purified GC B cells were cross-linked with 1% formaldehyde for 10 min at RT, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen. .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Agarose Gel Electrophoresis:

    Article Title: Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
    Article Snippet: Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus. .. Briefly, DNA (5µg) was fragmented using the Covaris shearing apparatus.

    Shotgun Sequencing:

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: Whole-genome shotgun sequencing of the four rice genomes was performed using the Illumina/Solexa GAII system. .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell.

    Mouse Assay:

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: Liver DNA samples from 12 mice were subjected to NGS analyses by Beckman Coulter Genomics (MA, USA). .. Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Chromatin Immunoprecipitation:

    Article Title: Epstein-Barr Virus-Encoded Latent Membrane Protein 1 Upregulates Glucose Transporter 1 Transcription via the mTORC1/NF-κB Signaling Pathways
    Article Snippet: The primer sequences used in qRT-PCR screening are as follows: 5′-GGTTGTGCCATACTCATGACC-3′ (forward) and 5′-CAGATAGGACATCCAGGGTAGC-3′ (reverse) for Glut-1, 5′-CCCTGTCTGTATCCAGCTTTG-3′ (forward) and 5′-TGTTTGCTACTAACATGGCTTTG-3′ for Glut-2, 5′-TTCTGATATTGCCGCACTAGG-3′ (forward) and 5′-AGTCTGAGGTTGGGGGAACT-3′ (reverse) for Glut-3, and 5′-TTTCTCAGTGGGACAAACCA-3′ (forward) and 5′-AAGGTGGTGGGAAACTGGAT-3′ (reverse) for Glut-4. .. Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations. .. The antibodies used were normal rabbit IgG against p65.

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation and sequencing (ChIP) ... Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris).

    Software:

    Article Title: Mutation assay using single-molecule real-time (SMRTTM) sequencing technology
    Article Snippet: The genomic DNA samples (5 μg each) were sheared to 50-1000 bp (average 280 bp) fragments by using a Covaris Shearing Device, and used to construct a PacBio DNA library using a SMRTbell Template Prep Kit 1.0 following the manufacturer’s guidelines ( http://www.pacb.com/samplenet/PC_250bp_Amplicon_Library_Preparation_and_Sequencing.pdf ). .. The genomic DNA samples (5 μg each) were sheared to 50-1000 bp (average 280 bp) fragments by using a Covaris Shearing Device, and used to construct a PacBio DNA library using a SMRTbell Template Prep Kit 1.0 following the manufacturer’s guidelines ( http://www.pacb.com/samplenet/PC_250bp_Amplicon_Library_Preparation_and_Sequencing.pdf ).

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions. .. Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions.

    Selection:

    Article Title: Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"
    Article Snippet: DNA sequencing, including construction of shotgun DNA libraries, was performed according to the methods recommended by the manufacturer (Illumina, San Diego, CA, USA). .. Briefly, whole-genome DNA shotgun paired-end sequencing libraries were generated by fragmentation of DNA into 500-bp segments using a Covaris DNA shearing machine (Covaris, CA, US), followed by ligation of paired-end adapters ligation of 53 and 68 bp for sequencing on the FlowCell, size selection of the adapter-ligated fragments within the desired size range (500-600 bp), and PCR enrichment using complete primer constructs required for binding and clustering on the FlowCell. .. Illumina GAII sequencing was performed by identifying the emission color of single-base extensions on the FlowCell.

    Sample Prep:

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: The sequence of AnchorX is 5′-GTCGACGGCGCGCCGGATCCATA-3′ and the sequence of AnchorY is 5′-ATATCTCGAGGGCGCGCCGGATCC-3′. .. Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols. .. The fragmented cDNAs were end-repaired, a single A base was added to the 3′ end, and then ligated with illumina PE adaptors.

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: All cell culture and nucleic acid extractions were performed at ATCC following their standard protocol. .. 500 ng of each DNA was prepared using the TruSeq DNA PCR-Free Sample Preparation Kit (Illumina® , cat# FC-121-3001) following the manufacturer’s protocol with modified Covaris DNA shearing settings: Duty cycle 10%, Cycles/Burst 200, Time 45 sec. .. The resulting libraries were sequenced on a HiSeq2500 in rapid mode with read length 101 × 101.

    Article Title: Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania
    Article Snippet: Genomic DNA was sheared into fragments of 100–1,200 bp (Nebulizer, Illumina) and was made into a DNA sequencing (DNA-seq) library by using the Genomic DNA Sample Preparation Kit (Illumina, San Diego, USA). .. Chromatin immunoprecipitation sequencing (ChIP-seq) libraries were prepared with the Illumina sample preparation kit and modified in the use of Covaris DNA Shearing (Covaris, MA, USA). .. Small RNA was purified by using 15% polyacrylamide/urea/TBE gel electrophoresis and ligated to 5′ and 3′ small RNA adapters, reverse transcribed, and prepared for sequencing.

    Article Title: Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells
    Article Snippet: Amplified cDNA (~5ng cDNA) was used to construct Illumina sequencing libraries using either Illumina’s “Ultra Low Input mRNA-Seq Guide” (the “PE” protocol) or a modification of Epicentre’s Nextera DNA sample preparation protocol (the “Tn5” protocol). .. With the PE protocol, the amplified cDNA was fragmented using a Covaris acoustic shearing instrument.

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Sequencing was accomplished using M13F and M13R primers, as well as φ52237-sequence guided primer walking of fragment clones and PCR amplicons using an ABI 3130xL Genetic Analyzer (Applied Biosystems, Carlsbad, CA) at the Colorado State University Proteomics and Metabolomics Facility. φX216 Illumina sequencing libraries were prepared using the TruSeq DNA Sample Preparation Kit v2, (Illumina, San Diego, CA), following the manufacturer's instructions. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Next-Generation Sequencing:

    Article Title: Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
    Article Snippet: Paragraph title: Sequencing library generation and next-generation sequencing of single cell cDNA samples ... Typically 200–300 ng amplified cDNAs were sonicated to around 200 bp long fragments using a Covaris acoustic shearing instrument and then used to construct Illumina sequencing libraries following Illumina’s TruSeq DNA sample preparation protocols.

    Article Title: Estimation of the frequency of inherited germline mutations by whole exome sequencing in ethyl nitrosourea-treated and untreated gpt delta mice
    Article Snippet: Liver DNA samples from 12 mice were subjected to NGS analyses by Beckman Coulter Genomics (MA, USA). .. Genomic DNA was fragmented using the Covaris DNA shearing system (Covaris, Inc., MA, USA).

    Article Title: Non-random DNA fragmentation in next-generation sequencing
    Article Snippet: For the first time we venture to show that the bias in NGS reads strongly correlates with the bias produced by sonication of pure restriction DNA fragments, which was shown to be sequence-specific . .. Hence we report and analyze bias produced by three DNA shearing methods, sonication, nebulization and Covaris, and demonstrate that the instances of bias in different fragmentation methods highly correlate with each other and are common for all of the hydrodynamic DNA shearing methods.

    Chromosome Walking:

    Article Title: ?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity
    Article Snippet: Sequencing was accomplished using M13F and M13R primers, as well as φ52237-sequence guided primer walking of fragment clones and PCR amplicons using an ABI 3130xL Genetic Analyzer (Applied Biosystems, Carlsbad, CA) at the Colorado State University Proteomics and Metabolomics Facility. φX216 Illumina sequencing libraries were prepared using the TruSeq DNA Sample Preparation Kit v2, (Illumina, San Diego, CA), following the manufacturer's instructions. .. Phage DNA was fragmented to a range of 300–400 bp using a Covaris acoustic shearing device, (Covaris Inc., Woburn, MA) followed by 3' adenylation and adapter ligation.

    Quantitation Assay:

    Article Title: Overexpression of X-Linked Genes in T Cells From Women With Lupus
    Article Snippet: Paragraph title: 2.10 Methylated DNA capture by affinity purification (MeCAP) and quantitation ... Genomic DNA was extracted from ~3×106 CD4+ T cells using the Qiagen DNeasy Blood & Tissue Kit, and 3–5 μg sonicated to an average length of ~500 bp using a Covaris DNA shearing system and fragment size-evaluated using an Agilent 2100 Bioanalyzer in the DNA Sequencing Core.

    Produced:

    Article Title: Non-random DNA fragmentation in next-generation sequencing
    Article Snippet: For the first time we venture to show that the bias in NGS reads strongly correlates with the bias produced by sonication of pure restriction DNA fragments, which was shown to be sequence-specific . .. Hence we report and analyze bias produced by three DNA shearing methods, sonication, nebulization and Covaris, and demonstrate that the instances of bias in different fragmentation methods highly correlate with each other and are common for all of the hydrodynamic DNA shearing methods. .. In 2006 we discovered that double-strand breaks resulting from sonication at 22 and 44 kHz of double-stranded DNA fragments with the known nucleotide sequences occurring preferentially in 5′-CpG-3′ dinucleotides .

    Article Title: Enhanced whole exome sequencing by higher DNA insert lengths
    Article Snippet: For exploring the effect of different genomic DNA insert lengths on the uniformity of coverage in whole exome sequencing (WES), we varied the DNA shearing by acoustic fragmentation (Covaris). .. For exploring the effect of different genomic DNA insert lengths on the uniformity of coverage in whole exome sequencing (WES), we varied the DNA shearing by acoustic fragmentation (Covaris).

    Immunoprecipitation:

    Article Title: Epstein-Barr Virus-Encoded Latent Membrane Protein 1 Upregulates Glucose Transporter 1 Transcription via the mTORC1/NF-κB Signaling Pathways
    Article Snippet: Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations. .. Chromatin immunoprecipitation (ChIP) was performed using a ChIP assay kit (Covaris, MA) according to the manufacturer's recommendations.

    Article Title: PDX1 dynamically regulates pancreatic ductal adenocarcinoma initiation and maintenance
    Article Snippet: Chromatin was prepared from isolated acinar cells or cell lines using the truChIP chromatin-shearing reagent kit (Covaris, 520154). .. Complexes were isolated using 50 μL of Dynabeads (Invitrogen, 10004D) previously blocked with 1 mg/mL BSA.

    DNA Purification:

    Article Title: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism
    Article Snippet: Genomic DNA from TCBQ or Control DMSO treated MRC-5 cells was purified by using Wizard genomic DNA purification kit (Promega) according to the manufacturer’s instructions. .. Genomic DNA samples were further sonicated into short fragments (about 300 bp) by using Covaris DNA shearing (Covaris S2 SonoLAB Single) with microTUBEs according to the manufacturer’s instructions.

    Article Title: Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages
    Article Snippet: The genomes of the ancestor R0 and the evolved cell population R7 were resequenced using a next-generation sequencer (Junior, Roche). .. Genomic DNA was purified with a Wizard Genomic DNA Purification kit (Promega) and fragmented using a DNA shearing system (Covaris), according to the manufacturer’s instructions. .. Whole-genome shotgun sequencing by the 454 GS Junior platform (Roche) was performed according to the manufacturer’s instructions.

    Marker:

    Article Title: A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
    Article Snippet: Peter Vos for assistance in the marker-trait analysis. .. We like to thank Dr. Alexander Hoischen for access to the Covaris DNA shearing apparatus at Radboud University, and Pieter van der Vlies of University Medical Centre Groningen for sequencing the DNA libraries.

    Lysis:

    Article Title: The Crebbp acetyltransferase is a haploinsufficient tumor suppressor in B cell lymphoma
    Article Snippet: To minimize potential biases between individual donors, ChIP was performed on two independent biological replicates each consisting of 3–5 GC B cell isolations. .. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). .. Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200–500bp.

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    Covaris acoustic shearing instrument
    Acoustic Shearing Instrument, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/acoustic shearing instrument/product/Covaris
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