dna  (Covaris)


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    Structured Review

    Covaris dna
    Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and <t>PBL</t> <t>DNA</t> samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation
    Dna, supplied by Covaris, used in various techniques. Bioz Stars score: 98/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dna - by Bioz Stars, 2019-11
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    Images

    1) Product Images from "Characterization of background noise in capture-based targeted sequencing data"

    Article Title: Characterization of background noise in capture-based targeted sequencing data

    Journal: Genome Biology

    doi: 10.1186/s13059-017-1275-2

    Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and PBL DNA samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation
    Figure Legend Snippet: Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and PBL DNA samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation

    Techniques Used: Sequencing, Standard Deviation

    Characterization of the DNA break point. a Fold changes in error rates across all substitution classes were compared between PBL and plasma DNA samples. The fold change was calculated by dividing the substitution rate at each position by the average rate of 1 − 50 bp. The distribution of fold changes in 1 − 50 bp was box-plotted. Above the box plots, the observed fold change at the first and the second bases was marked for comparison. For better discrimination between the groups, plasma data are displayed on a grey background . b The distribution of quality scores of total bases, including low quality bases, is plotted according to the position of reads. c Mononucleotide frequencies around the DNA break point. Note: except in ( b ), all analyses of background alleles were performed after filtering of bases with a quality score
    Figure Legend Snippet: Characterization of the DNA break point. a Fold changes in error rates across all substitution classes were compared between PBL and plasma DNA samples. The fold change was calculated by dividing the substitution rate at each position by the average rate of 1 − 50 bp. The distribution of fold changes in 1 − 50 bp was box-plotted. Above the box plots, the observed fold change at the first and the second bases was marked for comparison. For better discrimination between the groups, plasma data are displayed on a grey background . b The distribution of quality scores of total bases, including low quality bases, is plotted according to the position of reads. c Mononucleotide frequencies around the DNA break point. Note: except in ( b ), all analyses of background alleles were performed after filtering of bases with a quality score

    Techniques Used:

    The false positive rate. a The error rate of each background allele was calculated and their distribution was plotted, dependent on the total read counts. Data from 19 plasma DNA samples were down-sampled to a designated size of total reads in a range between 2.5 and 50 M. The x-axis denotes the frequency of background alleles, and the y-axis denotes the fraction of alleles with the designated background rate on the x-axis . b – d The fraction of background alleles present at a frequency greater than a given threshold is plotted against the depth of coverage after de-duplication ( x-axis ). b The effect of coverage depth on the false positive rate is shown in the down-sampled data set generated from 19 plasma DNA samples. c The effect of each DNA shearing condition on the false positive rate was estimated using the down-sampled data set from Fig. 3 . a–d indicate the fragmentation conditions, as described in Fig. 3 . d A comparison of plasma and fragmented PBL DNA samples
    Figure Legend Snippet: The false positive rate. a The error rate of each background allele was calculated and their distribution was plotted, dependent on the total read counts. Data from 19 plasma DNA samples were down-sampled to a designated size of total reads in a range between 2.5 and 50 M. The x-axis denotes the frequency of background alleles, and the y-axis denotes the fraction of alleles with the designated background rate on the x-axis . b – d The fraction of background alleles present at a frequency greater than a given threshold is plotted against the depth of coverage after de-duplication ( x-axis ). b The effect of coverage depth on the false positive rate is shown in the down-sampled data set generated from 19 plasma DNA samples. c The effect of each DNA shearing condition on the false positive rate was estimated using the down-sampled data set from Fig. 3 . a–d indicate the fragmentation conditions, as described in Fig. 3 . d A comparison of plasma and fragmented PBL DNA samples

    Techniques Used: Generated

    2) Product Images from "Improved Protocols for Illumina Sequencing"

    Article Title: Improved Protocols for Illumina Sequencing

    Journal:

    doi: 10.1002/0471142905.hg1802s62

    Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .
    Figure Legend Snippet: Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .

    Techniques Used: Purification, Chromatin Immunoprecipitation

    Related Articles

    Multiplexing:

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: Adapter-ligated fragments were amplified using Kapa HiFi polymerase (Kapa Biosystems cat. no. KK2602) as previously described [ ] with 200 nM final concentration of primer PE1.0 and modified multiplexing PE2.0 primers. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Amplification:

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: Adapter-ligated fragments were amplified using Kapa HiFi polymerase (Kapa Biosystems cat. no. KK2602) as previously described [ ] with 200 nM final concentration of primer PE1.0 and modified multiplexing PE2.0 primers. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: Prior to PCR amplification for sequence library construction, all bottled water and sample tubes used for shotgun library construction were processed under UV light irradiation at a clean bench and opened under the open clean system KOACH T 500-F to minimize microbial and nucleotide contamination. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
    Article Snippet: Briefly, genome-wide methylation was assessed using 500 ng of DNA fragmented by Covaris S2 (Covaris) and obtained from 6 pN0 OOSCC, 6 pN+ OOSCC, and 2 pools of leukocytes. .. Briefly, genome-wide methylation was assessed using 500 ng of DNA fragmented by Covaris S2 (Covaris) and obtained from 6 pN0 OOSCC, 6 pN+ OOSCC, and 2 pools of leukocytes.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry. .. Size selection was done on a 2% agarose gel to recover the target insert size (500 bp), followed by a gel purification step via QIAquick Gel Extraction kit (QIAGEN).

    Construct:

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: The library constructed from 1 ng of DNA was created following the manufacturers’ protocols. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Real-time Polymerase Chain Reaction:

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution. .. It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution.

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: All libraries were quantified by real-time PCR, using the SYBR Fast Illumina Library Quantification Kit (Kapa Biosystems cat. no. KK4834), prior to pooling and sequencing. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Incubation:

    Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice
    Article Snippet: In brief, 1.5-μg DNA samples were fragmented to approximately 5 kb by sonication (Covaris). .. After purification using bead columns, both oxBS and BS samples were denatured with 50 mM NaOH at 37 °C for 30 min. One microliter of oxidation solution included in the kit was added to the oxBS sample, while 1 μl of water was added to BS sample.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Can molecular profiling enhance radiotherapy? Impact of personalized targeted gold nanoparticles on radiosensitivity and imaging of adenoid cystic carcinoma
    Article Snippet: Briefly, 5μmeter sections of the formalin fixed paraffin embedded tumor resection block were marked for the cancer cell regions (identified from a consecutive cut stained with hematoxylin and eosin). .. DNA was fragmented with COVARIS® and construction of next generation sequencing library (attachment of sample-specific index and the Illumina adaptors to DNA fragments) was performed with NEBnext™ kit.

    Expressing:

    Article Title: Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels
    Article Snippet: 2.2 To determine if increased expression of ARID3a within SLE patient samples was associated with alterations in DNA methylation, genomic DNA was isolated using standard phenol/Chloroform extraction protocols from total PBMCs obtained from each of two SLE patient samples characterized as ARID3aH and two independent SLE samples characterized as ARID3a low. .. DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA).

    Genome Wide:

    Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
    Article Snippet: MethylCap-Seq analysis was performed as reported previously. .. Briefly, genome-wide methylation was assessed using 500 ng of DNA fragmented by Covaris S2 (Covaris) and obtained from 6 pN0 OOSCC, 6 pN+ OOSCC, and 2 pools of leukocytes. .. Methylated DNA was enriched using the methyl binding domain protein MeCP2 (MethylCap-kit, Diagenode) and followed by paired-end next generation sequencing on the Illumina GA II Sequencer (Illumina).

    Modification:

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: Adapter-ligated fragments were amplified using Kapa HiFi polymerase (Kapa Biosystems cat. no. KK2602) as previously described [ ] with 200 nM final concentration of primer PE1.0 and modified multiplexing PE2.0 primers. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    Article Snippet: DNA fragments were prepared into sequencing libraries according to modified manufacturer’s standard protocols, using the TruSeq Nano DNA library preparation protocols (FC-121-4001) and the QIAGEN Gene Reader DNA Library Prep I Kit (cat. no. 180984). .. 50–100 ng of sample DNA went through Covaris fragmentation to ~500 nucleotides.

    Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice
    Article Snippet: Paragraph title: Oxidative treatment and sodium bisulfite modification ... In brief, 1.5-μg DNA samples were fragmented to approximately 5 kb by sonication (Covaris).

    Gel Purification:

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry. .. Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry.

    Flow Cytometry:

    Article Title: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    Article Snippet: DNA fragments were prepared into sequencing libraries according to modified manufacturer’s standard protocols, using the TruSeq Nano DNA library preparation protocols (FC-121-4001) and the QIAGEN Gene Reader DNA Library Prep I Kit (cat. no. 180984). .. 50–100 ng of sample DNA went through Covaris fragmentation to ~500 nucleotides.

    Ligation:

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: After ligation, excess adapters and adapter dimers were removed using two Ampure XP clean-ups, first with a 1.1:1 ratio of standard AMPure XP beads to sample, followed by a 0.7:1 ratio. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    Article Snippet: 50–100 ng of sample DNA went through Covaris fragmentation to ~500 nucleotides. .. 50–100 ng of sample DNA went through Covaris fragmentation to ~500 nucleotides.

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: The Ovation SP+ Ultralow Library System (Ovation SP+) was worked in the MondrianTM SP+ Workstation. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase. .. The adaptor stock concentration was diluted to 0.3 to 150 nM to examine the best adaptor concentration for library construction with 1 to 100 pg DNA.

    DNA Sequencing:

    Article Title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae
    Article Snippet: DNA isolation needed for preparing the PacBio 10-kb library high molecular weight genomic DNA was performed according to Moore et al . .. DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA). .. Libraries were quantified by fluorometry, immobilised and processed onto a flow cell with a cBot followed by sequencing by synthesis by applying TruSeq v3 chemistry on a HiSeq2500 (all components by Illumina).

    Article Title: Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching
    Article Snippet: E. coli K12 (MG1655) genomic DNA was obtained from the American Type Culture Collection (ATCC 700926). .. For each DNA-seq library, the DNA (500 ng in 130 μl of 10 mM Tris-HCl, pH 7.5, 1 mM EDTA (TE)) was fragmented to a target size of 400 bp with a Covaris sonicator (S220, Woburn, MA) using a 10% duty cycle, intensity at 5, and 200 cycles per burst. .. After sequential size-selection with 0.6X and 1X Agencourt AMPure XP beads (Beckman Coulter) to remove larger and smaller DNA fragments, respectively, the remaining DNA fragments used for library preparation had an average length of ~250 bp.

    Sequencing:

    Article Title: Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility AllelesHeterozygous Mutations in DNA Repair Genes and Hereditary Breast Cancer: A Question of Power
    Article Snippet: Paragraph title: Whole-Exome Sequencing ... 2–3 µg of DNA was fragmented to approximately 200 bp by sonication (Covaris) and used to prepare single- or paired-end libraries using the SPRIworks Fragment Library System I for Illumina Genome Analyzer on the SPRI-TE Nucleic Acid Extractor (Beckman Coulter).

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution. .. It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution.

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Aliquots of DNA were also used for MiSeq sequencing according to the manufacturer’s protocols (Illumina, San Diego, CA, USA). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity
    Article Snippet: Whole genome sequencing of strain P5 was accomplished using a hybrid approach, combining Illumina short read data with PacBio long read data ( ). .. For PacBio sequencing, 5 μg of sample DNA was sheared to 10 Kb by a Covaris® g-TUBE® (Covaris, United States). .. A PacBio® SMRTbellTM Template Prep Kit (PacBio, United States) was used to construct the library.

    Article Title: Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
    Article Snippet: Paragraph title: Exome sequencing of germline DNA from 98 familial CRC cases ... Thirty-seven of the DNA samples were fragmented according to the Covaris 400 bp protocol and 61 samples were fragmented according to the SureSelect Protocol.

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: All libraries were quantified by real-time PCR, using the SYBR Fast Illumina Library Quantification Kit (Kapa Biosystems cat. no. KK4834), prior to pooling and sequencing. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae
    Article Snippet: Paragraph title: Sequencing and assembly of SBS data ... DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA).

    Article Title: Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels
    Article Snippet: DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA). .. DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA).

    Article Title: Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
    Article Snippet: DNA fragments were prepared into sequencing libraries according to modified manufacturer’s standard protocols, using the TruSeq Nano DNA library preparation protocols (FC-121-4001) and the QIAGEN Gene Reader DNA Library Prep I Kit (cat. no. 180984). .. 50–100 ng of sample DNA went through Covaris fragmentation to ~500 nucleotides.

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: Paragraph title: Metagenomic library construction and sequencing ... In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Article Title: Noncontiguous finished genome sequence and description of Bartonella mastomydis sp. nov.
    Article Snippet: Paragraph title: Genome sequencing and assembly ... The circularized DNA was mechanically sheared to small fragments with Optima on a bimodal curve at 593 and 1377 bp on a Covaris (Woburn, MA, USA) S2 device in T6 tubes.

    Article Title: Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
    Article Snippet: Paragraph title: Whole exome and targeted sequencing ... Prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads.

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: Paragraph title: RAD library construction and sequencing ... DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Paragraph title: Sample collection and sequencing ... Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry.

    Article Title: Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity
    Article Snippet: Finally, amplicons were diluted to 10 nM, quantified and sequenced on the Illumina MiSeq platform (reagent kit v.3; Illumina, United States). .. For metagenome sequencing, 1 μg of sample DNA was sheared to 500 bp by Covaris M220 (Covaris, United States). .. The library was constructed by NEBNext UltraTM DNA Library Prep Kit (NEB, United States).

    Article Title: Methylation of 23S rRNA Nucleotide G748 by RlmAII Methyltransferase Renders Streptococcus pneumoniae Telithromycin Susceptible
    Article Snippet: Relative mutations in the bacterial genome were estimated by sequencing the genomic DNA samples extracted from each strain. .. For preparation of the library DNA, 500 ng of each total DNA was sheared to 800 bp by Covaris (M & S).

    Sonication:

    Article Title: Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility AllelesHeterozygous Mutations in DNA Repair Genes and Hereditary Breast Cancer: A Question of Power
    Article Snippet: DNA for candidate gene mutation analysis underwent whole genome amplification (WGA) using Repli-G Phi-mediated amplification system (Qiagen) prior to mutation analysis. .. 2–3 µg of DNA was fragmented to approximately 200 bp by sonication (Covaris) and used to prepare single- or paired-end libraries using the SPRIworks Fragment Library System I for Illumina Genome Analyzer on the SPRI-TE Nucleic Acid Extractor (Beckman Coulter). .. Exome enrichment was performed using the NimbleGen Sequence Capture 2.1 M Exome Array, EZ Exome Library (Roche NimbleGen) or SureSelect Human All Exon version 2 or 50 Mb libraries (Agilent Technologies) according to the recommended protocols.

    Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice
    Article Snippet: Oxidative and sodium bisulfite treatments were performed using TrueMethyl Kit (Cambridge Epigenetix), according to the manufacturer’s instructions. .. In brief, 1.5-μg DNA samples were fragmented to approximately 5 kb by sonication (Covaris). .. Half the volume of the sample (equivalent to 750 ng of DNA) was subjected to oxidation followed by bisulfite modification (oxidative bisulfite sequencing, oxBS), and the other half was used for bisulfite modification only (bisulfite sequencing, BS).

    Article Title: Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
    Article Snippet: Briefly, DNA was extracted using the QIAGEN® QIAamp DNA Mini Kit according to the manufacturer’s protocol. .. Prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads. .. Size-selected DNA was then ligated to specific adapters during library preparation (Kapa Library Prep, Kapa Biosystems).

    Binding Assay:

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Libraries were bound to polymerase using the DNA/polymerase binding kit P5 or P6v2 and were then loaded on single-molecule real-time (SMRT) cells and sequenced with C3 (P5 polymerase) or C4v2 chemistry (P6v2 polymerase) for 270-min (10-kb libraries) or 360-min (20-kb libraries) movies on the RSII instrument (PacBio). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    DNA Extraction:

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Following DNA extraction, samples were shipped to BGI facilities in Tai Po, Hong Kong, where 500 bp insert-size libraries were prepared for each sample per manufacturer’s directions and sequenced using the Illumina HiSeq 2000 platform. .. Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry.

    Methylation:

    Article Title: Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels
    Article Snippet: 2.2 To determine if increased expression of ARID3a within SLE patient samples was associated with alterations in DNA methylation, genomic DNA was isolated using standard phenol/Chloroform extraction protocols from total PBMCs obtained from each of two SLE patient samples characterized as ARID3aH and two independent SLE samples characterized as ARID3a low. .. DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA). .. Illumina sequencing libraries were prepared from each sample using the Illumina Truseq DNA LT Sample Prep Kit (Illumina, San Diego, CA) by the Genomics Core facility at Oklahoma Medical Research Foundation.

    Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
    Article Snippet: MethylCap-Seq analysis was performed as reported previously. .. Briefly, genome-wide methylation was assessed using 500 ng of DNA fragmented by Covaris S2 (Covaris) and obtained from 6 pN0 OOSCC, 6 pN+ OOSCC, and 2 pools of leukocytes. .. Methylated DNA was enriched using the methyl binding domain protein MeCP2 (MethylCap-kit, Diagenode) and followed by paired-end next generation sequencing on the Illumina GA II Sequencer (Illumina).

    Isolation:

    Article Title: Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels
    Article Snippet: 2.2 To determine if increased expression of ARID3a within SLE patient samples was associated with alterations in DNA methylation, genomic DNA was isolated using standard phenol/Chloroform extraction protocols from total PBMCs obtained from each of two SLE patient samples characterized as ARID3aH and two independent SLE samples characterized as ARID3a low. .. DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA). .. Illumina sequencing libraries were prepared from each sample using the Illumina Truseq DNA LT Sample Prep Kit (Illumina, San Diego, CA) by the Genomics Core facility at Oklahoma Medical Research Foundation.

    Size-exclusion Chromatography:

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: Libraries in 96-well microtitre plates were prepared as above, with the following modifications. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform. .. A Caliper Zephyr liquid handler was used for a single post-PCR cleanup, using a 0.7:1 ratio of AMPure XP beads to DNA.

    Purification:

    Article Title: Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
    Article Snippet: Thirty-seven of the DNA samples were fragmented according to the Covaris 400 bp protocol and 61 samples were fragmented according to the SureSelect Protocol. .. An additional gel-based size selection step was performed for the 37 samples.

    Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice
    Article Snippet: In brief, 1.5-μg DNA samples were fragmented to approximately 5 kb by sonication (Covaris). .. Half the volume of the sample (equivalent to 750 ng of DNA) was subjected to oxidation followed by bisulfite modification (oxidative bisulfite sequencing, oxBS), and the other half was used for bisulfite modification only (bisulfite sequencing, BS).

    Article Title: Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
    Article Snippet: Briefly, DNA was extracted using the QIAGEN® QIAamp DNA Mini Kit according to the manufacturer’s protocol. .. Prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads. .. Size-selected DNA was then ligated to specific adapters during library preparation (Kapa Library Prep, Kapa Biosystems).

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples. .. DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples.

    Polymerase Chain Reaction:

    Article Title: Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
    Article Snippet: Thirty-seven of the DNA samples were fragmented according to the Covaris 400 bp protocol and 61 samples were fragmented according to the SureSelect Protocol. .. An additional gel-based size selection step was performed for the 37 samples.

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: After PCR, excess primers and any primer dimer were removed using two AMPure XP clean-ups, with a 0.7:1 ratio of AMPure XP beads. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae
    Article Snippet: DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA). .. DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA).

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: Prior to PCR amplification for sequence library construction, all bottled water and sample tubes used for shotgun library construction were processed under UV light irradiation at a clean bench and opened under the open clean system KOACH T 500-F to minimize microbial and nucleotide contamination. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples. .. DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry. .. Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry.

    Blocking Assay:

    Article Title: Can molecular profiling enhance radiotherapy? Impact of personalized targeted gold nanoparticles on radiosensitivity and imaging of adenoid cystic carcinoma
    Article Snippet: Briefly, 5μmeter sections of the formalin fixed paraffin embedded tumor resection block were marked for the cancer cell regions (identified from a consecutive cut stained with hematoxylin and eosin). .. DNA was fragmented with COVARIS® and construction of next generation sequencing library (attachment of sample-specific index and the Illumina adaptors to DNA fragments) was performed with NEBnext™ kit.

    Gel Extraction:

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples. .. The DNA was then ligated with a P2 adapter, followed by purification using 1.6 × AMPure XP Beads and then used for selective PCR using 2× Phusion PCR Master Mix (NEB) over 18 cycles.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry. .. Fragmented DNA was combined with End Repair Mix and incubated at 20° C for 30 min. We followed up this step with purification using the QIAquick PCR Purification Kit (QIAGEN), then added A-Tailing Mix and incubated at 37° C for 30 min. Adapters were added to this adenylated DNA mix using Adapter and Ligation Mix and an incubation reaction at 20° C for 15 min.

    Sample Prep:

    Article Title: Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
    Article Snippet: Sequencing libraries were prepared according to the TruSeq DNA Sample Preparation Kit EUC 15005180 or EUC 15026489 (Illumina). .. Thirty-seven of the DNA samples were fragmented according to the Covaris 400 bp protocol and 61 samples were fragmented according to the SureSelect Protocol.

    Article Title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae
    Article Snippet: DNA isolation needed for preparing the PacBio 10-kb library high molecular weight genomic DNA was performed according to Moore et al . .. DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA). .. Libraries were quantified by fluorometry, immobilised and processed onto a flow cell with a cBot followed by sequencing by synthesis by applying TruSeq v3 chemistry on a HiSeq2500 (all components by Illumina).

    Article Title: Noncontiguous finished genome sequence and description of Bartonella mastomydis sp. nov.
    Article Snippet: The genomic DNA was barcoded to be mixed with 11 other projects with the Nextera Mate Pair sample prep kit (Illumina). .. The circularized DNA was mechanically sheared to small fragments with Optima on a bimodal curve at 593 and 1377 bp on a Covaris (Woburn, MA, USA) S2 device in T6 tubes.

    Software:

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Sequence reads were assembled de novo using the Hierarchical Genome Assembly Process (HGAP3) from the SMRT Analysis Software suite (PacBio) ( ). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    Article Title: RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
    Article Snippet: Briefly, genome-wide methylation was assessed using 500 ng of DNA fragmented by Covaris S2 (Covaris) and obtained from 6 pN0 OOSCC, 6 pN+ OOSCC, and 2 pools of leukocytes. .. Methylated DNA was enriched using the methyl binding domain protein MeCP2 (MethylCap-kit, Diagenode) and followed by paired-end next generation sequencing on the Illumina GA II Sequencer (Illumina).

    Irradiation:

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: Prior to PCR amplification for sequence library construction, all bottled water and sample tubes used for shotgun library construction were processed under UV light irradiation at a clean bench and opened under the open clean system KOACH T 500-F to minimize microbial and nucleotide contamination. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Selection:

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution. .. It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution.

    Article Title: Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
    Article Snippet: Thirty-seven of the DNA samples were fragmented according to the Covaris 400 bp protocol and 61 samples were fragmented according to the SureSelect Protocol. .. After fragmentation, all samples were subjected to end-repair, A-tailing, and adaptor ligation of Illumina Multiplexing PE adaptors.

    Article Title: Noncontiguous finished genome sequence and description of Bartonella mastomydis sp. nov.
    Article Snippet: No size selection was performed, and 600 ng of tagmented fragments were circularized. .. The circularized DNA was mechanically sheared to small fragments with Optima on a bimodal curve at 593 and 1377 bp on a Covaris (Woburn, MA, USA) S2 device in T6 tubes.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry. .. Fragmented DNA was combined with End Repair Mix and incubated at 20° C for 30 min. We followed up this step with purification using the QIAquick PCR Purification Kit (QIAGEN), then added A-Tailing Mix and incubated at 37° C for 30 min. Adapters were added to this adenylated DNA mix using Adapter and Ligation Mix and an incubation reaction at 20° C for 15 min.

    Agarose Gel Electrophoresis:

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples. .. The DNA was then ligated with a P2 adapter, followed by purification using 1.6 × AMPure XP Beads and then used for selective PCR using 2× Phusion PCR Master Mix (NEB) over 18 cycles.

    Article Title: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee
    Article Snippet: Resulting DNA quality and quantity was measured using three methods: agarose gel electrophoresis (1%), Nanodrop (NanoDrop ND-1000), and Qubit Fluorometer (per the manufacturer’s instructions). .. Extracted DNA was fragmented via Covaris sonicator, and quality assessment followed using Gel-Electrophotometry.

    Electrophoresis:

    Article Title: A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage
    Article Snippet: DNA was processed to obtain RAD libraries and a Covaris S220 ultra-sonicator was used to break DNA to 300–700 bp in length, and 1.6× AMPure XP Beads were used to purify the DNA samples. .. The DNA was then ligated with a P2 adapter, followed by purification using 1.6 × AMPure XP Beads and then used for selective PCR using 2× Phusion PCR Master Mix (NEB) over 18 cycles.

    Next-Generation Sequencing:

    Article Title: Can molecular profiling enhance radiotherapy? Impact of personalized targeted gold nanoparticles on radiosensitivity and imaging of adenoid cystic carcinoma
    Article Snippet: DNA was extracted from the needle scratch of that region, using the standard protocol for Promega® robot. .. DNA was fragmented with COVARIS® and construction of next generation sequencing library (attachment of sample-specific index and the Illumina adaptors to DNA fragments) was performed with NEBnext™ kit. .. Target capture of an interval that includes all exons of 167 genes involved in a variety of carcinomas was performed using Agilent SureSelect.

    Article Title: Methylation of 23S rRNA Nucleotide G748 by RlmAII Methyltransferase Renders Streptococcus pneumoniae Telithromycin Susceptible
    Article Snippet: Paragraph title: Next-generation sequencing and data analysis. ... For preparation of the library DNA, 500 ng of each total DNA was sheared to 800 bp by Covaris (M & S).

    Chromosome Walking:

    Article Title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae
    Article Snippet: DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA). .. DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA).

    DNA Methylation Assay:

    Article Title: Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels
    Article Snippet: 2.2 To determine if increased expression of ARID3a within SLE patient samples was associated with alterations in DNA methylation, genomic DNA was isolated using standard phenol/Chloroform extraction protocols from total PBMCs obtained from each of two SLE patient samples characterized as ARID3aH and two independent SLE samples characterized as ARID3a low. .. DNA was fragmented on a Covaris S2 sonicator (Covaris, Woburn, MA) to an average size of ~350 bp in length and methylated DNA was isolated using the MethylMiner Methylated DNA Enrichment Kit (Life Technologies, Carlsbad, CA).

    Produced:

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: Different insert sizes can easily be obtained by adjusting the size selection step (ratio of DNA solution to AMPure beads) as recommended by the manufacturer. .. It is not necessary to adjust the shearing step, as the sheared DNA produced by Covaris has a very broad size distribution. .. NEBNext library process provides very consistent results in terms of library size and concentration, even when performed for the very first time.

    Concentration Assay:

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA). .. Dual-indexed sequencing libraries were prepared with NEBNext ultra DNA library prep kits for Illumina (New England Biolabs, Ipswich, MA, USA), and barcoding indices were synthesized in-house.

    Article Title: SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
    Article Snippet: Adapter-ligated fragments were amplified using Kapa HiFi polymerase (Kapa Biosystems cat. no. KK2602) as previously described [ ] with 200 nM final concentration of primer PE1.0 and modified multiplexing PE2.0 primers. .. DNA was sheared to a mean fragment size of 300 bp in Covaris 96 microTUBE plates (Covaris Inc., part no. 520078) using a Covaris E210 instrument with the settings: duty cycle 10, intensity 5, 200 cycles/burst, 60 sec. PrePCR processing was performed using a Beckman FxP dual arm liquid handling platform.

    Article Title: Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
    Article Snippet: Environmental DNA was diluted to a certain concentration with DNase and RNase-Free Water (NIPPON GENE) prior to shotgun metagenomic library construction. .. In order to prepare the starting DNA for KAPA HP and Ovation SP+, Covaris S220 (Woburn, MA, USA) was used for physical DNA fragmentation using the conditions described below to obtain a peak fragment size: 400 bp; Peak Power: 175.0, Duty Factor: 5.0, Cycles/Burst: 200, and Time: 55 s. In the KAPA HP kit, each 110 μL of the adaptor ligation reaction mixture consisted of 60 μL of input DNA, 5 μL of adaptor stock, 5 μL of water, 30 μL of ligation buffer, and 10 μL of DNA ligase.

    Staining:

    Article Title: Can molecular profiling enhance radiotherapy? Impact of personalized targeted gold nanoparticles on radiosensitivity and imaging of adenoid cystic carcinoma
    Article Snippet: Briefly, 5μmeter sections of the formalin fixed paraffin embedded tumor resection block were marked for the cancer cell regions (identified from a consecutive cut stained with hematoxylin and eosin). .. DNA was fragmented with COVARIS® and construction of next generation sequencing library (attachment of sample-specific index and the Illumina adaptors to DNA fragments) was performed with NEBnext™ kit.

    Variant Assay:

    Article Title: Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
    Article Snippet: Prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads. .. Prior to library preparation, DNA was fragmented (Covaris sonication) to 250 bp and further purified using Agentcourt AMPure XP beads.

    Article Title: Can molecular profiling enhance radiotherapy? Impact of personalized targeted gold nanoparticles on radiosensitivity and imaging of adenoid cystic carcinoma
    Article Snippet: DNA was fragmented with COVARIS® and construction of next generation sequencing library (attachment of sample-specific index and the Illumina adaptors to DNA fragments) was performed with NEBnext™ kit. .. NGS was performed on Illumina® HiSeq2500™, eight samples on each lane (typically 25-30 million reads per sample).

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  • dna  (Covaris)
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    Covaris dna
    Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and <t>PBL</t> <t>DNA</t> samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation
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    Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and PBL DNA samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation

    Journal: Genome Biology

    Article Title: Characterization of background noise in capture-based targeted sequencing data

    doi: 10.1186/s13059-017-1275-2

    Figure Lengend Snippet: Characterization of background errors in targeted deep sequencing data. a The background allele frequencies from plasma and PBL DNA samples were box-plotted (n = 19 for each group). b The frequency of error-free positions in each sample was calculated and box-plotted for each group. c The distribution of background allele frequencies across all possible 12 substitution classes. The y-axis denotes the frequency of each class in the pre-treatment PBL and plasma samples. The relative base substitution frequency is shown in the stacked bar plot on the right side. d The ratio of background errors in PBL compared to plasma DNA samples was plotted for each substitution class indicated on the x-axis. e The ratio of background allele frequencies for reciprocal base substitutions. Error bars indicate standard deviation

    Article Snippet: Given that the only difference between the protocols employed for plasma and PBL DNA samples was the fragmentation of DNA by adaptive focused acoustic technology (Covaris), we assumed that any observed PBL-specific errors were due to DNA damage incurred during the fragmentation step.

    Techniques: Sequencing, Standard Deviation

    Characterization of the DNA break point. a Fold changes in error rates across all substitution classes were compared between PBL and plasma DNA samples. The fold change was calculated by dividing the substitution rate at each position by the average rate of 1 − 50 bp. The distribution of fold changes in 1 − 50 bp was box-plotted. Above the box plots, the observed fold change at the first and the second bases was marked for comparison. For better discrimination between the groups, plasma data are displayed on a grey background . b The distribution of quality scores of total bases, including low quality bases, is plotted according to the position of reads. c Mononucleotide frequencies around the DNA break point. Note: except in ( b ), all analyses of background alleles were performed after filtering of bases with a quality score

    Journal: Genome Biology

    Article Title: Characterization of background noise in capture-based targeted sequencing data

    doi: 10.1186/s13059-017-1275-2

    Figure Lengend Snippet: Characterization of the DNA break point. a Fold changes in error rates across all substitution classes were compared between PBL and plasma DNA samples. The fold change was calculated by dividing the substitution rate at each position by the average rate of 1 − 50 bp. The distribution of fold changes in 1 − 50 bp was box-plotted. Above the box plots, the observed fold change at the first and the second bases was marked for comparison. For better discrimination between the groups, plasma data are displayed on a grey background . b The distribution of quality scores of total bases, including low quality bases, is plotted according to the position of reads. c Mononucleotide frequencies around the DNA break point. Note: except in ( b ), all analyses of background alleles were performed after filtering of bases with a quality score

    Article Snippet: Given that the only difference between the protocols employed for plasma and PBL DNA samples was the fragmentation of DNA by adaptive focused acoustic technology (Covaris), we assumed that any observed PBL-specific errors were due to DNA damage incurred during the fragmentation step.

    Techniques:

    The false positive rate. a The error rate of each background allele was calculated and their distribution was plotted, dependent on the total read counts. Data from 19 plasma DNA samples were down-sampled to a designated size of total reads in a range between 2.5 and 50 M. The x-axis denotes the frequency of background alleles, and the y-axis denotes the fraction of alleles with the designated background rate on the x-axis . b – d The fraction of background alleles present at a frequency greater than a given threshold is plotted against the depth of coverage after de-duplication ( x-axis ). b The effect of coverage depth on the false positive rate is shown in the down-sampled data set generated from 19 plasma DNA samples. c The effect of each DNA shearing condition on the false positive rate was estimated using the down-sampled data set from Fig. 3 . a–d indicate the fragmentation conditions, as described in Fig. 3 . d A comparison of plasma and fragmented PBL DNA samples

    Journal: Genome Biology

    Article Title: Characterization of background noise in capture-based targeted sequencing data

    doi: 10.1186/s13059-017-1275-2

    Figure Lengend Snippet: The false positive rate. a The error rate of each background allele was calculated and their distribution was plotted, dependent on the total read counts. Data from 19 plasma DNA samples were down-sampled to a designated size of total reads in a range between 2.5 and 50 M. The x-axis denotes the frequency of background alleles, and the y-axis denotes the fraction of alleles with the designated background rate on the x-axis . b – d The fraction of background alleles present at a frequency greater than a given threshold is plotted against the depth of coverage after de-duplication ( x-axis ). b The effect of coverage depth on the false positive rate is shown in the down-sampled data set generated from 19 plasma DNA samples. c The effect of each DNA shearing condition on the false positive rate was estimated using the down-sampled data set from Fig. 3 . a–d indicate the fragmentation conditions, as described in Fig. 3 . d A comparison of plasma and fragmented PBL DNA samples

    Article Snippet: Given that the only difference between the protocols employed for plasma and PBL DNA samples was the fragmentation of DNA by adaptive focused acoustic technology (Covaris), we assumed that any observed PBL-specific errors were due to DNA damage incurred during the fragmentation step.

    Techniques: Generated

    Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .

    Journal:

    Article Title: Improved Protocols for Illumina Sequencing

    doi: 10.1002/0471142905.hg1802s62

    Figure Lengend Snippet: Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .

    Article Snippet: DNA sample Covaris S2 or equivalent with chiller unit Life Technologies Qubit Fluorometer (or other fluorometric based method, e.g. SYBR green) 6-mm × 16-mm AFA fiber vials (Covaris, cat. no. 520045) Crimp caps (Covaris, cat no. 520028) Allow the Covaris chiller to reach 4°C, and degas the water for at least 30 min. During this time, prepare the DNA sample: Obtain concentration using the Qubit Fluorometer Dilute at least 500ng of DNA to 100 μl with EB buffer and transfer the DNA sample to a Covaris vial.

    Techniques: Purification, Chromatin Immunoprecipitation