microtube afa fiber  (Covaris)


Bioz Verified Symbol Covaris is a verified supplier
Bioz Manufacturer Symbol Covaris manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    8 microTUBE 50 AFA Fiber Strip V2
    Description:
    The Covaris microTUBE 50 is engineered to optimize DNA Shearing in a 50 µl sample volume with Focused ultrasonicators utilizing Adaptive Focused Acoustics AFA technology
    Catalog Number:
    520174
    Product Aliases:
    microTUBE-50
    Price:
    None
    Category:
    Consumable
    Score:
    85
    Quantity:
    12
    Buy from Supplier


    Structured Review

    Covaris microtube afa fiber
    8 microTUBE 50 AFA Fiber Strip V2
    The Covaris microTUBE 50 is engineered to optimize DNA Shearing in a 50 µl sample volume with Focused ultrasonicators utilizing Adaptive Focused Acoustics AFA technology
    https://www.bioz.com/result/microtube afa fiber/product/Covaris
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    microtube afa fiber - by Bioz Stars, 2019-10
    99/100 stars

    Images

    Related Articles

    Clone Assay:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Amplification:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Following either 5mC or 5hmC MeDIP, libraries were size-selected from 200–400 bp on a 2% agarose E-gel (Invitrogen) and extracted using a MinElute Gel DNA extraction kit (Qiagen) according to the manufacturer's instructions.

    Article Title: Mouse SCNT ESCs Have Lower Somatic Mutation Load Than Syngeneic iPSCs
    Article Snippet: Next, the DNA (3 μg in 50 μl volumes) was fragmented with Covaris AFA and then processed following the manufacturer’s protocol (NEBNext DNA Library Prep Master Mix Set for Illumina). .. Briefly, fragmented DNA was end polished, A tailed, and then ligated to adaptors compatible with Illumina sequencing primers.

    Lambda DNA Preparation:

    Article Title: The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
    Article Snippet: The ratio of genomic DNA to unmethylated lambda DNA should be kept at 200:1. .. 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions.

    SYBR Green Assay:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Incubation:

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: After incubation in the extracts, the plasmids were briefly washed with EB supplemented with 0.25% NP40 and 1.5 mM ATP; resuspended with 200 μl of EB supplemented with 0.25% NP40, 1.5 mM ATP, and 1% formaldehyde; and incubated for 10 min at room temperature. .. The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris).

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: Linear DNA was digested by adding 3.75 μl Exonuclease (Illumina) and incubation (30 min, 37 °C). .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Mass Spectrometry:

    Article Title: Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
    Article Snippet: DNA was sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using the Blue Pippin (Sage Science). .. Illumina libraries were constructed using either Illumina TruSeq LT kit (FC-121-2001), or with a PCR-free method using NEBNext End Repair (E6050S), NEBNext dA-tailing (E6053S) and Blunt T/A ligase (M0367S) New England Biolabs modules.

    Article Title: Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry
    Article Snippet: An Illumina library was also prepared for isolate 12008, with DNA sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using a Blue Pippin (Sage Science). .. The Illumina library was constructed with a PCR-free method using NEBNext End Repair (E6050S), NEBNext dA-tailing (E6053S) and Blunt T/A ligase (M0367S) New England Biolabs modules.

    Modification:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: MeDIP-Seq libraries for Ion Torrent semiconductor sequencing on the Ion Torrent PGM or Ion Torrent Proton instruments were generated using a modified protocol consisting of Life Technologies’ Ion Plus Fragment Library kit (Catalog # 4471252) in combination with a commercially available 5-methylcytosine (MagMeDIP Kit, Catalog # mc-magme-048) or 5-hydroxymethylcytosine (5hmC Kit, Catalog # AF-110–0016) immunoprecipitation kit (Diagenode). .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    Flow Cytometry:

    Article Title: Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Article Snippet: For each Reference Material, 12 (or 14 for NA12878) libraries were prepared in parallel using the Illumina TruSeq (LT) DNA PCR-Free Sample Prep Kits (FC-121–3001). .. Genomic DNA (1.5 ug) was fragmented using a Covaris S2 focused ultrasonicator in micro TUBE AFA Fiber Pre-Slit Snap-Cap 6×16 mm micro tubes and the Covaris MicroTUBE holder (covaris part numbers 520045 and 500114, respectively) under the following conditions for a target insert size of 550 base pairs.

    Sequencing:

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

    Article Title: Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
    Article Snippet: Paragraph title: DNA extraction, library preparation and sequencing ... DNA was sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using the Blue Pippin (Sage Science).

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: MeDIP-Seq libraries for Ion Torrent semiconductor sequencing on the Ion Torrent PGM or Ion Torrent Proton instruments were generated using a modified protocol consisting of Life Technologies’ Ion Plus Fragment Library kit (Catalog # 4471252) in combination with a commercially available 5-methylcytosine (MagMeDIP Kit, Catalog # mc-magme-048) or 5-hydroxymethylcytosine (5hmC Kit, Catalog # AF-110–0016) immunoprecipitation kit (Diagenode). .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    Article Title: Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses
    Article Snippet: The identification by 16S rDNA sequencing pointed at Pseudomonas xanthomarina since this strain shared 99.9% identity with 15 P. xanthomarina strains in GenBank ( ). .. Genomic DNA, extracted from a pure axenic culture according to an adapted protocol , was sheared in a 50-µL AFA microtube (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp.

    Article Title: Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry
    Article Snippet: Genomic DNA for isolate 12008 was prepared by extracting high molecular weight DNA from freeze-dried V. dahliae mycelium using the Macherey-Nagel Nucleospin Plant II kit (Fisher 11912262) for Illumina sequencing and QIAGEN Genomic-tip 500/G kit (Qiagen, Germany) for Pacbio sequencing, which was sequenced on an RSII machine. .. An Illumina library was also prepared for isolate 12008, with DNA sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using a Blue Pippin (Sage Science).

    Article Title: Emergence of the Virulence-Associated PB2 E627K Substitution in a Fatal Human Case of Highly Pathogenic Avian Influenza Virus A(H7N7) Infection as Determined by Illumina Ultra-Deep Sequencing
    Article Snippet: Paragraph title: Illumina sequencing. (i) Genome Analyzer IIx (GAIIx). ... Products from the full-genome influenza virus RT-PCR of the pooled chicken samples were diluted to a DNA concentration of 50 ng/μl and sheared to a length of 200 to 400 bp using a Covaris AFA (Covaris, Woburn, MA).

    Article Title: The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
    Article Snippet: 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions. .. 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions.

    Article Title: Viral population analysis and minority-variant detection using short read next-generation sequencing
    Article Snippet: Finally, equal volumes of both reactions were combined producing a near equimolar mixture of all influenza segments and total DNA concentration determined using the Quant-iT PicoGreen dsDNA Picogreen assay (Invitrogen). .. (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane. .. The products were sequenced on an Illumina GAIIx using a paired-end 54 bp run, following the manufacturer's instructions.

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Initially identified as a Mesorhizobium species by 16S sequencing, it shared 98 to 99% identity with many Mesorhizobium strains in GenBank ( ). .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: Paragraph title: Shotgun and mate-pair sequencing of MTP-BACs ... Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Ligation:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA). .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Hemagglutination Assay:

    Article Title: Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor
    Article Snippet: All samples were stored in LoBind Eppendorf tubes (Fisher Scientific, Hampton, NH) at 4 °C for short term use, or kept at −20 °C for long-term storage. .. A 50 μl solution of polydisperse HA concentrate (1 μg/μl) was placed in a microTUBE AFA fiber snap-cap (Covaris, Woburn, MA) and mechanically sheared in a 7 °C water bath using a Covaris S220 focused ultrasonicator (peak incident power of 175 W, 200 cycles per burst, 10% duty factor). .. HA fragmentation was monitored by gel electrophoresis using the methods described below.

    Generated:

    Article Title: Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
    Article Snippet: DNA was sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using the Blue Pippin (Sage Science). .. DNA was sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using the Blue Pippin (Sage Science).

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: MeDIP-Seq libraries for Ion Torrent semiconductor sequencing on the Ion Torrent PGM or Ion Torrent Proton instruments were generated using a modified protocol consisting of Life Technologies’ Ion Plus Fragment Library kit (Catalog # 4471252) in combination with a commercially available 5-methylcytosine (MagMeDIP Kit, Catalog # mc-magme-048) or 5-hydroxymethylcytosine (5hmC Kit, Catalog # AF-110–0016) immunoprecipitation kit (Diagenode). .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    Article Title: Viral population analysis and minority-variant detection using short read next-generation sequencing
    Article Snippet: (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane. .. (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane.

    DNA HS Assay:

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: The DNA concentration was measured using the Qubit device and the Quant-It DNA HS Assay (Invitrogen). .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Polymerase Chain Reaction:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Article Title: Base-resolution profiling of active DNA demethylation using methylase-assisted bisulfite sequencing (MAB-seq) and caMAB-seq
    Article Snippet: Illumina sequencing reagent for HiSeq 2500 or equivalent sequencers .. Eppendorf 0.2 mL PCR tube strips (Fisher Scientific, cat. no. E0030124286) Eppendorf RNA/DNA LoBind microcentrifuge tubes (1.5 mL, Sigma-Aldrich, cat. no. Z666548) Corning™ CentriStar™ centrifuge tubes (15 mL; Fisher Scientific, cat. no. 0553859A) Corning™ CentriStar™ centrifuge tubes (50 mL; Fisher Scientific, cat. no.0553860) Agilent 2100 Bioanalyzer (Agilent, cat. no. G2939AA) Qubit 2.0 Fluorometer (Life Technologies, cat. no. ) Qubit assay tubes (Life Technologies, cat. no. ) Branson Sonifier 450 (Branson Ultrasonics) M220 Focused-ultrasonicator (Covaris) microTUBE-50 AFA Fiber Screw-Cap (Covaris, cat. No. 5201660) Filter tips (10, 20, 200, 1000 μL; Genesee Scientific) Serological pipet (1, 5, 10, 25 mL; Genesee Scientific) C1000 thermal cycler (Biorad, cat. no. 185-1096) Eppendorf Thermomixer R (Fisher Scientific, cat. no. 05-400-203) Vortex-genie 2 (Scientific Industries, cat. no. SI-0286) Illumina sequencer (HiSeq 2500 or equivalent models) .. Trim galore (version 0.3.7): FastQC (version 0.10.1): Bismark (version 0.12.5) : Bowtie2 (version 2.2.2) : Picard (version 1.91): Samtools (version 0.1.19) : IGV genome browser : download from BEDTools (version 2.19.0) : BisSNP (version 0.82.2) :

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Following either 5mC or 5hmC MeDIP, libraries were size-selected from 200–400 bp on a 2% agarose E-gel (Invitrogen) and extracted using a MinElute Gel DNA extraction kit (Qiagen) according to the manufacturer's instructions.

    Article Title: Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Article Snippet: For each Reference Material, 12 (or 14 for NA12878) libraries were prepared in parallel using the Illumina TruSeq (LT) DNA PCR-Free Sample Prep Kits (FC-121–3001). .. Genomic DNA (1.5 ug) was fragmented using a Covaris S2 focused ultrasonicator in micro TUBE AFA Fiber Pre-Slit Snap-Cap 6×16 mm micro tubes and the Covaris MicroTUBE holder (covaris part numbers 520045 and 500114, respectively) under the following conditions for a target insert size of 550 base pairs.

    Article Title: The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
    Article Snippet: 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions. .. 4| Size selection can be performed in two ways: by using AmpurXP beads (option A) or by gel extraction (option B) (both methods are equally recommended).

    Article Title: Viral population analysis and minority-variant detection using short read next-generation sequencing
    Article Snippet: Finally, equal volumes of both reactions were combined producing a near equimolar mixture of all influenza segments and total DNA concentration determined using the Quant-iT PicoGreen dsDNA Picogreen assay (Invitrogen). .. (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane. .. The products were sequenced on an Illumina GAIIx using a paired-end 54 bp run, following the manufacturer's instructions.

    Article Title: Mouse SCNT ESCs Have Lower Somatic Mutation Load Than Syngeneic iPSCs
    Article Snippet: Next, the DNA (3 μg in 50 μl volumes) was fragmented with Covaris AFA and then processed following the manufacturer’s protocol (NEBNext DNA Library Prep Master Mix Set for Illumina). .. Briefly, fragmented DNA was end polished, A tailed, and then ligated to adaptors compatible with Illumina sequencing primers.

    Sonication:

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

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: A nonspecific mouse IgG was used for an immunoprecipitation reaction as a negative control. .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Sonicated DNA was end-repaired, purified with Agencourt AMPure XP reagent beads (Beckman Coulter), and ligated with Ion Torrent compatible sequencing adapters following the standard Ion Plus Fragment Library Kit protocol.

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: After incubation in the extracts, the plasmids were briefly washed with EB supplemented with 0.25% NP40 and 1.5 mM ATP; resuspended with 200 μl of EB supplemented with 0.25% NP40, 1.5 mM ATP, and 1% formaldehyde; and incubated for 10 min at room temperature. .. The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris). .. The plasmid DNA was sheared to ∼500 bp average size using Covaris S220 (Covaris, USA) with 30 cycles of 15 s sonication at 30 W. The sonicated samples were diluted to give a final concentration of 1 ng DNA/μl, with the sonication buffer containing 5 mg/ml BSA and 0.4 mg/ml salmon sperm, and the magnetic beads were removed with a magnet before immunoprecipitation.

    Affinity Purification:

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA). .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Methylated DNA Immunoprecipitation:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    DNA Extraction:

    Article Title: Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
    Article Snippet: Paragraph title: DNA extraction, library preparation and sequencing ... DNA was sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using the Blue Pippin (Sage Science).

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Adapter-ligated DNA was purified using Agencourt AMPure XP reagent beads and immunoprecipitated using either a 5-methylcytosine kit (MagMeDIP) or 5-hydroxymethylcytosine (hMeDIP) MeDIP kit according to the manufacturer's protocol.

    Article Title: Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry
    Article Snippet: For isolates, 12251, 12153, 12158 and 12161 DNA extraction was performed on freeze-dried mycelium using a GenElute plant DNA miniprep kit (Sigma-Aldrich). .. An Illumina library was also prepared for isolate 12008, with DNA sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using a Blue Pippin (Sage Science).

    Nucleic Acid Electrophoresis:

    Article Title: Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores
    Article Snippet: Mouse genomic DNA (1 μg/μL) extracted from brain tissue was obtained commercially (Zyagen, San Diego, CA) and stored at −20 °C prior to use. .. Sample fragmentation was performed by suspending 10 μg of genomic DNA in pure deionized water to a final volume of 50 μL in a microTUBE AFA fiber snap-cap (Covaris, Woburn, MA) followed by shearing with a Covaris S220 focused-ultrasonicator operated at the following settings: peak incident power = 175 W; duty factor = 10%; cycles per burst = 200; total treatment time = 280 s. Fragment length was confirmed by gel electrophoresis on 4% agarose gel as described above. .. For control material, fragmented genomic DNA was purified immediately using a QIAquick purification kit (Qiagen, Valencia, CA), eluted in pure deionized water, and stored at −20 °C prior to nanopore measurement.

    Methylated DNA Immunoprecipitation Sequencing:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: A nonspecific mouse IgG was used for an immunoprecipitation reaction as a negative control. .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Sonicated DNA was end-repaired, purified with Agencourt AMPure XP reagent beads (Beckman Coulter), and ligated with Ion Torrent compatible sequencing adapters following the standard Ion Plus Fragment Library Kit protocol.

    Isolation:

    Article Title: Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses
    Article Snippet: The strain UASWS0955 was isolated from the biomass of a sewage sludge treatment installation in Croatia. .. Genomic DNA, extracted from a pure axenic culture according to an adapted protocol , was sheared in a 50-µL AFA microtube (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp.

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Strain UASWS1009 was isolated from the sewage sludge of a coking plant in Hungary through a selection experiment for highly ammonia-tolerant nitrifying bacteria. .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Negative Control:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: A nonspecific mouse IgG was used for an immunoprecipitation reaction as a negative control. .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    Purification:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris). .. Sonicated DNA was end-repaired, purified with Agencourt AMPure XP reagent beads (Beckman Coulter), and ligated with Ion Torrent compatible sequencing adapters following the standard Ion Plus Fragment Library Kit protocol.

    Article Title: Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Article Snippet: Genomic DNA (1.5 ug) was fragmented using a Covaris S2 focused ultrasonicator in micro TUBE AFA Fiber Pre-Slit Snap-Cap 6×16 mm micro tubes and the Covaris MicroTUBE holder (covaris part numbers 520045 and 500114, respectively) under the following conditions for a target insert size of 550 base pairs. .. Genomic DNA (1.5 ug) was fragmented using a Covaris S2 focused ultrasonicator in micro TUBE AFA Fiber Pre-Slit Snap-Cap 6×16 mm micro tubes and the Covaris MicroTUBE holder (covaris part numbers 520045 and 500114, respectively) under the following conditions for a target insert size of 550 base pairs.

    Article Title: Mouse SCNT ESCs Have Lower Somatic Mutation Load Than Syngeneic iPSCs
    Article Snippet: Next, the DNA (3 μg in 50 μl volumes) was fragmented with Covaris AFA and then processed following the manufacturer’s protocol (NEBNext DNA Library Prep Master Mix Set for Illumina). .. Briefly, fragmented DNA was end polished, A tailed, and then ligated to adaptors compatible with Illumina sequencing primers.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Emergence of the Virulence-Associated PB2 E627K Substitution in a Fatal Human Case of Highly Pathogenic Avian Influenza Virus A(H7N7) Infection as Determined by Illumina Ultra-Deep Sequencing
    Article Snippet: Thermal cycling conditions were as follows: reverse transcription at 50°C for 1 h and denaturation at 95°C for 5 min; enzyme activation of 95°C for 15 min; 45 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 1 min; and final extension of 72°C for 10 min. .. Products from the full-genome influenza virus RT-PCR of the pooled chicken samples were diluted to a DNA concentration of 50 ng/μl and sheared to a length of 200 to 400 bp using a Covaris AFA (Covaris, Woburn, MA). .. The sheared fragments were end repaired, A-tailed, and ligated to Illumina sequencing adaptors containing molecular identifier (MID) tags using the NEBNext DNA Library Prep reagent set (New England BioLabs, United Kingdom) to allow for multiplex sequencing per lane.

    Immunoprecipitation:

    Article Title: Semiconductor-based sequencing of genome-wide DNA methylation states
    Article Snippet: A nonspecific mouse IgG was used for an immunoprecipitation reaction as a negative control. .. For both 5mC and 5hmC MeDIP-Seq, 1 μg of DNA was sheared to a mean fragment size of 300 bp by sonication with the Covaris M220 Focused-ultrasonicator instrument (Covaris) in a 50 μl microTUBE AFA Fiber Screw-CAP (Covaris).

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris). .. The plasmid DNA was sheared to ∼500 bp average size using Covaris S220 (Covaris, USA) with 30 cycles of 15 s sonication at 30 W. The sonicated samples were diluted to give a final concentration of 1 ng DNA/μl, with the sonication buffer containing 5 mg/ml BSA and 0.4 mg/ml salmon sperm, and the magnetic beads were removed with a magnet before immunoprecipitation.

    Gel Extraction:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Article Title: The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
    Article Snippet: 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions. .. For CMS-IP on the Illumina sequencing platform, the recommended target fragment size is 200 bp.

    Agarose Gel Electrophoresis:

    Article Title: Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores
    Article Snippet: Mouse genomic DNA (1 μg/μL) extracted from brain tissue was obtained commercially (Zyagen, San Diego, CA) and stored at −20 °C prior to use. .. Sample fragmentation was performed by suspending 10 μg of genomic DNA in pure deionized water to a final volume of 50 μL in a microTUBE AFA fiber snap-cap (Covaris, Woburn, MA) followed by shearing with a Covaris S220 focused-ultrasonicator operated at the following settings: peak incident power = 175 W; duty factor = 10%; cycles per burst = 200; total treatment time = 280 s. Fragment length was confirmed by gel electrophoresis on 4% agarose gel as described above. .. For control material, fragmented genomic DNA was purified immediately using a QIAquick purification kit (Qiagen, Valencia, CA), eluted in pure deionized water, and stored at −20 °C prior to nanopore measurement.

    Shotgun Sequencing:

    Article Title: Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses
    Article Snippet: Genomic DNA, extracted from a pure axenic culture according to an adapted protocol , was sheared in a 50-µL AFA microtube (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp. .. A library was created using the TruSeq DNA PCR-free library preparation kits (Illumina), and the insert size was checked in a Fragment analyzer (Advanced Analytical Technologies, Inc).

    Chromatin Immunoprecipitation:

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

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) assay ... The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris).

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: Size selected samples were collected in 40 μl of TRIS- TAPS buffer (pH 8.0) (Sage Science, Beverly, MA, USA), and analysed using the Agilent Bioanalyser (high sensitivity chip, Agilent, Stockport, UK) to determine the final library size. .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Plasmid Preparation:

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: Bead-coupled plasmids were incubated in the egg extracts to allow protein binding to the plasmid DNA. .. The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris).

    Real-time Polymerase Chain Reaction:

    Article Title: RNA-Seq analysis to capture the transcriptome landscape of a single cell
    Article Snippet: For the genes with mRNAs longer than 3 kb, which constitute about 36% of all known genes, the 5′ end part of the mRNA can not be detected. .. Ac-BSA (Sigma, cat. no. B8894) Acidic Tyrode’s solution (Sigma, cat. no. T1788) 1× PBS (pH 7.2) (Gibco, cat. no. 14249-95) 10× PCR Buffer II and 25 mM MgCl2 (Applied Biosystems, cat. no. 4379878) Nonidet P-40 SP (Roche, cat. no. 11332473001) SuperScript III Reverse Transcriptase with 0.1 M DTT (Invitrogen, cat. no. 18080-044 or 18080-085) RNase Inhibitor (Cloned) (40 U μl−1 ) (Applied Biosystems, cat. no. AM2682) SUPERase-In™ (20 U μl−1 ) (Applied Biosystems, cat. no. AM2694) T4 gene 32 Protein (Roche, cat. no. 972983) Exonuclease I (New England Biolabs, cat. no. M0293S) Terminal Transferase (TdT) (Invitrogen, cat. no. 10533-065 or 10533-073) 100 mM dATP (Promega, cat. no. U1201) Nuclease-free Water, 1 L (Applied Biosystems, cat. no. AM9932) RNase H (Invitrogen, cat. no. 18021-014 or 18021-071) TaKaRa Ex Taq™ HS (Includes: 10× ExTaq Buffer (mg2+ plus) and dNTP mixture) (Takara Bio Inc, cat. no. RR006A or RR006B) QIAquick PCR Purification Kit (250) (Qiagen, cat. no. 28106) QIAquick Gel Extraction Kit (250) (Qiagen, cat. no. 28706) RNeasy Mini Kit (50) (Qiagen, cat. no. 74104) PCR tubes, 0.5 ml (Eppendorf, cat. no. 951010057) PCR tubes, 0.2 ml thin-wall (MLS) Filtered pipettor tips (MLS) SYBR Green PCR Mastermix (Applied Biosystems, cat. no. 4334973) GeneAmp® dNTP Blend (100 mM) (Applied Biosystems, cat. no. N8080261) 3 M sodium acetate (pH 5.5) (Applied Biosystems/Ambion, cat. no. AM9740) 1 M Tris, pH 8.0 (100 ml) (Applied Biosystems/Ambion, AM9855G) Nuclease-free Water (1 L) (Applied Biosystems/Ambion, cat. no. AM9932) 10× NEBuffer2 (New England BioLabs® Inc., B7002S) Ethanol (Sigma-Aldrich®, cat. no. E7023) Ethylene glycol (American Bioanalytical, cat. no. AB00455-01000) Covaris microTUBE with AFA fiber and Snap-Cap with pre-slit Teflon/silicone/Teflon septa (Covaris™ Inc., cat. no. 520045) End-It™ DNA End-Repair Kit (Epicentre®, cat. no. ER0720) DNA Polymerase I (E. coli), (10U μl−1 ) (New England BioLabs® Inc., cat. no. M0209L) Quick Ligation™ kit (New England Biolabs, cat. no. M2200L) SYBR GreenER® qPCR SuperMix Universal (Invitrogen™ Corporation, cat. no. 11762-100) OR SYBR Green PCR Master Mix (Applied Biosystems, cat. no. 4309155) Agilent DNA 1000 Kit (Agilent Technologies, cat. no. 5067-1504) Agencourt® AMPure® 60 ml kit (Agencourt, cat. no. 000130) AmpliTaq® DNA Polymerase, LD with Buffer I (Applied Biosystems, cat. no. N8080157) Cloned Pfu polymerase (2.5 U μl−1 ) (Stratagene, cat. no. 600153) Invitrogen Platinum® PCR SuperMix (Invitrogen™ Corporation, cat. no. 11306-016) Quant-iT™ dsDNA HS Assay Kit, 100 assays (Invitrogen™ Corporation, cat. no. ) SOLiD™ Fragment Library Oligos Kit (Applied Biosystems, cat. no. 4401151) .. Brown-flaming micropipette puller (Sutter Instrument Co., Model P-80) Covaris™ S2 System, (for system materials summary, see “Covaris™ S2 System Materials Summary,” SOLiD ™ System 2.0 Site Preparation Guide .)

    Multiplex Assay:

    Article Title: Viral population analysis and minority-variant detection using short read next-generation sequencing
    Article Snippet: Finally, equal volumes of both reactions were combined producing a near equimolar mixture of all influenza segments and total DNA concentration determined using the Quant-iT PicoGreen dsDNA Picogreen assay (Invitrogen). .. (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane. .. The products were sequenced on an Illumina GAIIx using a paired-end 54 bp run, following the manufacturer's instructions.

    Selection:

    Article Title: The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
    Article Snippet: Paragraph title: DNA preparation and size selection ● TIMING 3 h, depending on the number of samples ... 3| Shear genomic DNA in a microtube using Covaris AFA, according to the manufacturer’s instructions.

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Strain UASWS1009 was isolated from the sewage sludge of a coking plant in Hungary through a selection experiment for highly ammonia-tolerant nitrifying bacteria. .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Sample Prep:

    Article Title: Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry
    Article Snippet: Paired-end genomic libraries were prepared using a Nextera sample preparation kit (Illumina), according to the manufacturer’s protocol. .. An Illumina library was also prepared for isolate 12008, with DNA sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using a Blue Pippin (Sage Science).

    Article Title: Extensive sequencing of seven human genomes to characterize benchmark reference materials
    Article Snippet: For each Reference Material, 12 (or 14 for NA12878) libraries were prepared in parallel using the Illumina TruSeq (LT) DNA PCR-Free Sample Prep Kits (FC-121–3001). .. Genomic DNA (1.5 ug) was fragmented using a Covaris S2 focused ultrasonicator in micro TUBE AFA Fiber Pre-Slit Snap-Cap 6×16 mm micro tubes and the Covaris MicroTUBE holder (covaris part numbers 520045 and 500114, respectively) under the following conditions for a target insert size of 550 base pairs.

    Protein Binding:

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: Bead-coupled plasmids were incubated in the egg extracts to allow protein binding to the plasmid DNA. .. The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris).

    Concentration Assay:

    Article Title: Emergence of the Virulence-Associated PB2 E627K Substitution in a Fatal Human Case of Highly Pathogenic Avian Influenza Virus A(H7N7) Infection as Determined by Illumina Ultra-Deep Sequencing
    Article Snippet: Thermal cycling conditions were as follows: reverse transcription at 50°C for 1 h and denaturation at 95°C for 5 min; enzyme activation of 95°C for 15 min; 45 cycles of 94°C for 30 s, 50°C for 30 s, and 72°C for 1 min; and final extension of 72°C for 10 min. .. Products from the full-genome influenza virus RT-PCR of the pooled chicken samples were diluted to a DNA concentration of 50 ng/μl and sheared to a length of 200 to 400 bp using a Covaris AFA (Covaris, Woburn, MA). .. The sheared fragments were end repaired, A-tailed, and ligated to Illumina sequencing adaptors containing molecular identifier (MID) tags using the NEBNext DNA Library Prep reagent set (New England BioLabs, United Kingdom) to allow for multiplex sequencing per lane.

    Article Title: Viral population analysis and minority-variant detection using short read next-generation sequencing
    Article Snippet: Finally, equal volumes of both reactions were combined producing a near equimolar mixture of all influenza segments and total DNA concentration determined using the Quant-iT PicoGreen dsDNA Picogreen assay (Invitrogen). .. (b) Products from the eight-segment PCR with a DNA concentration of approximately 50 ng µl−1 were sheared to lengths of between 200 and 400 bp using a Covaris AFA (Covaris, Woburn, MA, USA), end-repaired, A-tailed and ligated with Illumina sequencing adaptors containing identifying tags allowing multiplex sequencing of 12 samples per lane. .. The products were sequenced on an Illumina GAIIx using a paired-end 54 bp run, following the manufacturer's instructions.

    Article Title: Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
    Article Snippet: The DNA concentration was measured using the Qubit device and the Quant-It DNA HS Assay (Invitrogen). .. Circularised DNA (130 μl) was sheared in a Covaris MicroTube AFA Fiber (Pre-slit, Snap-cap, 6×16 mm; 2 cycles of 37 s, 10% duty cycle, 200 cycles per burst, 4 intensity, 4 °C) using the Covaris S2 device (Covaris, Massachusetts, USA).

    Molecular Weight:

    Article Title: Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry
    Article Snippet: Genomic DNA for isolate 12008 was prepared by extracting high molecular weight DNA from freeze-dried V. dahliae mycelium using the Macherey-Nagel Nucleospin Plant II kit (Fisher 11912262) for Illumina sequencing and QIAGEN Genomic-tip 500/G kit (Qiagen, Germany) for Pacbio sequencing, which was sequenced on an RSII machine. .. An Illumina library was also prepared for isolate 12008, with DNA sheared using the Covaris M220 with microTUBE-50 (Covaris 520166) and size selected using a Blue Pippin (Sage Science).

    Lysis:

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

    Article Title: RecQ4 promotes the conversion of the pre-initiation complex at a site-specific origin for DNA unwinding in Xenopus egg extracts
    Article Snippet: After incubation in the extracts, the plasmids were briefly washed with EB supplemented with 0.25% NP40 and 1.5 mM ATP; resuspended with 200 μl of EB supplemented with 0.25% NP40, 1.5 mM ATP, and 1% formaldehyde; and incubated for 10 min at room temperature. .. The cross-linked products were washed 3 times with 150 μl of EB containing 0.25% NP40 and 2 times with 150 μl of lysis buffer (140 mM NaCl, 1% TritonX-100, 20 mM β-glycerophosphate, 50 mM NaF, 0.1 mM Na3 VO4 , 0.5 mM sodium pyrophosphate, 1 mM EDTA, and 50 mM HEPES-KOH, pH 7.5), and then resuspended with 130 μl of sonication buffer (lysis buffer supplemented with 1× complete Mini (Roche) and 1 mM PMSF) and transferred into a microTUBE (Covaris). .. The plasmid DNA was sheared to ∼500 bp average size using Covaris S220 (Covaris, USA) with 30 cycles of 15 s sonication at 30 W. The sonicated samples were diluted to give a final concentration of 1 ng DNA/μl, with the sonication buffer containing 5 mg/ml BSA and 0.4 mg/ml salmon sperm, and the magnetic beads were removed with a magnet before immunoprecipitation.

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Covaris microtube afa fiber
    Microtube Afa Fiber, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microtube afa fiber/product/Covaris
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    microtube afa fiber - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    87
    Covaris microtube afa fiber pre slit snap cap
    Microtube Afa Fiber Pre Slit Snap Cap, supplied by Covaris, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/microtube afa fiber pre slit snap cap/product/Covaris
    Average 87 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    microtube afa fiber pre slit snap cap - by Bioz Stars, 2019-10
    87/100 stars
      Buy from Supplier

    99
    Covaris s220
    S220, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s220/product/Covaris
    Average 99 stars, based on 22 article reviews
    Price from $9.99 to $1999.99
    s220 - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    Image Search Results