covaris s2  (Covaris)


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    Structured Review

    Covaris covaris s2
    Covaris S2, supplied by Covaris, used in various techniques. Bioz Stars score: 94/100, based on 219 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/covaris s2/product/Covaris
    Average 94 stars, based on 219 article reviews
    Price from $9.99 to $1999.99
    covaris s2 - by Bioz Stars, 2020-07
    94/100 stars

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    Related Articles

    Sample Prep:

    Article Title: LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization.
    Article Snippet: .. Detailed procedures were according to Chavez's publication.26 Briefly, DNA (3 μg) was sonicated at intensity 4 for 200 cycles per burst for 55 seconds (Covaris S2), and DNA fragments were end-repaired, ATPtailed, and adapter-ligated with the Sample Preparation Kit (Illumina). .. Then DNA was recovered by AMPure XP Beads and used for methylated DNA immunoprecipitation (MeDIP) using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode) according to the manufacturer's protocol.

    Methylation:

    Article Title: Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
    Article Snippet: .. EM-seq libraries and Methylation analysis Fifty nanograms of cannabis genomic DNA (with spike-in controls: unmethylated lambda DNA and CpG methylated pUC19 DNA) was sheared to 300bp with a Covaris S2. .. This DNA was end repaired and adaptor ligated utilizing the NEBNext EM-Seq protocol according to the manufacturers instruction.

    Lambda DNA Preparation:

    Article Title: Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
    Article Snippet: .. EM-seq libraries and Methylation analysis Fifty nanograms of cannabis genomic DNA (with spike-in controls: unmethylated lambda DNA and CpG methylated pUC19 DNA) was sheared to 300bp with a Covaris S2. .. This DNA was end repaired and adaptor ligated utilizing the NEBNext EM-Seq protocol according to the manufacturers instruction.

    Purification:

    Article Title: MeCP2 mediates transgenerational transmission of chronic pain.
    Article Snippet: .. The purified cDNA was sheared by Covaris S2 into 150–350 bp fragments. .. The sequencing library was constructed by over 10 ng of the purified cDNA from each neuron with Ovation Ultralow Library System V2 (Nugen) following the manufacturer’s protocol.

    Sequencing:

    Article Title: NF1 patient missense variants predict a role for ATM in modifying neurofibroma initiation.
    Article Snippet: .. In Neurofibromatosis type 1, NF1 gene mutations in Schwann cells (SC) drive benign plexiform neurofibroma (PNF), and no additional SC changes explain patient-to-patient variability in tumor number. ..

    Sonication:

    Article Title: LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization.
    Article Snippet: .. Detailed procedures were according to Chavez's publication.26 Briefly, DNA (3 μg) was sonicated at intensity 4 for 200 cycles per burst for 55 seconds (Covaris S2), and DNA fragments were end-repaired, ATPtailed, and adapter-ligated with the Sample Preparation Kit (Illumina). .. Then DNA was recovered by AMPure XP Beads and used for methylated DNA immunoprecipitation (MeDIP) using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode) according to the manufacturer's protocol.

    Article Title: NF1 patient missense variants predict a role for ATM in modifying neurofibroma initiation.
    Article Snippet: .. In Neurofibromatosis type 1, NF1 gene mutations in Schwann cells (SC) drive benign plexiform neurofibroma (PNF), and no additional SC changes explain patient-to-patient variability in tumor number. ..

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  • 92
    Covaris sonicator covaris s2
    Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a <t>Covaris</t> S2 sonicator.
    Sonicator Covaris S2, supplied by Covaris, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sonicator covaris s2/product/Covaris
    Average 92 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    sonicator covaris s2 - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    94
    Covaris covaris s2
    Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a <t>Covaris</t> S2 sonicator.
    Covaris S2, supplied by Covaris, used in various techniques. Bioz Stars score: 94/100, based on 219 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/covaris s2/product/Covaris
    Average 94 stars, based on 219 article reviews
    Price from $9.99 to $1999.99
    covaris s2 - by Bioz Stars, 2020-07
    94/100 stars
      Buy from Supplier

    90
    Covaris reference germline dna
    Analysis of the primary tumour reveals tumour heterogeneity. (A) Single-nucleotide variations in chromosomal <t>DNA</t> from the diagnostic biopsy of the primary tumour and the radical surgery 2 months after the initial biopsy. n.d., not detected. (B) Copy number determination of KIT and NLGN4X in the diagnostic biopsy and in tissue from the subsequent surgical excision when compared with <t>germline</t> DNA by using droplet digital PCR. *** P
    Reference Germline Dna, supplied by Covaris, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/reference germline dna/product/Covaris
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    reference germline dna - by Bioz Stars, 2020-07
    90/100 stars
      Buy from Supplier

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    Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Journal: Scientific Reports

    Article Title: Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads

    doi: 10.1038/s41598-018-27819-x

    Figure Lengend Snippet: Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Article Snippet: After conducting the three different Y chromosome isolation processes, physical fragmentation was performed with a sonicator Covaris S2, workflow of all the samples was described in Fig. .

    Techniques: Flow Cytometry, Cytometry, Laser Capture Microdissection, Cell Culture, Incubation, Staining, Centrifugation, Sequencing

    Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Journal: Scientific Reports

    Article Title: Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads

    doi: 10.1038/s41598-018-27819-x

    Figure Lengend Snippet: Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Article Snippet: Samples quantification After conducting the three different Y chromosome isolation processes, physical fragmentation was performed with a sonicator Covaris S2, workflow of all the samples was described in Fig. .

    Techniques: Flow Cytometry, Cytometry, Laser Capture Microdissection, Cell Culture, Incubation, Staining, Centrifugation, Sequencing

    Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Journal: Scientific Reports

    Article Title: Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads

    doi: 10.1038/s41598-018-27819-x

    Figure Lengend Snippet: Overview of the three technologies used in this study (flow cytometry capture, laser capture microdissection, magnetic streptavidin-bead capture). For all three processes, human lymphocytes were cultured overnight, then phytohaemagglutinin (PHA) and colcemid were added to achieve a high mitotic index and accumulation of cells in metaphase. Later, metaphase chromosomes were extracted from the lymphocytes. ( A ) For flow cytometry capture, the extracted chromosomes were incubated with a specific biotin Y chromosome probe and stained with streptavidin-PE and DAPI. Y chromosomes were then sorted in a FACSAria flow cytometer. The sorted chromosomes were collected in Eppendorf (Hamburg, Germany) tubes in ddH 2 O (double-distilled water) for further processing. ( B ) For laser capture microdissection, individual chromosomes were hybridized with Y chromosome-specific probes conjugated with FITC (green), counterstained with DAPI (blue) and mounted on slides covered by polyethylene membranes. On these slides, they were selected and catapulted by the laser pressure catapulting (LPC) function in a Zeiss PALM MicroBeam IV Laser Microdissector. Y chromosomes were captured within the cap and dissolved in TE buffer. The cap was closed and the sample was spun down by centrifugation. ( C ) For magnetic streptavidin-bead capture, chromosomes were incubated with a specific biotin Y chromosome probe as in the previous procedure. Dynabeads MyOne streptavidin beads were added to the probe Y chromosome mixture and magnetic separation was performed to capture the Y chromosome on a magnetic rack. Finally, in all cases, physical fragmentation was performed before library prep and sequencing with a Covaris S2 sonicator.

    Article Snippet: We degassed the samples in a Covaris S2 instrument for 30 min before use, chilled to 5 °C and set up the Covaris S2 for shearing as described in Table .

    Techniques: Flow Cytometry, Cytometry, Laser Capture Microdissection, Cell Culture, Incubation, Staining, Centrifugation, Sequencing

    Analysis of the primary tumour reveals tumour heterogeneity. (A) Single-nucleotide variations in chromosomal DNA from the diagnostic biopsy of the primary tumour and the radical surgery 2 months after the initial biopsy. n.d., not detected. (B) Copy number determination of KIT and NLGN4X in the diagnostic biopsy and in tissue from the subsequent surgical excision when compared with germline DNA by using droplet digital PCR. *** P

    Journal: Annals of Oncology

    Article Title: Distinct subclonal tumour responses to therapy revealed by circulating cell-free DNA

    doi: 10.1093/annonc/mdw278

    Figure Lengend Snippet: Analysis of the primary tumour reveals tumour heterogeneity. (A) Single-nucleotide variations in chromosomal DNA from the diagnostic biopsy of the primary tumour and the radical surgery 2 months after the initial biopsy. n.d., not detected. (B) Copy number determination of KIT and NLGN4X in the diagnostic biopsy and in tissue from the subsequent surgical excision when compared with germline DNA by using droplet digital PCR. *** P

    Article Snippet: For cfDNA analysis, 2 ng cfDNA or reference germline DNA (sheared to ∼150 bp using an S2 series focused-ultrasonicator, Covaris, Woburn, MA) was used directly for analysis.

    Techniques: Diagnostic Assay, Digital PCR