amplicons  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 90

    Structured Review

    New England Biolabs amplicons
    DNA methylation and H3K9me3 analysis in Atf7ip and Zmym2 KO cells. a ) Boxplots indicating average DNA methylation over all CpGs covered at least 10x in the mouse genome. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated b) Bisulphite conversion controls from spiked-in Lambda and methylated T7 phage DNA show complete conversion of DNA molecules. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated. c) WGBS data analysis of all annotated ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. d) Individual methylation profiles from targeted bisulfite sequencing experiments for Airn , Kcnqot1 and Peg10 ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. 1000 <t>amplicons</t> per sample were randomly sampled for better visualization. e ) Heatmap showing H3K9me3 at all ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. Shown are library-normalized reads per 20 bp.
    Amplicons, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/New England Biolabs
    Average 90 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    amplicons - by Bioz Stars, 2022-11
    90/100 stars

    Images

    1) Product Images from "DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions"

    Article Title: DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions

    Journal: Nature Genetics

    doi: 10.1038/s41588-022-01210-z

    DNA methylation and H3K9me3 analysis in Atf7ip and Zmym2 KO cells. a ) Boxplots indicating average DNA methylation over all CpGs covered at least 10x in the mouse genome. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated b) Bisulphite conversion controls from spiked-in Lambda and methylated T7 phage DNA show complete conversion of DNA molecules. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated. c) WGBS data analysis of all annotated ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. d) Individual methylation profiles from targeted bisulfite sequencing experiments for Airn , Kcnqot1 and Peg10 ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. 1000 amplicons per sample were randomly sampled for better visualization. e ) Heatmap showing H3K9me3 at all ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. Shown are library-normalized reads per 20 bp.
    Figure Legend Snippet: DNA methylation and H3K9me3 analysis in Atf7ip and Zmym2 KO cells. a ) Boxplots indicating average DNA methylation over all CpGs covered at least 10x in the mouse genome. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated b) Bisulphite conversion controls from spiked-in Lambda and methylated T7 phage DNA show complete conversion of DNA molecules. Interquartile range is shown as a box (IQR) and the lowest and highest values within the range of 1.5 x IQR around the box as whiskers. Number of independent CpGs analyzed are indicated. c) WGBS data analysis of all annotated ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. d) Individual methylation profiles from targeted bisulfite sequencing experiments for Airn , Kcnqot1 and Peg10 ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. 1000 amplicons per sample were randomly sampled for better visualization. e ) Heatmap showing H3K9me3 at all ICRs in wild type, Atf7ip -KO, and Zmym2 -KO mESCs. Shown are library-normalized reads per 20 bp.

    Techniques Used: DNA Methylation Assay, Methylation, Methylation Sequencing

    2) Product Images from "A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome"

    Article Title: A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

    Journal: Nature Communications

    doi: 10.1038/s41467-022-33530-3

    Multiple mtDNA deletions in a clinical sample. a , b Circos plot of the lrPCR products of sample AW6506 showing three full-length lrPCR amplicons – two deletions and wild type, sequenced by Illumina short-read ( a ) and ONT long-read ( b ) instruments. White arrows at positions m.2120 and m.2119 represent forward and reverse primers, respectively. c – e Circos plots of sample AW6506 targeted with the Cas9-mtDNA-enrichment sequenced on a GridIon flow cell showing three populations of mtDNA. c Targeted with the gRNA mt3 (m.3127), all three populations can be observed – two deletions and the wild type; d gRNA mt5 (m.5142) results in two populations – the small deletion and the wild type; e gRNA mt11 (m.11239) results in capturing the wild-type population only. In the circos plots, the reference circle colours denote genes encoding protein subunits of complex I (green), III (sky blue), IV (royal blue), V (light steel blue), ribosomal RNAs (ocean blue), transfer RNAs (ivory), and non-coding region D-loop (grey). f Summary of mean coverage of selected full-length reads and SV proportions in lrPCR amplicons, sequenced on Illumina and GridIon, and Cas9-mtDNA-enriched native molecules, sequenced on GridIon. Source data are provided as a Source Data file.
    Figure Legend Snippet: Multiple mtDNA deletions in a clinical sample. a , b Circos plot of the lrPCR products of sample AW6506 showing three full-length lrPCR amplicons – two deletions and wild type, sequenced by Illumina short-read ( a ) and ONT long-read ( b ) instruments. White arrows at positions m.2120 and m.2119 represent forward and reverse primers, respectively. c – e Circos plots of sample AW6506 targeted with the Cas9-mtDNA-enrichment sequenced on a GridIon flow cell showing three populations of mtDNA. c Targeted with the gRNA mt3 (m.3127), all three populations can be observed – two deletions and the wild type; d gRNA mt5 (m.5142) results in two populations – the small deletion and the wild type; e gRNA mt11 (m.11239) results in capturing the wild-type population only. In the circos plots, the reference circle colours denote genes encoding protein subunits of complex I (green), III (sky blue), IV (royal blue), V (light steel blue), ribosomal RNAs (ocean blue), transfer RNAs (ivory), and non-coding region D-loop (grey). f Summary of mean coverage of selected full-length reads and SV proportions in lrPCR amplicons, sequenced on Illumina and GridIon, and Cas9-mtDNA-enriched native molecules, sequenced on GridIon. Source data are provided as a Source Data file.

    Techniques Used:

    3) Product Images from "Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool"

    Article Title: Optimization of Oxford Nanopore Technology Sequencing Workflow for Detection of Amplicons in Real Time Using ONT-DART Tool

    Journal: Genes

    doi: 10.3390/genes13101785

    Detected organism counts. Counts for each method out of a total of 36, per method per flow cell type (Green is detected, Pink is not detected). Detection in this analysis means all expected amplicons had a filtered aligned read count ≥1. NTCs are not included.
    Figure Legend Snippet: Detected organism counts. Counts for each method out of a total of 36, per method per flow cell type (Green is detected, Pink is not detected). Detection in this analysis means all expected amplicons had a filtered aligned read count ≥1. NTCs are not included.

    Techniques Used:

    4) Product Images from "Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater"

    Article Title: Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater

    Journal: Environmental Science & Technology

    doi: 10.1021/acs.est.2c04727

    Detection Mechanisms of HF-RT-LAMP In the presence of SARS-CoV-2, quantities of amplicons are generated via RT-LAMP, which could activate the trans-cleavage of the Cas12a–gRNA complex. Then, the complex unspecifically and readily cleaves ssDNA probes. Fluorescence is generated due to the separation of the fluorophore (FAM) and quencher (BHQ1) in the fluorescence method. In the lateral flow method, a strong test-stained band is produced due to the separation of FAM and biotin because the former could combine with modified GNPs and becomes immobilized on the test line, while the latter is fixed on the control line. However, in the absence of SARS-CoV-2, no amplicons are generated, and the Cas12a–gRNA complex cannot be activated. Therefore, the probes remain intact, and no fluorescence is observed due to the short distance between the quencher and fluorophore in the fluorescence method, while a slight test band is observed with the probes that are mostly fixed on the control line due to their biotin groups.
    Figure Legend Snippet: Detection Mechanisms of HF-RT-LAMP In the presence of SARS-CoV-2, quantities of amplicons are generated via RT-LAMP, which could activate the trans-cleavage of the Cas12a–gRNA complex. Then, the complex unspecifically and readily cleaves ssDNA probes. Fluorescence is generated due to the separation of the fluorophore (FAM) and quencher (BHQ1) in the fluorescence method. In the lateral flow method, a strong test-stained band is produced due to the separation of FAM and biotin because the former could combine with modified GNPs and becomes immobilized on the test line, while the latter is fixed on the control line. However, in the absence of SARS-CoV-2, no amplicons are generated, and the Cas12a–gRNA complex cannot be activated. Therefore, the probes remain intact, and no fluorescence is observed due to the short distance between the quencher and fluorophore in the fluorescence method, while a slight test band is observed with the probes that are mostly fixed on the control line due to their biotin groups.

    Techniques Used: Generated, Fluorescence, Staining, Produced, Modification

    RT-LAMP performance for the detection of N, E, and S gene fragments. (a–c) Gel electrophoretic characterization of the N, E, and S gene amplicons. Lines 1 and 2 of panel (a–c) represent the marker and negative control, respectively, lines a3–12: 1.5 × 10 0 to 1.5 × 10 9 copies/μL according to a 10-fold increase; b3–12: 2.6 × 10 0 to 2.6 × 10 9 copies/μL according to a 10-fold increase; and c3–12: 5 × 10 –1 to 5 × 10 8 copies/μL according to a 10-fold increase. (d–f) Normalized intensity at the endpoint of the N, E, and S gene fragments. (g–i) Quantitative curves of the N, E, and S genes.
    Figure Legend Snippet: RT-LAMP performance for the detection of N, E, and S gene fragments. (a–c) Gel electrophoretic characterization of the N, E, and S gene amplicons. Lines 1 and 2 of panel (a–c) represent the marker and negative control, respectively, lines a3–12: 1.5 × 10 0 to 1.5 × 10 9 copies/μL according to a 10-fold increase; b3–12: 2.6 × 10 0 to 2.6 × 10 9 copies/μL according to a 10-fold increase; and c3–12: 5 × 10 –1 to 5 × 10 8 copies/μL according to a 10-fold increase. (d–f) Normalized intensity at the endpoint of the N, E, and S gene fragments. (g–i) Quantitative curves of the N, E, and S genes.

    Techniques Used: Marker, Negative Control

    5) Product Images from "Rapid Amplicon Nanopore Sequencing (RANS) for the Differential Diagnosis of Monkeypox Virus and Other Vesicle-Forming Pathogens"

    Article Title: Rapid Amplicon Nanopore Sequencing (RANS) for the Differential Diagnosis of Monkeypox Virus and Other Vesicle-Forming Pathogens

    Journal: Viruses

    doi: 10.3390/v14081817

    The RANS approach for the differential diagnosis of MPXV and other vesicle-forming pathogens. The figure elaborates on the rapid and comprehensive RANS procedure. The procedure starts with a suspected clinical sample and ends with a specific sequence-based identification in a timeframe of a few hours. (I). Multiplex PCR amplification, in which primers that are mutual for a group of viruses (for example OPVs) are used to amplify the whole group. A 5′ phosphate (using a phosphorylated primer) and a dA tail (using the terminal transferase activity of the DNA polymerase and a final extension step of 15 min) were concurrently added at this stage. Next (II), an adapter ligation was performed, wherein the ONT-proprietary adapters, which were attached to a motor enzyme, ligated to the ends of the strands. The final step (III) involved library loading, sequencing, and base calling: The amplicons were loaded onto a Flongle apparatus and based-called FASTQ files were generated as the DNA was translocated through the nanopores. Finally, bioinformatic comparisons between the resulting sequences to a relevant database pinpointed the specific agent (in bold). The different viruses’ abbreviations are detailed in Table 1 legend.
    Figure Legend Snippet: The RANS approach for the differential diagnosis of MPXV and other vesicle-forming pathogens. The figure elaborates on the rapid and comprehensive RANS procedure. The procedure starts with a suspected clinical sample and ends with a specific sequence-based identification in a timeframe of a few hours. (I). Multiplex PCR amplification, in which primers that are mutual for a group of viruses (for example OPVs) are used to amplify the whole group. A 5′ phosphate (using a phosphorylated primer) and a dA tail (using the terminal transferase activity of the DNA polymerase and a final extension step of 15 min) were concurrently added at this stage. Next (II), an adapter ligation was performed, wherein the ONT-proprietary adapters, which were attached to a motor enzyme, ligated to the ends of the strands. The final step (III) involved library loading, sequencing, and base calling: The amplicons were loaded onto a Flongle apparatus and based-called FASTQ files were generated as the DNA was translocated through the nanopores. Finally, bioinformatic comparisons between the resulting sequences to a relevant database pinpointed the specific agent (in bold). The different viruses’ abbreviations are detailed in Table 1 legend.

    Techniques Used: Sequencing, Multiplex Assay, Polymerase Chain Reaction, Amplification, Activity Assay, Ligation, Generated

    6) Product Images from "Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet"

    Article Title: Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet

    Journal: Animals : an Open Access Journal from MDPI

    doi: 10.3390/ani12162011

    Principal Coordinate Analysis (PCoA) showing the weighted UniFrac distance matrix of bacterial 16S rRNA amplicons from fecal samples of cow (red color) and goat (blue color) groups. Each dot represents one sample. The percentage of variation explained by the plotted principal coordinates is indicated on the axes.
    Figure Legend Snippet: Principal Coordinate Analysis (PCoA) showing the weighted UniFrac distance matrix of bacterial 16S rRNA amplicons from fecal samples of cow (red color) and goat (blue color) groups. Each dot represents one sample. The percentage of variation explained by the plotted principal coordinates is indicated on the axes.

    Techniques Used:

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    New England Biolabs nebnext single cell low input cdna synthesis amplification module
    Nebnext Single Cell Low Input Cdna Synthesis Amplification Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext single cell low input cdna synthesis amplification module/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nebnext single cell low input cdna synthesis amplification module - by Bioz Stars, 2022-11
    94/100 stars
      Buy from Supplier

    97
    New England Biolabs isothermal amplification buffer
    Isothermal Amplification Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/isothermal amplification buffer/product/New England Biolabs
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    isothermal amplification buffer - by Bioz Stars, 2022-11
    97/100 stars
      Buy from Supplier

    90
    New England Biolabs insert amplificate
    Insert Amplificate, supplied by New England Biolabs, 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/insert amplificate/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    insert amplificate - by Bioz Stars, 2022-11
    90/100 stars
      Buy from Supplier

    Image Search Results