thermolabile exonuclease i  (New England Biolabs)


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    Structured Review

    New England Biolabs thermolabile exonuclease i
    Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).
    Thermolabile Exonuclease I, 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/thermolabile exonuclease i/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermolabile exonuclease i - by Bioz Stars, 2022-07
    94/100 stars

    Images

    1) Product Images from "Accurate measurement of microsatellite length by disrupting its tandem repeat structure"

    Article Title: Accurate measurement of microsatellite length by disrupting its tandem repeat structure

    Journal: bioRxiv

    doi: 10.1101/2021.12.09.471828

    Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).
    Figure Legend Snippet: Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).

    Techniques Used: Mutagenesis, Amplification, Purification, Polymerase Chain Reaction, Sequencing

    2) Product Images from "McQ – An open-source multiplexed SARS-CoV-2 quantification platform"

    Article Title: McQ – An open-source multiplexed SARS-CoV-2 quantification platform

    Journal: medRxiv

    doi: 10.1101/2020.12.02.20242628

    Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.
    Figure Legend Snippet: Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.

    Techniques Used:

    3) Product Images from "McQ – An open-source multiplexed SARS-CoV-2 quantification platform"

    Article Title: McQ – An open-source multiplexed SARS-CoV-2 quantification platform

    Journal: medRxiv

    doi: 10.1101/2020.12.02.20242628

    Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.
    Figure Legend Snippet: Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.

    Techniques Used:

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    New England Biolabs thermolabile exonuclease i
    Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).
    Thermolabile Exonuclease I, 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/thermolabile exonuclease i/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    thermolabile exonuclease i - by Bioz Stars, 2022-07
    94/100 stars
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    Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).

    Journal: bioRxiv

    Article Title: Accurate measurement of microsatellite length by disrupting its tandem repeat structure

    doi: 10.1101/2021.12.09.471828

    Figure Lengend Snippet: Bench protocol for partial mutagenesis. In step 1, each of the two synthetic templates containing C was partially bisulfite converted. In steps 2-3, about 6*10^4 of these templates underwent 9 cycles of linear amplification by using a biotinylated oligo. In step 4, double-stranded DNA fragments were obtained in another round of linear amplification by using UP1. In step 5, extra free oligo was removed by exonuclease I. After adding carrier DNA, biotinylated DNA fragments were purified by streptavidin beads. In step 6, the exponential PCR was carried out using UP1 and UP3 to generate enough material to prepare the DNA libraries for sequencing. These were sequenced as 2 × 150 bp paired-end runs on MiSeq (steps 7-8).

    Article Snippet: In step 5 extra free oligo was removed by Thermolabile Exonuclease I (NEB).

    Techniques: Mutagenesis, Amplification, Purification, Polymerase Chain Reaction, Sequencing

    Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.

    Journal: medRxiv

    Article Title: McQ – An open-source multiplexed SARS-CoV-2 quantification platform

    doi: 10.1101/2020.12.02.20242628

    Figure Lengend Snippet: Free-floating index primers are a source of background reads. Scatterplots depict number of UMI detected for viral E (pink) and nsp14 (purple) targets in non-template control (NTC) samples (containing only human RNA i.e. representing background levels) in the original samples and the same samples sequenced after an additional Exonuclease I treatment after PCR2 to remove excess index primers. Black line indicates a slope of 1. Sample pool ID and number of NTC samples present in each sample pool are indicated in grey boxes above panels. Sample pools S025 and S066 were present in four variations, but each with identical sample composition.

    Article Snippet: Exonuclease I digest to remove excess indexed P5 and P7 primersTo reduce contamination during sequencing caused by leftover indexed primers, the PCR2 products were optionally treated with thermolabile Exonuclease I (NEB) for 30 min at 37°C followed by 5 min at 85°C.

    Techniques: