nextera dna flex enrichment  (New England Biolabs)


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    Name:
    NEBNext rRNA Depletion Kit Bacteria
    Description:
    The NEBNext rRNA Depletion Kits Bacteria employ the NEBNext RNase H based RNA depletion workflow to deplete ribosomal rRNA 5S 16S and 23S from gram positive and gram negative organisms The kit is effective with both intact and degraded RNA preparations from monocultures or samples with mixed bacterial species
    Catalog Number:
    e7850l
    Price:
    1080
    Size:
    24 rxns
    Category:
    RNA Purification Kit Components
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    New England Biolabs nextera dna flex enrichment
    NEBNext rRNA Depletion Kit Bacteria
    The NEBNext rRNA Depletion Kits Bacteria employ the NEBNext RNase H based RNA depletion workflow to deplete ribosomal rRNA 5S 16S and 23S from gram positive and gram negative organisms The kit is effective with both intact and degraded RNA preparations from monocultures or samples with mixed bacterial species
    https://www.bioz.com/result/nextera dna flex enrichment/product/New England Biolabs
    Average 84 stars, based on 138 article reviews
    Price from $9.99 to $1999.99
    nextera dna flex enrichment - by Bioz Stars, 2020-10
    84/100 stars

    Images

    1) Product Images from "A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2"

    Article Title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2

    Journal: bioRxiv

    doi: 10.1101/2020.05.11.088724

    Performance metrics for Illumina DNA Flex Enrichment Protocol. Number of total reads generated per sample using the Illumina Nextera DNA Flex Enrichment workflow relative to: A) Sample N1 Ct value; B) Sample N2 Ct value. Percentage of reads aligned to a human reference genome using the Illumina Nextera DNA Flex Enrichment workflow relative to: C) Sample N1 Ct value; D) Sample N2 Ct value.
    Figure Legend Snippet: Performance metrics for Illumina DNA Flex Enrichment Protocol. Number of total reads generated per sample using the Illumina Nextera DNA Flex Enrichment workflow relative to: A) Sample N1 Ct value; B) Sample N2 Ct value. Percentage of reads aligned to a human reference genome using the Illumina Nextera DNA Flex Enrichment workflow relative to: C) Sample N1 Ct value; D) Sample N2 Ct value.

    Techniques Used: Generated

    Comparison of sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows on clinical specimens spanning a range of viral loads. A) Samples with N1 and N2 Ct values ranging from approximately 20-35 chosen for testing of SARS-CoV-2 sequencing workflows. B) Evenness of representation of amplicons for different workflows as a function of sample N1 Ct value. Percentage of genome coverage at 100x at different subsampled read depths for each sample when sequenced using the following approaches: D) Illumina Nextera DNA Enrichment; E) ARTIC v3 with TruSeq library preparation. F) Tailed amplicon v1 (2 pool amplification); G) Tailed amplicon v2 (4 pool amplification)
    Figure Legend Snippet: Comparison of sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows on clinical specimens spanning a range of viral loads. A) Samples with N1 and N2 Ct values ranging from approximately 20-35 chosen for testing of SARS-CoV-2 sequencing workflows. B) Evenness of representation of amplicons for different workflows as a function of sample N1 Ct value. Percentage of genome coverage at 100x at different subsampled read depths for each sample when sequenced using the following approaches: D) Illumina Nextera DNA Enrichment; E) ARTIC v3 with TruSeq library preparation. F) Tailed amplicon v1 (2 pool amplification); G) Tailed amplicon v2 (4 pool amplification)

    Techniques Used: Sequencing, Amplification

    Methods for SARS-CoV-2 genome sequencing compared in this study. A) In Illumina’s Nextera DNA Flex Enrichment protocol cDNA is tagmented and made into barcoded sequencing libraries, which are then enriched using sequence capture with a respiratory virus panel containing probes against SARS-CoV-2. B) In the ARTIC protocol, first strand cDNA is enriched by amplifying with two pools of primers to generate amplicons tiling the SARS-CoV-2 genome. These amplicons are then subjected to either Illumina or Oxford Nanopore library preparation, using methods that either directly add adapters to the ends of the amplicons or fragment them to enable sequencing on a wider variety of Illumina instruments. C) The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. This allows functional sequencing libraries to be created through a second indexing PCR reaction that adds sample-specific barcodes and flow cell adapters.
    Figure Legend Snippet: Methods for SARS-CoV-2 genome sequencing compared in this study. A) In Illumina’s Nextera DNA Flex Enrichment protocol cDNA is tagmented and made into barcoded sequencing libraries, which are then enriched using sequence capture with a respiratory virus panel containing probes against SARS-CoV-2. B) In the ARTIC protocol, first strand cDNA is enriched by amplifying with two pools of primers to generate amplicons tiling the SARS-CoV-2 genome. These amplicons are then subjected to either Illumina or Oxford Nanopore library preparation, using methods that either directly add adapters to the ends of the amplicons or fragment them to enable sequencing on a wider variety of Illumina instruments. C) The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. This allows functional sequencing libraries to be created through a second indexing PCR reaction that adds sample-specific barcodes and flow cell adapters.

    Techniques Used: Sequencing, Amplification, Functional Assay, Polymerase Chain Reaction

    Coverage metrics by method for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. Percentage of genome coverage at 10x at different subsampled read depths for each sample when sequenced using the following approaches: A) Illumina Nextera DNA Enrichment; B) ARTIC v3 with TruSeq library preparation. C) Tailed amplicon v1 (2 pool amplification); D) Tailed amplicon v2 (4 pool amplification).
    Figure Legend Snippet: Coverage metrics by method for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. Percentage of genome coverage at 10x at different subsampled read depths for each sample when sequenced using the following approaches: A) Illumina Nextera DNA Enrichment; B) ARTIC v3 with TruSeq library preparation. C) Tailed amplicon v1 (2 pool amplification); D) Tailed amplicon v2 (4 pool amplification).

    Techniques Used: Sequencing, Amplification

    2) Product Images from "A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2"

    Article Title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2

    Journal: bioRxiv

    doi: 10.1101/2020.05.11.088724

    Performance metrics for Illumina DNA Flex Enrichment Protocol. Number of total reads generated per sample using the Illumina Nextera DNA Flex Enrichment workflow relative to: A) Sample N1 Ct value; B) Sample N2 Ct value. Percentage of reads aligned to a human reference genome using the Illumina Nextera DNA Flex Enrichment workflow relative to: C) Sample N1 Ct value; D) Sample N2 Ct value.
    Figure Legend Snippet: Performance metrics for Illumina DNA Flex Enrichment Protocol. Number of total reads generated per sample using the Illumina Nextera DNA Flex Enrichment workflow relative to: A) Sample N1 Ct value; B) Sample N2 Ct value. Percentage of reads aligned to a human reference genome using the Illumina Nextera DNA Flex Enrichment workflow relative to: C) Sample N1 Ct value; D) Sample N2 Ct value.

    Techniques Used: Generated

    Comparison of sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows on clinical specimens spanning a range of viral loads. A) Samples with N1 and N2 Ct values ranging from approximately 20-35 chosen for testing of SARS-CoV-2 sequencing workflows. B) Evenness of representation of amplicons for different workflows as a function of sample N1 Ct value. Percentage of genome coverage at 100x at different subsampled read depths for each sample when sequenced using the following approaches: D) Illumina Nextera DNA Enrichment; E) ARTIC v3 with TruSeq library preparation. F) Tailed amplicon v1 (2 pool amplification); G) Tailed amplicon v2 (4 pool amplification)
    Figure Legend Snippet: Comparison of sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows on clinical specimens spanning a range of viral loads. A) Samples with N1 and N2 Ct values ranging from approximately 20-35 chosen for testing of SARS-CoV-2 sequencing workflows. B) Evenness of representation of amplicons for different workflows as a function of sample N1 Ct value. Percentage of genome coverage at 100x at different subsampled read depths for each sample when sequenced using the following approaches: D) Illumina Nextera DNA Enrichment; E) ARTIC v3 with TruSeq library preparation. F) Tailed amplicon v1 (2 pool amplification); G) Tailed amplicon v2 (4 pool amplification)

    Techniques Used: Sequencing, Amplification

    Methods for SARS-CoV-2 genome sequencing compared in this study. A) In Illumina’s Nextera DNA Flex Enrichment protocol cDNA is tagmented and made into barcoded sequencing libraries, which are then enriched using sequence capture with a respiratory virus panel containing probes against SARS-CoV-2. B) In the ARTIC protocol, first strand cDNA is enriched by amplifying with two pools of primers to generate amplicons tiling the SARS-CoV-2 genome. These amplicons are then subjected to either Illumina or Oxford Nanopore library preparation, using methods that either directly add adapters to the ends of the amplicons or fragment them to enable sequencing on a wider variety of Illumina instruments. C) The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. This allows functional sequencing libraries to be created through a second indexing PCR reaction that adds sample-specific barcodes and flow cell adapters.
    Figure Legend Snippet: Methods for SARS-CoV-2 genome sequencing compared in this study. A) In Illumina’s Nextera DNA Flex Enrichment protocol cDNA is tagmented and made into barcoded sequencing libraries, which are then enriched using sequence capture with a respiratory virus panel containing probes against SARS-CoV-2. B) In the ARTIC protocol, first strand cDNA is enriched by amplifying with two pools of primers to generate amplicons tiling the SARS-CoV-2 genome. These amplicons are then subjected to either Illumina or Oxford Nanopore library preparation, using methods that either directly add adapters to the ends of the amplicons or fragment them to enable sequencing on a wider variety of Illumina instruments. C) The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. This allows functional sequencing libraries to be created through a second indexing PCR reaction that adds sample-specific barcodes and flow cell adapters.

    Techniques Used: Sequencing, Amplification, Functional Assay, Polymerase Chain Reaction

    Coverage metrics by method for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. Percentage of genome coverage at 10x at different subsampled read depths for each sample when sequenced using the following approaches: A) Illumina Nextera DNA Enrichment; B) ARTIC v3 with TruSeq library preparation. C) Tailed amplicon v1 (2 pool amplification); D) Tailed amplicon v2 (4 pool amplification).
    Figure Legend Snippet: Coverage metrics by method for sequence capture, ARTIC v3 amplicon, and tailed amplicon workflows. Percentage of genome coverage at 10x at different subsampled read depths for each sample when sequenced using the following approaches: A) Illumina Nextera DNA Enrichment; B) ARTIC v3 with TruSeq library preparation. C) Tailed amplicon v1 (2 pool amplification); D) Tailed amplicon v2 (4 pool amplification).

    Techniques Used: Sequencing, Amplification

    Related Articles

    RNA Sequencing Assay:

    Article Title: A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries
    Article Snippet: .. RNA-seq data analysis indicated that the RTR2D method yielded highly correlative transcriptomic landscape with that of the NEBNext rRNA Depletion Kit at both mRNA and lncRNA levels. .. RNA-seq data analysis indicated that the RTR2D method yielded highly correlative transcriptomic landscape with that of the NEBNext rRNA Depletion Kit at both mRNA and lncRNA levels.

    Article Title: A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries
    Article Snippet: .. RNA-seq data analysis indicated that RTR2D yielded highly correlative transcriptome landscape with that of NEBNext rRNA Depletion Kit at both mRNA and lncRNA levels. .. In a proof-of-principle study, we found that RNA-seq dataset from RTR2D-depleted rRNA samples identified more differentially expressed mRNAs and lncRNAs regulated by Nutlin3A in human osteosarcoma cells than that from NEBNext rRNA Depletion samples, suggesting that RTR2D may have lower off-target depletion of non-rRNA transcripts.

    Article Title: A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries
    Article Snippet: .. RNA-seq analysis reveals that the transcriptomic profiles of the RTR2D-depleted samples are comparable with those of the NEB kit-depleted samples We further analyzed the RNA-seq data quality of the libraries prepared from the RTR2D-based rRNA-depleted samples, compared with those prepared from the NEBNext rRNA Depletion Kit. .. RNA-seq analysis reveals that the transcriptomic profiles of the RTR2D-depleted samples are comparable with those of the NEB kit-depleted samples We further analyzed the RNA-seq data quality of the libraries prepared from the RTR2D-based rRNA-depleted samples, compared with those prepared from the NEBNext rRNA Depletion Kit.

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    New England Biolabs nebnext ultra ii rna first strand synthesis module
    Nebnext Ultra Ii Rna First Strand Synthesis Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 4 article reviews
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