microbiome dna enrichment kit  (New England Biolabs)


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    Name:
    NEBNext Microbiome DNA Enrichment Kit
    Description:
    NEBNext Microbiome DNA Enrichment Kit 24 rxns
    Catalog Number:
    e2612l
    Price:
    729
    Size:
    24 rxns
    Category:
    Genomic DNA Purification Kits
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    Structured Review

    New England Biolabs microbiome dna enrichment kit
    NEBNext Microbiome DNA Enrichment Kit
    NEBNext Microbiome DNA Enrichment Kit 24 rxns
    https://www.bioz.com/result/microbiome dna enrichment kit/product/New England Biolabs
    Average 95 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    microbiome dna enrichment kit - by Bioz Stars, 2020-02
    95/100 stars

    Images

    1) Product Images from "Phylogenomics and barcoding of Panax: toward the identification of ginseng species"

    Article Title: Phylogenomics and barcoding of Panax: toward the identification of ginseng species

    Journal: BMC Evolutionary Biology

    doi: 10.1186/s12862-018-1160-y

    Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA
    Figure Legend Snippet: Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA

    Techniques Used: Methylation

    2) Product Images from "Phylogenomics and barcoding of Panax: toward the identification of ginseng species"

    Article Title: Phylogenomics and barcoding of Panax: toward the identification of ginseng species

    Journal: BMC Evolutionary Biology

    doi: 10.1186/s12862-018-1160-y

    Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA
    Figure Legend Snippet: Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA

    Techniques Used: Methylation

    3) Product Images from "Gut Microbial Dynamics during Conventionalization of Germfree Chicken"

    Article Title: Gut Microbial Dynamics during Conventionalization of Germfree Chicken

    Journal: mSphere

    doi: 10.1128/mSphere.00035-19

    Genus-level distribution of gut microbiome in the gnotobiotic chicken inoculated with intestinal material from feral chickens. The pooled inoculum, derived from 6 healthy feral chickens, was orally inoculated to gnotobiotic chicken on day 3 after hatch. Birds were euthanized on day 9 ( n = 7) and day 18 ( n = 9) of age, and cecal contents were collected for DNA isolation. The metagenomic functional analysis was performed in MG-RAST using the RefSeq database with a maximum E value at 10 −5 and minimum identity of 60%. Phylogenetic tables were generated in MG-RAST, and analysis was conducted using Explicet software.
    Figure Legend Snippet: Genus-level distribution of gut microbiome in the gnotobiotic chicken inoculated with intestinal material from feral chickens. The pooled inoculum, derived from 6 healthy feral chickens, was orally inoculated to gnotobiotic chicken on day 3 after hatch. Birds were euthanized on day 9 ( n = 7) and day 18 ( n = 9) of age, and cecal contents were collected for DNA isolation. The metagenomic functional analysis was performed in MG-RAST using the RefSeq database with a maximum E value at 10 −5 and minimum identity of 60%. Phylogenetic tables were generated in MG-RAST, and analysis was conducted using Explicet software.

    Techniques Used: Derivative Assay, DNA Extraction, Functional Assay, RAST Test, Generated, Software

    Predicted functional profile at the subsystem level of the microbiome in feral and gnotobiotic chickens. The pooled inoculum was derived from 6 healthy feral chickens. Birds were inoculated on day 3 after hatch and were euthanized at 9 days ( n = 7) and 18 days ( n = 9) of age, and cecal contents were collected for DNA isolation. The functional analysis was performed using subsystems information based on contigs from the MG-RAST database with an E value at 10 −5 , minimum identity at 60%, and a minimum read length of 100. Heat map was constructed in the Morpheus server ( https://software.broadinstitute.org/morpheus ) with a Euclidean distance matrix and average clustering method.
    Figure Legend Snippet: Predicted functional profile at the subsystem level of the microbiome in feral and gnotobiotic chickens. The pooled inoculum was derived from 6 healthy feral chickens. Birds were inoculated on day 3 after hatch and were euthanized at 9 days ( n = 7) and 18 days ( n = 9) of age, and cecal contents were collected for DNA isolation. The functional analysis was performed using subsystems information based on contigs from the MG-RAST database with an E value at 10 −5 , minimum identity at 60%, and a minimum read length of 100. Heat map was constructed in the Morpheus server ( https://software.broadinstitute.org/morpheus ) with a Euclidean distance matrix and average clustering method.

    Techniques Used: Functional Assay, Derivative Assay, DNA Extraction, RAST Test, Construct, Software

    Related Articles

    Functional Assay:

    Article Title: Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
    Article Snippet: Genomic DNA (gDNA) was extracted with phenol/chloroform/isoamylalcohol solution (25:24:1, v /v ) adhering to the protocol provided by Pacific Biosciences in combination with phase lock gels for phase separation (VWR International, Radnor, USA). gDNA was concentrated and washed using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol from New England Biolabs . .. The library construction and Single-Molecule Real-Time sequencing (SMRT) was done on the Pacific Biosciences RS II platform at the Functional Genomic Center Zurich, Zurich, Switzerland.

    Centrifugation:

    Article Title: Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno
    Article Snippet: .. Strain Cad16T was anaerobically grown in Pfennigs medium [ ] Cells were collected by centrifugation for 15 min at 10,600 g. DNA was extracted using phenol/chloroform/isoamylalcohol solution (25:24:1, v / v , Sigma, Buchs, Switzerland) following the protocol provided by Pacific Biosciences [ ] in combination with phase lock gels (VWR International). gDNA was purified using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol form New England Biolabs [ ]. .. Purity of the DNA was tested using the Qbit U V /VIS absorption reader (Thermo Fisher Scientific, Rheinach, Switzerland).

    Article Title: Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno
    Article Snippet: .. Growth conditions and genomic DNA preparation Strain Cad16T was anaerobically grown in Pfennigs medium [ ] Cells were collected by centrifugation for 15 min at 10,600 g. DNA was extracted using phenol/chloroform/isoamylalcohol solution (25:24:1, v /v , Sigma, Buchs, Switzerland) following the protocol provided by Pacific Biosciences [ ] in combination with phase lock gels (VWR International). gDNA was purified using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol form New England Biolabs [ ]. .. Purity of the DNA was tested using the Qbit UV /VIS absorption reader (Thermo Fisher Scientific, Rheinach, Switzerland).

    Amplification:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA. .. The ligated DNA was cleaned with HighPrep beads and subjected to amplification via PCR as follows: initial denaturation at 98˚C for 2 min; 10 cycles of denaturation at 98˚C for 30 sec, annealing at 65˚C for 30 sec and extension at 72˚C for 60 sec; and a final extension at 72˚C for 4 min) using the primers provided by NEXTFlex DNA Sequencing kit.

    Article Title: A comprehensive analysis of breast cancer microbiota and host gene expression
    Article Snippet: The DNA concentrations were measured by Qubit dsDNA HS Assay Kit (PN Q32854 Thermo Fisher Scientific Inc., Waltham, MA) and samples with sufficient DNA were enriched for microbial DNA using the NEBNext® Microbiome DNA Enrichment Kit (PN E2612L, New England Biolabs, Ipswich, MA). .. The V3-V5 region of the 16S-rRNA gene were amplified with a two-step PCR protocol, and then Illumina flow cell adaptors containing indices were incorporated [ ].

    Construct:

    Article Title: Draft Genome Sequence of Sinorhizobium meliloti Strain AK170
    Article Snippet: Genomic purification was done by using a Pacific Biosciences protocol with Phase Lock Gel (VWR International) and AMPure beads (Agencourt Bioscience, Beckman Coulter Life Sciences), following the E2612 protocol from New England BioLabs. .. The DNA library was constructed using the dual-index NEBNext multiplex oligos (NEB) and the NEBNext Ultra II DNA library prep kit for Illumina (NEB).

    Article Title: Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
    Article Snippet: Genomic DNA (gDNA) was extracted with phenol/chloroform/isoamylalcohol solution (25:24:1, v /v ) adhering to the protocol provided by Pacific Biosciences in combination with phase lock gels for phase separation (VWR International, Radnor, USA). gDNA was concentrated and washed using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol from New England Biolabs . .. A 10 kb SMRTbell library was constructed using the DNA Template Prep Kit 1.0 (Pacific Biosciences, Menlo Park, USA).

    Incubation:

    Article Title: Draft Genome Sequence of Sinorhizobium meliloti Strain AK170
    Article Snippet: A glycerol stock was used to inoculate a tryptone-yeast extract (TY) agar plate ( ); the resulting single colony was incubated overnight in TY broth (28°C, 180 rpm). .. Genomic purification was done by using a Pacific Biosciences protocol with Phase Lock Gel (VWR International) and AMPure beads (Agencourt Bioscience, Beckman Coulter Life Sciences), following the E2612 protocol from New England BioLabs.

    Article Title: Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
    Article Snippet: Microbial DNA enrichment and sequencing Selective enrichment of microbial genomic DNA was performed using NEBNext® Microbiome DNA Enrichment Kit (New England Biolabs, Inc. MA) . .. Briefly, 0.5 µg of genomic DNA was treated with 80 µl of MBD2-Fcbound magnetic beads in the presence of binding buffer and incubated at room temperature for 15 min with rotation.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). .. A volume of 10 μL of washed beads was mixed with 21.25–50 μL of aDNA extract, 20 μL of 5X Bind/Wash Buffer and supplemented with sterile water up to 100 μL, before being incubated for 20 minutes at RT with agitation.

    Article Title: Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles
    Article Snippet: The solution was then incubated for 20 min at room temperature, centrifuged at 13,000 g for 20 min and the top aqueous layer was collected. .. For the “Antibody Depletion” method, 1 μg of total extracted DNA was processed with the NEBNext Microbiome DNA Enrichment Kit (NEB E2612S) according to the manufacturer’s instructions.

    Derivative Assay:

    Article Title: Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues 1
    Article Snippet: .. The input DNA sources for the latter two libraries represent the supernatant and bead fractions derived from the application of the NEBNext Microbiome DNA Enrichment Kit (#E2612S; New England Biolabs, Ipswich, Massachusetts, USA). ..

    Hybridization:

    Article Title: Draft Genome Sequence of Sinorhizobium meliloti Strain AK170
    Article Snippet: This region is a part of a modern center of alfalfa intrоgressive hybridization in northwest Kazakhstan, which has been suffering from manmade salinization since the 1960s ( , ). .. Genomic purification was done by using a Pacific Biosciences protocol with Phase Lock Gel (VWR International) and AMPure beads (Agencourt Bioscience, Beckman Coulter Life Sciences), following the E2612 protocol from New England BioLabs.

    Flow Cytometry:

    Article Title: A comprehensive analysis of breast cancer microbiota and host gene expression
    Article Snippet: The DNA concentrations were measured by Qubit dsDNA HS Assay Kit (PN Q32854 Thermo Fisher Scientific Inc., Waltham, MA) and samples with sufficient DNA were enriched for microbial DNA using the NEBNext® Microbiome DNA Enrichment Kit (PN E2612L, New England Biolabs, Ipswich, MA). .. The V3-V5 region of the 16S-rRNA gene were amplified with a two-step PCR protocol, and then Illumina flow cell adaptors containing indices were incorporated [ ].

    Ligation:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA. .. The fragmented mitochondrial DNA was cleaned up using HighPrep beads (MagBio Genomics, Inc, Gaithersburg, Maryland) and subjected to end-repair, A-tailing and ligation with multiplex adaptors using the NEXTFlex DNA Sequencing kit (Catalogue # 5140–02, Bioo Scientific).

    Methylation:

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates. .. By using the methylated CpG-specific binding protein MBD2 fused to a human IgG Fc fragment, human DNA is selectively bound and separated using Protein A-bound magnetic beads ( ).

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: .. MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). ..

    CpG Methylation Assay:

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: .. One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates. .. By using the methylated CpG-specific binding protein MBD2 fused to a human IgG Fc fragment, human DNA is selectively bound and separated using Protein A-bound magnetic beads ( ).

    DNA Sequencing:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Paragraph title: Sample processing, DNA sequencing and assembly ... Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA.

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: Without the ability to target DNA sequencing, low microbial burden means that the overwhelming majority of DNA sequenced then comes from host cells rather than the pathogen(s). .. One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates.

    Sequencing:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: The complete overview of sequencing and analysis of mitochondrial genome of A . assamensis is represented in . .. Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA.

    Article Title: Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
    Article Snippet: Paragraph title: DNA Extraction, Sequencing and Genomic Analysis ... Genomic DNA (gDNA) was extracted with phenol/chloroform/isoamylalcohol solution (25:24:1, v /v ) adhering to the protocol provided by Pacific Biosciences in combination with phase lock gels for phase separation (VWR International, Radnor, USA). gDNA was concentrated and washed using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol from New England Biolabs .

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: This increased sequencing depth can quickly escalate the costs of sequencing. .. One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates.

    Article Title: A comprehensive analysis of breast cancer microbiota and host gene expression
    Article Snippet: Paragraph title: 16S ribosomal sequencing validation ... The DNA concentrations were measured by Qubit dsDNA HS Assay Kit (PN Q32854 Thermo Fisher Scientific Inc., Waltham, MA) and samples with sufficient DNA were enriched for microbial DNA using the NEBNext® Microbiome DNA Enrichment Kit (PN E2612L, New England Biolabs, Ipswich, MA).

    Article Title: Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
    Article Snippet: .. Microbial DNA enrichment and sequencing Selective enrichment of microbial genomic DNA was performed using NEBNext® Microbiome DNA Enrichment Kit (New England Biolabs, Inc. MA) . ..

    Binding Assay:

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates. .. By using the methylated CpG-specific binding protein MBD2 fused to a human IgG Fc fragment, human DNA is selectively bound and separated using Protein A-bound magnetic beads ( ).

    Article Title: Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
    Article Snippet: Microbial DNA enrichment and sequencing Selective enrichment of microbial genomic DNA was performed using NEBNext® Microbiome DNA Enrichment Kit (New England Biolabs, Inc. MA) . .. Briefly, 0.5 µg of genomic DNA was treated with 80 µl of MBD2-Fcbound magnetic beads in the presence of binding buffer and incubated at room temperature for 15 min with rotation.

    DNA Extraction:

    Article Title: Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
    Article Snippet: Paragraph title: DNA Extraction, Sequencing and Genomic Analysis ... Genomic DNA (gDNA) was extracted with phenol/chloroform/isoamylalcohol solution (25:24:1, v /v ) adhering to the protocol provided by Pacific Biosciences in combination with phase lock gels for phase separation (VWR International, Radnor, USA). gDNA was concentrated and washed using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol from New England Biolabs .

    Article Title: Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont
    Article Snippet: Paragraph title: Sponge sampling, DNA isolation, and microbial DNA purification. ... The microbial DNA fraction was enriched using New England Biolab's NEBNext microbiome DNA enrichment kit.

    Article Title: A comprehensive analysis of breast cancer microbiota and host gene expression
    Article Snippet: The MoBio PowerSoil® DNA Isolation Kit (PN 12888 Mo Bio Laboratories, Inc. Carlsbad, CA) were used for DNA extraction according to the manufacturer’s protocol. .. The DNA concentrations were measured by Qubit dsDNA HS Assay Kit (PN Q32854 Thermo Fisher Scientific Inc., Waltham, MA) and samples with sufficient DNA were enriched for microbial DNA using the NEBNext® Microbiome DNA Enrichment Kit (PN E2612L, New England Biolabs, Ipswich, MA).

    Article Title: Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles
    Article Snippet: Paragraph title: DNA Extraction ... For the “Antibody Depletion” method, 1 μg of total extracted DNA was processed with the NEBNext Microbiome DNA Enrichment Kit (NEB E2612S) according to the manufacturer’s instructions.

    Fluorescence:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Subsequently, mitochondrial DNA was enriched from total DNA extracted once the integrity, quantity and purity of extracted DNA was confirmed by agarose gel electrophoresis, light absorbance and fluorescence spectroscopy. .. Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA.

    Magnetic Beads:

    Article Title: Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
    Article Snippet: One method, New England Biolab’s NEBNext Microbiome DNA Enrichment kit, takes advantage of human and other higher order eukaryotic DNA having high CpG methylation rates. .. By using the methylated CpG-specific binding protein MBD2 fused to a human IgG Fc fragment, human DNA is selectively bound and separated using Protein A-bound magnetic beads ( ).

    Article Title: Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues 1
    Article Snippet: Enrichments followed manufacturer’s recommendations (#E2612S; New England Biolabs). .. In short, we used a ratio of 1 μg of gDNA for 160-μL protein A magnetic beads and 16-μL MBD2-Fc protein.

    Article Title: Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle
    Article Snippet: Microbial DNA enrichment and sequencing Selective enrichment of microbial genomic DNA was performed using NEBNext® Microbiome DNA Enrichment Kit (New England Biolabs, Inc. MA) . .. Briefly, 0.5 µg of genomic DNA was treated with 80 µl of MBD2-Fcbound magnetic beads in the presence of binding buffer and incubated at room temperature for 15 min with rotation.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). .. MBD2−Fc/Protein A Magnetic Beads were then concentrated using a magnetic rack and washed twice using 1 mL 1X Bind/Wash Buffer before being re-suspended in 11 μL 1X Bind/Wash Buffer.

    Size-exclusion Chromatography:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA. .. The ligated DNA was cleaned with HighPrep beads and subjected to amplification via PCR as follows: initial denaturation at 98˚C for 2 min; 10 cycles of denaturation at 98˚C for 30 sec, annealing at 65˚C for 30 sec and extension at 72˚C for 60 sec; and a final extension at 72˚C for 4 min) using the primers provided by NEXTFlex DNA Sequencing kit.

    Purification:

    Article Title: Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno
    Article Snippet: .. Strain Cad16T was anaerobically grown in Pfennigs medium [ ] Cells were collected by centrifugation for 15 min at 10,600 g. DNA was extracted using phenol/chloroform/isoamylalcohol solution (25:24:1, v / v , Sigma, Buchs, Switzerland) following the protocol provided by Pacific Biosciences [ ] in combination with phase lock gels (VWR International). gDNA was purified using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol form New England Biolabs [ ]. .. Purity of the DNA was tested using the Qbit U V /VIS absorption reader (Thermo Fisher Scientific, Rheinach, Switzerland).

    Article Title: Draft Genome Sequence of Sinorhizobium meliloti Strain AK170
    Article Snippet: .. Genomic purification was done by using a Pacific Biosciences protocol with Phase Lock Gel (VWR International) and AMPure beads (Agencourt Bioscience, Beckman Coulter Life Sciences), following the E2612 protocol from New England BioLabs. .. Total DNA was fragmented with medium-sized fragments of about 600 bp in a microTUBE Adaptive Focused Acoustics (AFA) fiber snap-cap tube using a Covaris S2 instrument.

    Article Title: Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno
    Article Snippet: .. Growth conditions and genomic DNA preparation Strain Cad16T was anaerobically grown in Pfennigs medium [ ] Cells were collected by centrifugation for 15 min at 10,600 g. DNA was extracted using phenol/chloroform/isoamylalcohol solution (25:24:1, v /v , Sigma, Buchs, Switzerland) following the protocol provided by Pacific Biosciences [ ] in combination with phase lock gels (VWR International). gDNA was purified using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol form New England Biolabs [ ]. .. Purity of the DNA was tested using the Qbit UV /VIS absorption reader (Thermo Fisher Scientific, Rheinach, Switzerland).

    Polymerase Chain Reaction:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA. .. The ligated DNA was cleaned with HighPrep beads and subjected to amplification via PCR as follows: initial denaturation at 98˚C for 2 min; 10 cycles of denaturation at 98˚C for 30 sec, annealing at 65˚C for 30 sec and extension at 72˚C for 60 sec; and a final extension at 72˚C for 4 min) using the primers provided by NEXTFlex DNA Sequencing kit.

    Article Title: A comprehensive analysis of breast cancer microbiota and host gene expression
    Article Snippet: The DNA concentrations were measured by Qubit dsDNA HS Assay Kit (PN Q32854 Thermo Fisher Scientific Inc., Waltham, MA) and samples with sufficient DNA were enriched for microbial DNA using the NEBNext® Microbiome DNA Enrichment Kit (PN E2612L, New England Biolabs, Ipswich, MA). .. The V3-V5 region of the 16S-rRNA gene were amplified with a two-step PCR protocol, and then Illumina flow cell adaptors containing indices were incorporated [ ].

    Spectroscopy:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Subsequently, mitochondrial DNA was enriched from total DNA extracted once the integrity, quantity and purity of extracted DNA was confirmed by agarose gel electrophoresis, light absorbance and fluorescence spectroscopy. .. Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA.

    CRISPR:

    Article Title: Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno
    Article Snippet: Agencourt AMPure XP Bead Clean-up - NEBNext Microbiome DNA Enrichment Kit (E2612) | NEB [Internet]. .. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

    Multiplex Assay:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA. .. The fragmented mitochondrial DNA was cleaned up using HighPrep beads (MagBio Genomics, Inc, Gaithersburg, Maryland) and subjected to end-repair, A-tailing and ligation with multiplex adaptors using the NEXTFlex DNA Sequencing kit (Catalogue # 5140–02, Bioo Scientific).

    Article Title: Draft Genome Sequence of Sinorhizobium meliloti Strain AK170
    Article Snippet: Genomic purification was done by using a Pacific Biosciences protocol with Phase Lock Gel (VWR International) and AMPure beads (Agencourt Bioscience, Beckman Coulter Life Sciences), following the E2612 protocol from New England BioLabs. .. The DNA library was constructed using the dual-index NEBNext multiplex oligos (NEB) and the NEBNext Ultra II DNA library prep kit for Illumina (NEB).

    Agarose Gel Electrophoresis:

    Article Title: The mitochondrial genome of Muga silkworm (Antheraea assamensis) and its comparative analysis with other lepidopteran insects
    Article Snippet: Subsequently, mitochondrial DNA was enriched from total DNA extracted once the integrity, quantity and purity of extracted DNA was confirmed by agarose gel electrophoresis, light absorbance and fluorescence spectroscopy. .. Briefly, the preferential enrichment of mitochondrial DNA was carried out with NEBNext microbiome DNA enrichment kit (New England Biolabs, USA) which selectively removes CpG-methylated eukaryotic nuclear DNA.

    Laser Capture Microdissection:

    Article Title: Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues 1
    Article Snippet: METHODS To test the potential utility of methyl-CpG capture on plant systems, we sequenced gDNA from A. thaliana , Glycine max (L.) Merr., Leucaena leucocephala (Lam.) de Wit, O. sativa , and Zea mays L. For each sample, three gDNA libraries were sequenced using a MiSeq instrument (Illumina, San Diego, California, USA): (1) untreated gDNA, (2) a fraction depleted of methyl-CpG, and (3) a fraction enriched for methyl-CpG. .. The input DNA sources for the latter two libraries represent the supernatant and bead fractions derived from the application of the NEBNext Microbiome DNA Enrichment Kit (#E2612S; New England Biolabs, Ipswich, Massachusetts, USA).

    dsDNA Assay:

    Article Title: Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues 1
    Article Snippet: In addition, a double-stranded DNA (dsDNA) assay was also used to calculate concentration using the Qubit dsDNA BR Assay Kit (#Q32850; Life Technologies, Grand Island, New York, USA). .. Enrichments followed manufacturer’s recommendations (#E2612S; New England Biolabs).

    Sampling:

    Article Title: Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont
    Article Snippet: Paragraph title: Sponge sampling, DNA isolation, and microbial DNA purification. ... The microbial DNA fraction was enriched using New England Biolab's NEBNext microbiome DNA enrichment kit.

    Concentration Assay:

    Article Title: Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
    Article Snippet: Genomic DNA (gDNA) was extracted with phenol/chloroform/isoamylalcohol solution (25:24:1, v /v ) adhering to the protocol provided by Pacific Biosciences in combination with phase lock gels for phase separation (VWR International, Radnor, USA). gDNA was concentrated and washed using AMPure beads (Agencourt, Beckman Coulter Life Sciences, Indianapolis, USA) following the E2612 protocol from New England Biolabs . .. Concentration of the DNA was assessed using a Qubit UV/VIS absorption reader (Thermo Fisher Scientific, Rheinach, Switzerland).

    Article Title: Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues 1
    Article Snippet: Differences in concentration between NanoDrop and Qubit are likely due to single-stranded RNA contamination in genomic preps or other contaminants absorbing at A260. .. Enrichments followed manufacturer’s recommendations (#E2612S; New England Biolabs).

    DNA Purification:

    Article Title: Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont
    Article Snippet: Paragraph title: Sponge sampling, DNA isolation, and microbial DNA purification. ... The microbial DNA fraction was enriched using New England Biolab's NEBNext microbiome DNA enrichment kit.

    Lysis:

    Article Title: Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles
    Article Snippet: For the “Antibody Depletion” method, 1 μg of total extracted DNA was processed with the NEBNext Microbiome DNA Enrichment Kit (NEB E2612S) according to the manufacturer’s instructions. .. For the “Cell Lysis” method , prior to Standard DNA extraction sputum was suspended in 1 mL PBS, vortexed and centrifuged at 13,000 g for 2 min.

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    New England Biolabs microbiome enrichment kit
    The <t>microbiota</t> of breast tissue is distinct from skin tissue in rare bacterial lineages. ( A ) Barplots of the taxonomic profiles of the breast and skin tissue microbiota at phylum, family and genus level for taxa with a relative abundance > 0.5%. ( B , C ) Rarefaction curves compare the two alpha-diversity measures (observed OTU number ( B ) and Shannon index ( C )) between the two tissue types. ( D ) Heat map shows the OTU presence and absence of all the tissue samples (column: samples, row: O TUs). The hierarchical clustering (top) is built based on the Euclidean distance of the OTU presence/absence profiles with a complete linkage. ( E , F ) Ordination plots show the clustering pattern of the two tissue samples based on unweighted ( E ) and weighted ( F ) UniFrac distance. ( G , H ) Differential taxa between breast and skin tissue microbiota based on a permutation test. Taxa with a nominal p value
    Microbiome Enrichment Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The microbiota of breast tissue is distinct from skin tissue in rare bacterial lineages. ( A ) Barplots of the taxonomic profiles of the breast and skin tissue microbiota at phylum, family and genus level for taxa with a relative abundance > 0.5%. ( B , C ) Rarefaction curves compare the two alpha-diversity measures (observed OTU number ( B ) and Shannon index ( C )) between the two tissue types. ( D ) Heat map shows the OTU presence and absence of all the tissue samples (column: samples, row: O TUs). The hierarchical clustering (top) is built based on the Euclidean distance of the OTU presence/absence profiles with a complete linkage. ( E , F ) Ordination plots show the clustering pattern of the two tissue samples based on unweighted ( E ) and weighted ( F ) UniFrac distance. ( G , H ) Differential taxa between breast and skin tissue microbiota based on a permutation test. Taxa with a nominal p value

    Journal: Scientific Reports

    Article Title: The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

    doi: 10.1038/srep30751

    Figure Lengend Snippet: The microbiota of breast tissue is distinct from skin tissue in rare bacterial lineages. ( A ) Barplots of the taxonomic profiles of the breast and skin tissue microbiota at phylum, family and genus level for taxa with a relative abundance > 0.5%. ( B , C ) Rarefaction curves compare the two alpha-diversity measures (observed OTU number ( B ) and Shannon index ( C )) between the two tissue types. ( D ) Heat map shows the OTU presence and absence of all the tissue samples (column: samples, row: O TUs). The hierarchical clustering (top) is built based on the Euclidean distance of the OTU presence/absence profiles with a complete linkage. ( E , F ) Ordination plots show the clustering pattern of the two tissue samples based on unweighted ( E ) and weighted ( F ) UniFrac distance. ( G , H ) Differential taxa between breast and skin tissue microbiota based on a permutation test. Taxa with a nominal p value

    Article Snippet: NEBNext Microbiome Enrichment Kit (New England BioLabs, NEB #2612S) was applied to remove the methylated host DNA in the genomic DNA for tissue samples.

    Techniques:

    Ordination plot of samples from 33 women shows a distinct clustering pattern of different sample types (breast tissue, breast skin tissue, skin swab and buccal swab). The microbiota samples are embedded in the two-dimensional space based on the first two principal coordinates (PCs) from PCoA on the unweighted UniFrac distance. The percentage of explained variability of each PC is indicated on the axis. Each point represents a sample and is colored by sample types (blue diamonds - skin swab, green squares - buccal swab, purple triangles - breast skin tissue, red circles - breast tissue). The ellipse reflects the probability distribution of each sample type.

    Journal: Scientific Reports

    Article Title: The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

    doi: 10.1038/srep30751

    Figure Lengend Snippet: Ordination plot of samples from 33 women shows a distinct clustering pattern of different sample types (breast tissue, breast skin tissue, skin swab and buccal swab). The microbiota samples are embedded in the two-dimensional space based on the first two principal coordinates (PCs) from PCoA on the unweighted UniFrac distance. The percentage of explained variability of each PC is indicated on the axis. Each point represents a sample and is colored by sample types (blue diamonds - skin swab, green squares - buccal swab, purple triangles - breast skin tissue, red circles - breast tissue). The ellipse reflects the probability distribution of each sample type.

    Article Snippet: NEBNext Microbiome Enrichment Kit (New England BioLabs, NEB #2612S) was applied to remove the methylated host DNA in the genomic DNA for tissue samples.

    Techniques:

    The microbiota of breast tissue adjacent to invasive cancer is distinguishable from that adjacent to benign disease (BBD-non-atypia). ( A ) Ordination plot based on unweighted UniFrac distance shows the clustering pattern of the breast tissue microbiota between the two disease states. ( B ) Differential taxa between the breast tissue microbiota of malignant and benign states based on a permutation test. Taxa with a nominal p value

    Journal: Scientific Reports

    Article Title: The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease

    doi: 10.1038/srep30751

    Figure Lengend Snippet: The microbiota of breast tissue adjacent to invasive cancer is distinguishable from that adjacent to benign disease (BBD-non-atypia). ( A ) Ordination plot based on unweighted UniFrac distance shows the clustering pattern of the breast tissue microbiota between the two disease states. ( B ) Differential taxa between the breast tissue microbiota of malignant and benign states based on a permutation test. Taxa with a nominal p value

    Article Snippet: NEBNext Microbiome Enrichment Kit (New England BioLabs, NEB #2612S) was applied to remove the methylated host DNA in the genomic DNA for tissue samples.

    Techniques:

    Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA

    Journal: BMC Evolutionary Biology

    Article Title: Phylogenomics and barcoding of Panax: toward the identification of ginseng species

    doi: 10.1186/s12862-018-1160-y

    Figure Lengend Snippet: Proportion of mitochondrial, plastid and microbiome reads from the methylated and non-methylated fraction for the four enriched libraries. These results show that the enrichment procedure successfully capture more than 99.5% of the plastid sequences contained in the total DNA

    Article Snippet: In order to test the efficacy of the NEBNext Microbiome DNA Enrichment Kit the proportion of reads belonging to the plastome was estimated for both the methylated and the non-methylated fraction.

    Techniques: Methylation

    Genus-level distribution of gut microbiome in the gnotobiotic chicken inoculated with intestinal material from feral chickens. The pooled inoculum, derived from 6 healthy feral chickens, was orally inoculated to gnotobiotic chicken on day 3 after hatch. Birds were euthanized on day 9 ( n = 7) and day 18 ( n = 9) of age, and cecal contents were collected for DNA isolation. The metagenomic functional analysis was performed in MG-RAST using the RefSeq database with a maximum E value at 10 −5 and minimum identity of 60%. Phylogenetic tables were generated in MG-RAST, and analysis was conducted using Explicet software.

    Journal: mSphere

    Article Title: Gut Microbial Dynamics during Conventionalization of Germfree Chicken

    doi: 10.1128/mSphere.00035-19

    Figure Lengend Snippet: Genus-level distribution of gut microbiome in the gnotobiotic chicken inoculated with intestinal material from feral chickens. The pooled inoculum, derived from 6 healthy feral chickens, was orally inoculated to gnotobiotic chicken on day 3 after hatch. Birds were euthanized on day 9 ( n = 7) and day 18 ( n = 9) of age, and cecal contents were collected for DNA isolation. The metagenomic functional analysis was performed in MG-RAST using the RefSeq database with a maximum E value at 10 −5 and minimum identity of 60%. Phylogenetic tables were generated in MG-RAST, and analysis was conducted using Explicet software.

    Article Snippet: Selective enrichment of bacterial genomic DNA was performed using a NEBNext microbiome DNA enrichment kit (New England Biolabs, Inc., MA) following methods previously published by our group ( ).

    Techniques: Derivative Assay, DNA Extraction, Functional Assay, RAST Test, Generated, Software

    Predicted functional profile at the subsystem level of the microbiome in feral and gnotobiotic chickens. The pooled inoculum was derived from 6 healthy feral chickens. Birds were inoculated on day 3 after hatch and were euthanized at 9 days ( n = 7) and 18 days ( n = 9) of age, and cecal contents were collected for DNA isolation. The functional analysis was performed using subsystems information based on contigs from the MG-RAST database with an E value at 10 −5 , minimum identity at 60%, and a minimum read length of 100. Heat map was constructed in the Morpheus server ( https://software.broadinstitute.org/morpheus ) with a Euclidean distance matrix and average clustering method.

    Journal: mSphere

    Article Title: Gut Microbial Dynamics during Conventionalization of Germfree Chicken

    doi: 10.1128/mSphere.00035-19

    Figure Lengend Snippet: Predicted functional profile at the subsystem level of the microbiome in feral and gnotobiotic chickens. The pooled inoculum was derived from 6 healthy feral chickens. Birds were inoculated on day 3 after hatch and were euthanized at 9 days ( n = 7) and 18 days ( n = 9) of age, and cecal contents were collected for DNA isolation. The functional analysis was performed using subsystems information based on contigs from the MG-RAST database with an E value at 10 −5 , minimum identity at 60%, and a minimum read length of 100. Heat map was constructed in the Morpheus server ( https://software.broadinstitute.org/morpheus ) with a Euclidean distance matrix and average clustering method.

    Article Snippet: Selective enrichment of bacterial genomic DNA was performed using a NEBNext microbiome DNA enrichment kit (New England Biolabs, Inc., MA) following methods previously published by our group ( ).

    Techniques: Functional Assay, Derivative Assay, DNA Extraction, RAST Test, Construct, Software