monarch dna gel extraction kit  (New England Biolabs)


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    Name:
    Monarch DNA Gel Extraction Kit
    Description:
    Monarch DNA Gel Extraction Kit 250 preps
    Catalog Number:
    t1020l
    Price:
    460
    Size:
    250 preps
    Category:
    DNA Fragment Purification from Gels
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    Structured Review

    New England Biolabs monarch dna gel extraction kit
    Monarch DNA Gel Extraction Kit
    Monarch DNA Gel Extraction Kit 250 preps
    https://www.bioz.com/result/monarch dna gel extraction kit/product/New England Biolabs
    Average 90 stars, based on 77 article reviews
    Price from $9.99 to $1999.99
    monarch dna gel extraction kit - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice"

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23830-4

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .
    Figure Legend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .

    Techniques Used: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    2) Product Images from "Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice"

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23830-4

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .
    Figure Legend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .

    Techniques Used: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    3) Product Images from "Filter paper-based spin column method for cost-efficient DNA or RNA purification"

    Article Title: Filter paper-based spin column method for cost-efficient DNA or RNA purification

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203011

    The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.
    Figure Legend Snippet: The efficiency of filter paper for purification of nucleic acids from various sources using respective Qiagen kits. (A) Tomato genomic DNAs purified using Qiagen DNeasy plant mini kit. (B) Tomato total RNAs purified using Qiagen RNeasy plant mini kit. (C) PCR products of a GUS fragment purified using Qiagen QIAquick PCR purification kit. (D) PCR products of GUS fragment recovered from an agarose gel using a Qiagen QIAquick gel extraction kit. (E) pUC -19 plasmid DNAs purified using a Qiagen QIAprep spin miniprep kit. For each panel, from left to right are (Q) nucleic acid purified in experiments using original Qiagen spin column, (G) reassembled spin column using two layers of Whatman glass microfiber filters (Grade GF/F), and (P) reassembled spin column using two layers of Whatman qualitative filter paper, (Grade 3) respectively. Upper panel is quantification data based on three experimental replicates normalized according to performance of the Qiagen kit; lower panel is an image of agarose gel electrophoresis for the same volume of purified nucleic acids.

    Techniques Used: Purification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Gel Extraction, Plasmid Preparation

    Related Articles

    Methylation Sequencing:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: Paragraph title: Bisulfite sequencing ... PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates.

    Clone Assay:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies). .. Amplicons were then cloned into linearized and dephosphorylated pGRG36 using Quick-Stick T4 Ligase (Bioline).

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Amplification:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: To construct the pMRE-Tn7 family, fluorescent protein genes and antibiotic resistance genes were amplified from the pMRE1XX series using primers FWD_pMRE-Tn7 and REV_pMRE-Tn7. .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies).

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: For the verification of amplified SAM gRNA library, 10 ng of input plasmid DNA was used. .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The Tci-mptl-1 gene was amplified in two sections using a nested-PCR approach: 5′ section amplified with MPTL-SL1 (5′-ATTACCCAAGTTTGAGATCTCAAGG-3′) and MPTL-degR1 (5′-TTTTGCGCATAGGCYTGYTTCAT-3′), followed with semi-nested-PCR with primer pair MTPL-SL1 and MPTL-degR2 (5′-CATRAGAAGCGGCATCTCCAT-3′); the 3′ section was initially amplified with primer pair MPTL-F2 (5′-TGGTCATATACGTACAGAAGCAGG-3′) and MPTL-degR3 (5′-GGMTCTTCMATAGATTTATRAAAATAC-3′) followed by semi-nested-PCR with primer pair MPTL-F2 and MPTL-degR4 (5′-GTGCAGTCAAACGGAACACTTCG-3′). .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs).

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: Briefly, the total viral RNA/DNA derived from the lymph nodes of three necropsied cats were individually amplified using a Qiagen OneStep RT-PCR kit (Qiagen GmbH, Hilden, Germany) with a combination of reverse transcriptase and DNA polymerase, and specific primers. .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea).

    Article Title: All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo
    Article Snippet: In the second-step PCR, equimolar amounts of DNA were amplified with a universal forward primer and an indexed reverse primer using Phusion High Fidelity DNA Polymerase (98 °C, 15 s; 61 °C, 25 s; 72 °C, 18 s; nine cycles) to ligate the TruSeq adaptors. .. The resultant amplicons were separated in a 2.5% agarose gel and the corresponding ~ 250-bp product bands were extracted using Monarch DNA Gel Extraction Kit (New England Biolabs).

    Positive Control:

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: Nuclease free water was used as negative control and female tsetse fly DNA (Glossina fuscipes fuscipes ) obtained from the field in Uganda was used as a positive control. .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.).

    Construct:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: To construct the pMRE-Tn7 family, fluorescent protein genes and antibiotic resistance genes were amplified from the pMRE1XX series using primers FWD_pMRE-Tn7 and REV_pMRE-Tn7. .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies).

    Electrophoresis:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions. .. NGS libraries were prepared from amplicons by GATC Biotech (Konstanz, Germany) and 125 bp paired end sequencing was carried out on an Illumina HiSeq 4000 with 15 million reads per condition.

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. Hybridization of complementary oligonucleotides or long overhangs was done in a thermocycler by heating the samples at 65°C for 15 min and then decreasing the temperature in 5°C steps every 5 min, until reaching 25°C.

    Incubation:

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly. .. Gibson Assembly reactions were carried out using NEB Gibson Assembly Master Mix where the fragments were combined at 200 ng of DNA and incubated at 50 °C for 1 h. After the assembly, reactions were purified using KAPA Pure beads.

    Cell Culture:

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: Genomic DNA was isolated from faecal and larynx samples (infected and non-infected, each n = 4) and cultured B. pseudohinzii (n = 1) with the ISOLATE Faecal DNA Kit (Bioline, Luckenwalde, Germany) according to the manufacturer’s protocol. .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. Transformed cells were cultured and recombinant plasmid was extracted using the QIAprep Spin Miniprep Kit (Qiagen, Valencia CA).

    Touchdown PCR:

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: Amplification was conducted using Q5® high-fidelity DNA polymerase (New England Biolabs) in a final volume of 25 μl (Q5®high-fidelity reaction buffer, 0.2 mM dNTPs, 0.5 μM of each primer, 0.02 U/μl Q5® high-fidelity DNA polymerase and 1 μl template cDNA), using touchdown PCR thermocycling conditions as follows: initial denaturing step at 98 °C for 2 min; 10 three-step cycles of 98 °C for 10 s, Tanneal for 20 s and 72 °C for 90 s, with decreasing annealing temperature by 0.5 °C per cycle from the (Tanneal + 5 °C) to the Tanneal ; this was followed by 30 three-step cycles of 98 °C for 10 s, Tanneal for 20 s and 72 °C for 90 s with a final extension step of 72 °C for 5 min. .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs).

    Modification:

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: DNA manipulation, plasmid construction and conjugation The enzymes for DNA modification were purchased from New England Biolabs (NEB) and Takara Biomedical Technology. .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively.

    Transformation Assay:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: For isothermal assemblies, EcoRV-digested pAG408 was mixed with the insert fragments in a 1:3:3 ratio as described above and assembled plasmids were transformed into chemically competent E. coli S17-1. .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies).

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. Transformed cells were cultured and recombinant plasmid was extracted using the QIAprep Spin Miniprep Kit (Qiagen, Valencia CA).

    Derivative Assay:

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: Briefly, the total viral RNA/DNA derived from the lymph nodes of three necropsied cats were individually amplified using a Qiagen OneStep RT-PCR kit (Qiagen GmbH, Hilden, Germany) with a combination of reverse transcriptase and DNA polymerase, and specific primers. .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea).

    Gel Purification:

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: .. Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB). .. Unless otherwise stated, all site-directed mutagenesis was carried out by iPCR ( ) followed by PCR purification column cleanup and blunt end ligation.

    Conjugation Assay:

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: Paragraph title: DNA manipulation, plasmid construction and conjugation ... All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively.

    Sequencing:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: To control for representation, PCR with gRNAs sequence primer listed in Additional file : Table S1b was performed on genomic DNA equivalent to 500 cells per guide, corresponding to a total of 231 μg from 35 million cells (assuming 6.6 pg in a single diploid cell). .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: Paragraph title: High-throughput sequencing of genomic DNA. ... PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols.

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: Paragraph title: 2.5. Sequencing and Phylogeny ... PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States).

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. Sequencing of the purified plasmid DNA was outsourced to Eurofins Genomics (Germany) using the pJET1.2for and pJET1.2rev sequencing primers.

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea). ..

    DNA Ligation:

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: T4 DNA ligase was used for DNA ligations 1h or overnight at 16°C in 1× T4 DNA ligation buffer. .. When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB).

    Ligation:

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB). .. Unless otherwise stated, all site-directed mutagenesis was carried out by iPCR ( ) followed by PCR purification column cleanup and blunt end ligation.

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: Paragraph title: Restriction enzyme digest and ligation ... When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB).

    Infection:

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: Genomic DNA was isolated from faecal and larynx samples (infected and non-infected, each n = 4) and cultured B. pseudohinzii (n = 1) with the ISOLATE Faecal DNA Kit (Bioline, Luckenwalde, Germany) according to the manufacturer’s protocol. .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Generated:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. Obtained sequences were analyzed and DNA methylation plots were generated using the QUMA quantification tool for methylation analysis .

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: The amplicons were generated by thermocycling at 50 °C for 30 min, 94 °C for 15 min and then 40 cycles of 94 °C for 30 s, 50 °C for 30 s and 72 °C for 1 min, before a final 72 °C for 7 min. .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea).

    DNA Sequencing:

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified DNA was sequenced in at the Yale Keck DNA Sequencing Facility.

    Polymerase Chain Reaction:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: PCR products were purified using GeneJET PCR Purification Kits (Thermo Fisher Scientific, Waltham MA, USA), Nucleospin Gel and PCR Clean-up (Machery-Nagel GmbH, Düren, Germany) or Monarch PCR and DNA Cleanup kits (NEB). .. Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB).

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. For the DNA annealing strategy, PCR products obtained with Taq DNA polymerase were treated with T4 DNA polymerase (NEB) for 15 min at 12°C in 1× buffer 2.1 (NEB), to remove 3′-A overhangs.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The resulting PCR products were analyzed by agarose gel-electrophoresis on a 1% gel, stained with ethidium bromide and recorded using the Gel Doc EQ quantification analysis software (Bio-Rad, Image Lab Software Version 4.1). .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.).

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea). ..

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: .. PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly. .. Gibson Assembly reactions were carried out using NEB Gibson Assembly Master Mix where the fragments were combined at 200 ng of DNA and incubated at 50 °C for 1 h. After the assembly, reactions were purified using KAPA Pure beads.

    Article Title: All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo
    Article Snippet: In the second-step PCR, equimolar amounts of DNA were amplified with a universal forward primer and an indexed reverse primer using Phusion High Fidelity DNA Polymerase (98 °C, 15 s; 61 °C, 25 s; 72 °C, 18 s; nine cycles) to ligate the TruSeq adaptors. .. The resultant amplicons were separated in a 2.5% agarose gel and the corresponding ~ 250-bp product bands were extracted using Monarch DNA Gel Extraction Kit (New England Biolabs).

    Hybridization:

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. Hybridization of complementary oligonucleotides or long overhangs was done in a thermocycler by heating the samples at 65°C for 15 min and then decreasing the temperature in 5°C steps every 5 min, until reaching 25°C.

    Multiplexing:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: PCR was conducted using Phusion Flash High-Fidelity PCR master mix (Life Technologies) for 28 cycles as 98 °C for 90 s, 98 °C for 1 s, 60 °C for 5 s, 72 °C for 15 s, followed by final extension of 72 °C for 1 min. To enable multiplexing during NGS, an 8 bp unique barcode was added at the beginning of the forward primer as TCGCCTTG, ATAGCGTC, GAAGAAGT, ATTCTAGG or CGTTACCA. .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    Nucleic Acid Electrophoresis:

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Methylation:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: Bisulfite-converted DNA was subjected to methylation-specific PCR using specific primers for the BCL2 promoter listed in Supplementary Table . .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates.

    Mutagenesis:

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB). .. Unless otherwise stated, all site-directed mutagenesis was carried out by iPCR ( ) followed by PCR purification column cleanup and blunt end ligation.

    Isolation:

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: Genomic DNA was isolated from faecal and larynx samples (infected and non-infected, each n = 4) and cultured B. pseudohinzii (n = 1) with the ISOLATE Faecal DNA Kit (Bioline, Luckenwalde, Germany) according to the manufacturer’s protocol. .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Marker:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: To construct the pMRE-Tn5 plasmid series, pMRE1XX plasmids were used as a template to amplify the desired DNA fragments, which include one of the eight fluorescent protein gene and one of the four antibiotic resistance marker combinations. .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies).

    Multiplex Assay:

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: PCR 2 reactions used 1.25 μL each of 10 μM forward and reverse Illumina barcoding primers and 1 μL of unpurified PCR 1 reaction product, all diluted to 12.5 μL with nuclease-free water, and 12.5 μL Phusion U Green Multiplex PCR MasterMix (Thermo Fisher Scientific). .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols.

    Purification:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies). .. Following dephosphorylation, plasmids were purified using the DNA Clean & ConcentratorTM -5 Kit (Zymo).

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: PCR products were purified using GeneJET PCR Purification Kits (Thermo Fisher Scientific, Waltham MA, USA), Nucleospin Gel and PCR Clean-up (Machery-Nagel GmbH, Düren, Germany) or Monarch PCR and DNA Cleanup kits (NEB). .. Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB).

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea). ..

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly. .. Gibson Assembly reactions were carried out using NEB Gibson Assembly Master Mix where the fragments were combined at 200 ng of DNA and incubated at 50 °C for 1 h. After the assembly, reactions were purified using KAPA Pure beads.

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. The ssDNA fragments were identified using a blue light transilluminator , cut out of the gel and purified using the Monarch® DNA Gel Extraction Kit. ..

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: Briefly, the total viral RNA/DNA derived from the lymph nodes of three necropsied cats were individually amplified using a Qiagen OneStep RT-PCR kit (Qiagen GmbH, Hilden, Germany) with a combination of reverse transcriptase and DNA polymerase, and specific primers. .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea).

    Selection:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    De-Phosphorylation Assay:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies). .. Following dephosphorylation, plasmids were purified using the DNA Clean & ConcentratorTM -5 Kit (Zymo).

    Gel Extraction:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: .. The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies). .. Following dephosphorylation, plasmids were purified using the DNA Clean & ConcentratorTM -5 Kit (Zymo).

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions. .. NGS libraries were prepared from amplicons by GATC Biotech (Konstanz, Germany) and 125 bp paired end sequencing was carried out on an Illumina HiSeq 4000 with 15 million reads per condition.

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Article Title: Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis
    Article Snippet: .. Gel purification was carried out using Monarch DNA Gel Extraction Kit (NEB). .. Unless otherwise stated, all site-directed mutagenesis was carried out by iPCR ( ) followed by PCR purification column cleanup and blunt end ligation.

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. Hybridization of complementary oligonucleotides or long overhangs was done in a thermocycler by heating the samples at 65°C for 15 min and then decreasing the temperature in 5°C steps every 5 min, until reaching 25°C.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea). ..

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: .. PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly. .. Gibson Assembly reactions were carried out using NEB Gibson Assembly Master Mix where the fragments were combined at 200 ng of DNA and incubated at 50 °C for 1 h. After the assembly, reactions were purified using KAPA Pure beads.

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. The ssDNA fragments were identified using a blue light transilluminator , cut out of the gel and purified using the Monarch® DNA Gel Extraction Kit. ..

    Article Title: All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo
    Article Snippet: .. The resultant amplicons were separated in a 2.5% agarose gel and the corresponding ~ 250-bp product bands were extracted using Monarch DNA Gel Extraction Kit (New England Biolabs). .. The libraries were then sequenced on an Illumina MiSeq in paired-end mode with a read length of 150 bp.

    Nested PCR:

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The Tci-mptl-1 gene was amplified in two sections using a nested-PCR approach: 5′ section amplified with MPTL-SL1 (5′-ATTACCCAAGTTTGAGATCTCAAGG-3′) and MPTL-degR1 (5′-TTTTGCGCATAGGCYTGYTTCAT-3′), followed with semi-nested-PCR with primer pair MTPL-SL1 and MPTL-degR2 (5′-CATRAGAAGCGGCATCTCCAT-3′); the 3′ section was initially amplified with primer pair MPTL-F2 (5′-TGGTCATATACGTACAGAAGCAGG-3′) and MPTL-degR3 (5′-GGMTCTTCMATAGATTTATRAAAATAC-3′) followed by semi-nested-PCR with primer pair MPTL-F2 and MPTL-degR4 (5′-GTGCAGTCAAACGGAACACTTCG-3′). .. The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs).

    Polymerase Cycling Assembly:

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: Gibson assembly PCR reactions were cleaned-up using KAPA Pure beads (Roche Cat # KK8000) before added to the first Gibson Assembly. .. PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly.

    Plasmid Preparation:

    Article Title: Chromatic Bacteria – A Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    Article Snippet: Paragraph title: Plasmid Construction ... The amplicons were gel purified using the Monarch DNA Gel Extraction Kit (NEB) and phosphorylated using T4 polynucleotide kinase (Life Technologies). pGRG36 was SmaI digested and dephosphorylated using thermosensitive alkaline phosphatase according to the manufacturers’ recommendations (Fast AP, Life Technologies).

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: For the verification of amplified SAM gRNA library, 10 ng of input plasmid DNA was used. .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. The blunt-ended amplicons were ligated into pJET1.2/blunt cloning vector using the CloneJET PCR cloning kit (ThermoFisher Scientific) as per the manufacturer's instructions and were used to directly transform JM109 competent E. coli cells (Promega).

    Software:

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The resulting PCR products were analyzed by agarose gel-electrophoresis on a 1% gel, stained with ethidium bromide and recorded using the Gel Doc EQ quantification analysis software (Bio-Rad, Image Lab Software Version 4.1). .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.).

    Article Title: Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta
    Article Snippet: The amplicons were confirmed with gel electrophoresis and cDNA was purified from excised gel slices using the Monarch® DNA Gel Extraction Kit (New England Biolabs). .. Sequence data were aligned and analysed using SeqMan Pro™ software from DNASTAR® Lasergene® v15 with default parameters.

    Negative Control:

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: Nuclease free water was used as negative control and female tsetse fly DNA (Glossina fuscipes fuscipes ) obtained from the field in Uganda was used as a positive control. .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.).

    Recombinant:

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Agarose Gel Electrophoresis:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: .. This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions. .. NGS libraries were prepared from amplicons by GATC Biotech (Konstanz, Germany) and 125 bp paired end sequencing was carried out on an Illumina HiSeq 4000 with 15 million reads per condition.

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: .. PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. DNA of single colonies was extracted using the NucleoSpin Plasmid EasyPure Mini Kit (Macherey-Nagel) and submitted to Sanger sequencing using sequencing primers M13-for and M13-rev (see Supplementary Table ).

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. Hybridization of complementary oligonucleotides or long overhangs was done in a thermocycler by heating the samples at 65°C for 15 min and then decreasing the temperature in 5°C steps every 5 min, until reaching 25°C.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.). .. The purified PCR products were ligated into pGEM-T Vector (Promega, Madison, WI) and recombinant plasmids were used to transform competent Escherichia coli strain DH5α.

    Article Title: Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
    Article Snippet: .. The PCR products were visualized on 1% (w/w) agarose gel electrophoresis and further purified using a Monarch DNA Gel extraction kit (New England Biolab, Frankfurt, Germany) prior to commercial Sanger sequencing (Macrogen Inc, Seoul, South Korea). ..

    Article Title: DNA assembly for nanopore data storage readout
    Article Snippet: .. PCR reactions were gel-purified using a 1% agarose gel and NEB Monarch DNA Gel Extraction kit for the second Gibson Assembly reactions in order to select out any side products from the first assembly. .. Gibson Assembly reactions were carried out using NEB Gibson Assembly Master Mix where the fragments were combined at 200 ng of DNA and incubated at 50 °C for 1 h. After the assembly, reactions were purified using KAPA Pure beads.

    Article Title: All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo
    Article Snippet: .. The resultant amplicons were separated in a 2.5% agarose gel and the corresponding ~ 250-bp product bands were extracted using Monarch DNA Gel Extraction Kit (New England Biolabs). .. The libraries were then sequenced on an Illumina MiSeq in paired-end mode with a read length of 150 bp.

    Next-Generation Sequencing:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: Paragraph title: Genomic DNA extraction and next-generation sequencing (NGS) ... This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    DNA Methylation Assay:

    Article Title: MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer
    Article Snippet: PCR product was resolved on a 2% agarose gel and purified using the Monarch DNA Gel Extraction Kit (New England BioLabs), cloned into pCR4-TOPO TA Vector (Thermo Fisher Scientific), transformed into XL10-Gold Ultracompetent Cells (Agilent Technologies), and plated onto ampicillin selection LB-agar plates. .. Obtained sequences were analyzed and DNA methylation plots were generated using the QUMA quantification tool for methylation analysis .

    DNA Extraction:

    Article Title: Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer
    Article Snippet: Paragraph title: Genomic DNA extraction and next-generation sequencing (NGS) ... This was subjected to electrophoresis on a 2% agarose gel and the band of interest was extracted using Monarch DNA Gel extraction kit (NEB GmbH, Frankfurt, Germany) according to manufacturer’s instructions.

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: Paragraph title: DNA isolation and PCR ... For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Concentration Assay:

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: .. PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols. ..

    High Throughput Screening Assay:

    Article Title: Continuous directed evolution of proteins with improved soluble expression
    Article Snippet: Paragraph title: High-throughput sequencing of genomic DNA. ... PCR 2 conditions: 98 °C for 2 min, then 12 cycles of (98 °C for 15 s, 61 °C for 20 s, 72 °C for 20 s), followed by a final 72 °C extension for 2 min. PCR products were pooled and purified by electrophoresis with a 2% agarose gel using a Monarch DNA Gel Extraction Kit (New England BioLabs) eluting with 30 μL H2 O. DNA concentration was quantified with the KAPA Library Quantification Kit-Illumina (KAPA Biosystems) and sequenced on an Illumina MiSeq instrument (paired-end read – R1: 220 cycles, R2: 0 cycles) according to the manufacturer’s protocols.

    Staining:

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: .. When necessary, final products were separated from non-ligated fragments by electrophoresis using a 0.8–1.5% (m/V) agarose gel stained with Sybr™ Gold (Thermo Fisher Scientific) ( ) and extracted from the gel with the Monarch® DNA Gel Extraction Kit (NEB). .. Hybridization of complementary oligonucleotides or long overhangs was done in a thermocycler by heating the samples at 65°C for 15 min and then decreasing the temperature in 5°C steps every 5 min, until reaching 25°C.

    Article Title: Investigation of Wolbachia spp. and Spiroplasma spp. in Phlebotomus species by molecular methods
    Article Snippet: The resulting PCR products were analyzed by agarose gel-electrophoresis on a 1% gel, stained with ethidium bromide and recorded using the Gel Doc EQ quantification analysis software (Bio-Rad, Image Lab Software Version 4.1). .. The amplified DNA fragments of the correct size were excised from the agarose gel and extracted using the Monarch DNA Gel Extraction Kit (New England Biolabs, Inc.).

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    New England Biolabs monarch dna gel extraction kit
    Monarch Dna Gel Extraction Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs monarch plasmid miniprep kit
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    Monarch RNA Wash Buffer 50 ml
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