dna library preparation kit  (New England Biolabs)


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    Name:
    NEBNext DNA Library Prep Master Mix Set for 454
    Description:
    NEBNext DNA Library Prep Master Mix Set for 454 50 rxns
    Catalog Number:
    E6070L
    Price:
    1260
    Size:
    50 rxns
    Category:
    DNA Analysis
    Score:
    85
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    Structured Review

    New England Biolabs dna library preparation kit
    NEBNext DNA Library Prep Master Mix Set for 454
    NEBNext DNA Library Prep Master Mix Set for 454 50 rxns
    https://www.bioz.com/result/dna library preparation kit/product/New England Biolabs
    Average 99 stars, based on 539 article reviews
    Price from $9.99 to $1999.99
    dna library preparation kit - by Bioz Stars, 2019-11
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: Paragraph title: Sequencing of MTP BAC clones ... After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland).

    Centrifugation:

    Article Title: Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish
    Article Snippet: Bacterial cells were cultured in medium (1% soluble starch, 0.5% yeast extract, 0.5% peptone, 0.1% K2 HPO4 , 0.02% MgSO4 ·7H2 O, and 5% NaCl) at 30°C and were collected by centrifugation (10,000 × g , 15 min, 4°C). .. A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

    Article Title: Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States
    Article Snippet: Fungal tissue was collected by centrifugation at 4000 rpm for 5 min and ground with liquid nitrogen. .. A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Amplification:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb. .. We added 5 µl Adapter Fill-in Reaction Buffer and 3 µl Bst DNA polymerase, Large Fragment to the full eluate volume and incubated the reaction at 37°C for 20 min. For AT libraries, we used the NEBNext Quick DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref : E6090), without the small fragment removal step, and with 10 pmol Illumina inPE adapter.

    Article Title: An efficient approach for the development of genome-specific markers in allohexaploid wheat (Triticum aestivum L.) and its application in the construction of high-density linkage maps of the D genome
    Article Snippet: An NEBNext Quick DNA Library Prep Master Mix set for 454 (New England Biolabs Inc., Beverly, MA, USA) was used to construct two genomic libraries. .. These libraries were amplified and fractionated from 500 to 700 bp before hybridization using a SeqCap EZ reagent Kit.

    Article Title: Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
    Article Snippet: Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States). .. Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States).

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA). .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: Amplification and sequencing of the strain molecular barcodes ... The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs).

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs).

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Following an extensive study of the impact of DNA amount, amplification and library preparation protocol , the method developed at Genoscope and described in detail at https://www.protocols.io/groups/sullivan-lab was chosen for preparation of all viral metagenomics libraries from Tara Oceans stations. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions. .. The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions.

    Methylated DNA Immunoprecipitation Sequencing:

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Paragraph title: MeDIP-seq ... Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    Construct:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: BAC DNAs were prepared in a 96-deepwell plate, extracted using the alkaline lysis method and purified with the MultiScreen Filter plate (Millipore, Billerica, MA, USA). .. After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland). .. The tagged DNAs were subjected to size selection using agarose gel electrophoresis to obtain DNA fragments of the appropriate size (600–1200 bp) and then quantified using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Article Title: An efficient approach for the development of genome-specific markers in allohexaploid wheat (Triticum aestivum L.) and its application in the construction of high-density linkage maps of the D genome
    Article Snippet: In total, 1,000 ng of each DNA sample was sheared using a Covaris LE220 (Covaris Inc., Woburn, MA, USA) focused ultrasonicator to fragments that averaged 600 bp. .. An NEBNext Quick DNA Library Prep Master Mix set for 454 (New England Biolabs Inc., Beverly, MA, USA) was used to construct two genomic libraries. .. These libraries were amplified and fractionated from 500 to 700 bp before hybridization using a SeqCap EZ reagent Kit.

    Article Title: Holo-Seq: single-cell sequencing of holo-transcriptome
    Article Snippet: cDNA from 1 ng of total mESC RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells. .. Then, 2 ng of cDNA was sheared into 150- to 350-bp fragments by sonication, and a NEBNext DNA library preparation kit (E7645) was used to construct the sequencing library. .. cDNA from 1 ng mESC total RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells.

    Article Title: Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish
    Article Snippet: Five micrograms of genomic DNA dissolved in Tris-EDTA (TE) buffer was digested by a Covaris S-2 sonicator (Covaris, Woburn, MA, USA), with an average size of 500 bases. .. A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol. .. The library was sequenced by a massively parallel sequencer (MiSeq; Illumina KK, Tokyo, Japan) with a 300-base paired-end format, and finally, 2.90 Gb of sequence reads was obtained.

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: ChIRP oligos and pools are listed in the Supplemental Material. .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs). .. Sequencing libraries were barcoded using TruSeq adapters and sequenced on HiSeq or NextSeq instruments (Illumina) using single-end 50-bp reads.

    Real-time Polymerase Chain Reaction:

    Article Title: Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
    Article Snippet: Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States). .. The adapter was ligated to the A-tailed DNA fragments and 200 ng of the adapter-ligated DNA fragments was amplified over 22 cycles using the primers Tra_Fp and Tra_Mp_Rp which contain unique 7-bp indexes (indicated by N) for sample multiplexing ( ).

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: Relative fold enrichment of SRF was determined by adding DNA to Brilliant II SYBR Green qPCR Master Mix Kit (Agilent Technologies). .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Incubation:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: Each library building reaction was purified on a MinElute column (QIAGEN) and eluted in 32 µl EB buffer following 15 min incubation at 37°C. .. For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb.

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: ChIP with non-specific IgG control antibody incubated with ASZ001 extract was used as a control to calculate fold enrichment. .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Activity Assay:

    Article Title: Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin
    Article Snippet: Streptomyces canus C-509 (ATCC 12647) is a notable member of this group and was previously isolated by researchers of the Bristol-Myers Company (now Bristol-Myers Squibb Co.) in the 1950s, who identified its production of telomycin, an antibiotic with noteworthy bactericidal activity ( , ). .. The associated library was prepared using a NEBNext DNA library preparation kit (New England BioLabs) and sequenced via a 2 × 151-bp reagent kit, providing approximately 14.5 million reads and 100× average coverage.

    Expressing:

    Article Title: Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila
    Article Snippet: Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform. .. Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform.

    Derivative Assay:

    Article Title: An efficient approach for the development of genome-specific markers in allohexaploid wheat (Triticum aestivum L.) and its application in the construction of high-density linkage maps of the D genome
    Article Snippet: Most of the remaining 3,997 sequences were EST sequences derived from mapped 9K iSelect probes showing polymorphisms in Japanese varieties, and additional sequences to fill in gaps in coverage were based on bin-mapped wheat ESTs that were selected based on the barley physical map. .. An NEBNext Quick DNA Library Prep Master Mix set for 454 (New England Biolabs Inc., Beverly, MA, USA) was used to construct two genomic libraries.

    Hybridization:

    Article Title: An efficient approach for the development of genome-specific markers in allohexaploid wheat (Triticum aestivum L.) and its application in the construction of high-density linkage maps of the D genome
    Article Snippet: An NEBNext Quick DNA Library Prep Master Mix set for 454 (New England Biolabs Inc., Beverly, MA, USA) was used to construct two genomic libraries. .. These libraries were amplified and fractionated from 500 to 700 bp before hybridization using a SeqCap EZ reagent Kit.

    Article Title: Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin
    Article Snippet: Sequencing was performed by the Farncombe Metagenomics Facility at McMaster University on an Illumina HiSeq DNA sequencer using TruSeq Rapid version 1 chemistry with cBot hybridization. .. The associated library was prepared using a NEBNext DNA library preparation kit (New England BioLabs) and sequenced via a 2 × 151-bp reagent kit, providing approximately 14.5 million reads and 100× average coverage.

    Ligation:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: Each library was built using an aliquot of 16 µl of DNA extract and following two different protocols: the first using A-tailed adapters (inPE adapters), and the second based on blunt-ended adapter ligation . .. For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb.

    Article Title: Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species. Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species
    Article Snippet: 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070). .. 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070).

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA). .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Briefly, 10–15 ng DNA were fragmented to a 150–600 bp size range using the E210 Covaris instrument. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs). .. After two consecutive 1x AMPure XP clean ups, the ligated product was amplified by 12 cycles PCR using Platinium Pfx DNA polymerase followed by 0.6x AMPure XP purification.

    Protease Inhibitor:

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: Cross-linked material was resuspended in 7 mL of nuclear lysis buffer supplemented with protease inhibitor cocktail and Superase-In and then solubilized and sheared by sonication using a Covaris E-series focused ultrasonicator (850 µL per tube, 4°C water bath, 5% duty cycle, 140 PIP, 60 min total). .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: Beads were washed with ChIP wash buffer (100mM Tris pH 9.0, 500mM LiCl, 1% Igepal, 1% Deoxycholic Acid, protease inhibitor cocktail [Roche]) and protein/DNA complexes were eluted with IP elution buffer (1%SDS, 50mM NaCOH3 ). .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Cell Culture:

    Article Title: Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish
    Article Snippet: Bacterial cells were cultured in medium (1% soluble starch, 0.5% yeast extract, 0.5% peptone, 0.1% K2 HPO4 , 0.02% MgSO4 ·7H2 O, and 5% NaCl) at 30°C and were collected by centrifugation (10,000 × g , 15 min, 4°C). .. A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

    Generated:

    Article Title: Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila
    Article Snippet: Briefly, total RNA from dissected ovaries was purified using Trizol, and ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (human/mouse/rat) (Epicenter) with additional probes. .. Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform. .. The RNA-seq reads were first mapped against Drosophila rRNA using Bowtie version 0.12.7 ( ) with the following settings: “-v3 -a.” The remaining reads were aligned against the Drosophila melanogaster genome (dm3) with settings “-v0 -m1,” and reads corresponding to RefSeq-annotated genes and piRNA clusters were calculated using eXpress or custom Python scripts.

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: ChIP with non-specific IgG control antibody incubated with ASZ001 extract was used as a control to calculate fold enrichment. .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs). .. ChIP libraries were sequenced using the Illumina HiSeq 4000 platform.

    other:

    Article Title: Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
    Article Snippet: E6070L).

    CpG Methylation Assay:

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. Sequencing reads were filtered to remove low-quality calls and adapters were removed using v0.2.2 of Trim Galore ( www.bioinformatics.babraham.ac.uk/projects/trim_galore ) with default parameters.

    Sequencing:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: BAC DNAs were prepared in a 96-deepwell plate, extracted using the alkaline lysis method and purified with the MultiScreen Filter plate (Millipore, Billerica, MA, USA). .. After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland). .. The tagged DNAs were subjected to size selection using agarose gel electrophoresis to obtain DNA fragments of the appropriate size (600–1200 bp) and then quantified using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Article Title: Holo-Seq: single-cell sequencing of holo-transcriptome
    Article Snippet: cDNA from 1 ng of total mESC RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells. .. Then, 2 ng of cDNA was sheared into 150- to 350-bp fragments by sonication, and a NEBNext DNA library preparation kit (E7645) was used to construct the sequencing library. .. cDNA from 1 ng mESC total RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells.

    Article Title: Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin
    Article Snippet: Sequencing was performed by the Farncombe Metagenomics Facility at McMaster University on an Illumina HiSeq DNA sequencer using TruSeq Rapid version 1 chemistry with cBot hybridization. .. The associated library was prepared using a NEBNext DNA library preparation kit (New England BioLabs) and sequenced via a 2 × 151-bp reagent kit, providing approximately 14.5 million reads and 100× average coverage.

    Article Title: Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
    Article Snippet: Paragraph title: Preparation of TraDIS Sequencing Libraries ... Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States).

    Article Title: Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish
    Article Snippet: A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol. .. The library was sequenced by a massively parallel sequencer (MiSeq; Illumina KK, Tokyo, Japan) with a 300-base paired-end format, and finally, 2.90 Gb of sequence reads was obtained.

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: MeDIP DNA libraries were prepared for multiplexed-paired-end sequencing on the Illumina GAIIx platform as follows. .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Both tags were amplified in a single 20 μl PCR reaction using the SequalPrep Long PCR Kit (Invitrogen). .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs). .. The sequencing was done on Illumina HiSequation 2000 or MiSeq instruments with paired ends of 101 or 150 bp, respectively.

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. Final library amplification (11 cycles) was performed with KAPA Uracil+ (Kapa Biosystems), after which the libraries were purified using 1x Ampure beads.

    Article Title: Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States
    Article Snippet: Paragraph title: Genomic DNA extraction and sequencing ... A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Genome-Wide Binding Patterns of Thyroid Hormone Receptor Beta
    Article Snippet: Paragraph title: Sequencing ... Solexa libraries were prepared using the NEBNext DNA Sample Preparation Kit (NEB) and Illumina PE adapters (Illumina) from three pooled replicates of control cell line and TRβ-expressing cells +/−T3.

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: Paragraph title: 2.1. Genomic DNA extraction and sequencing ... A 450 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Paragraph title: [4] Sequencing library preparation ... End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: In order to locate the Tn in the selected mutant strain and to verify the insertion of only one Tn in its genome, Ion Torrent genome sequencing was performed. .. The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions. .. The adapter ligated library fragments were separated by gel electrophoresis followed by extraction of approximately 500 bp fragments from a 2% ( w / v ) E‐gel (Life Technologies).

    Sonication:

    Article Title: Holo-Seq: single-cell sequencing of holo-transcriptome
    Article Snippet: cDNA from 1 ng of total mESC RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells. .. Then, 2 ng of cDNA was sheared into 150- to 350-bp fragments by sonication, and a NEBNext DNA library preparation kit (E7645) was used to construct the sequencing library. .. cDNA from 1 ng mESC total RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells.

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: Cross-linked material was resuspended in 7 mL of nuclear lysis buffer supplemented with protease inhibitor cocktail and Superase-In and then solubilized and sheared by sonication using a Covaris E-series focused ultrasonicator (850 µL per tube, 4°C water bath, 5% duty cycle, 140 PIP, 60 min total). .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Each sample was sonicated for 6 cycles of 10 mins (30s on/off) cycle at +4°C. .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA). .. MeDIP was performed using 4μg of each library, using a previously described method ( ).

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Peak areas for the fragment ions were obtained from extracted ion chromatograms of the relevant scans and quantified by external calibration relative to standards obtained by digestion of nucleotide triphosphates. .. Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. DNA was subsequently bisulfite-treated using the Sigma Imprint kit according to the manufacturer’s instructions (one step protocol).

    Binding Assay:

    Article Title: Genome-Wide Binding Patterns of Thyroid Hormone Receptor Beta
    Article Snippet: Solexa libraries were prepared using the NEBNext DNA Sample Preparation Kit (NEB) and Illumina PE adapters (Illumina) from three pooled replicates of control cell line and TRβ-expressing cells +/−T3. .. Solexa sequencing data was aligned to HG19 with Bowtie 0.12.7 .

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: Paragraph title: Locating the transposon in the mutant strain with altered binding to anti‐FHbp antibody ... The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions.

    Multiplexing:

    Article Title: Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
    Article Snippet: Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States). .. Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States).

    Methylated DNA Immunoprecipitation:

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: MeDIP DNA libraries were prepared for multiplexed-paired-end sequencing on the Illumina GAIIx platform as follows. .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    DNA Extraction:

    Article Title: Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States
    Article Snippet: Paragraph title: Genomic DNA extraction and sequencing ... A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: Paragraph title: 2.1. Genomic DNA extraction and sequencing ... A 450 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Library preparation from viral samples (Method ID: MetaG_virus) Due to very low DNA extraction yields obtained from concentrated viral samples (usually only a few nanograms), library preparation protocol was adapted in order to improve its efficiency starting from very low input DNA. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    In Vivo:

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: Paragraph title: In vivo ChIRP-seq ... The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

    RNA Sequencing Assay:

    Article Title: Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila
    Article Snippet: Paragraph title: RNA-seq library preparation and high-throughput data analyses ... Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform.

    BAC Assay:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: Paragraph title: Sequencing of MTP BAC clones ... After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland).

    Methylation:

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Peak areas for the fragment ions were obtained from extracted ion chromatograms of the relevant scans and quantified by external calibration relative to standards obtained by digestion of nucleotide triphosphates. .. Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. DNA was subsequently bisulfite-treated using the Sigma Imprint kit according to the manufacturer’s instructions (one step protocol).

    Mutagenesis:

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: Paragraph title: Locating the transposon in the mutant strain with altered binding to anti‐FHbp antibody ... The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions.

    Isolation:

    Article Title: Draft Genome Sequence of Streptomyces canus ATCC 12647, a Producer of Telomycin
    Article Snippet: Bacterial DNA was isolated using a GenElute bacterial genomic DNA kit (Sigma). .. The associated library was prepared using a NEBNext DNA library preparation kit (New England BioLabs) and sequenced via a 2 × 151-bp reagent kit, providing approximately 14.5 million reads and 100× average coverage.

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: RNA was digested with 0.2ug/ml RNase A at 37°C for 30 min. DNA was isolated using Qiagen min elute columns using manufacturers instructions. .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Purification:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: Each library building reaction was purified on a MinElute column (QIAGEN) and eluted in 32 µl EB buffer following 15 min incubation at 37°C. .. For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb.

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: BAC DNAs were prepared in a 96-deepwell plate, extracted using the alkaline lysis method and purified with the MultiScreen Filter plate (Millipore, Billerica, MA, USA). .. After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland).

    Article Title: Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species. Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species
    Article Snippet: 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070). .. 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070).

    Article Title: Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model
    Article Snippet: Briefly, 1 μg of genomic DNA was sheared to fragments of 100–1,500 bp, followed by end repair and A-tailing with the NEBNext DNA library preparation kit (New England Biolabs, United States). .. The adapter was ligated to the A-tailed DNA fragments and 200 ng of the adapter-ligated DNA fragments was amplified over 22 cycles using the primers Tra_Fp and Tra_Mp_Rp which contain unique 7-bp indexes (indicated by N) for sample multiplexing ( ).

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: ChIRP oligos and pools are listed in the Supplemental Material. .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs). .. Sequencing libraries were barcoded using TruSeq adapters and sequenced on HiSeq or NextSeq instruments (Illumina) using single-end 50-bp reads.

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Both tags were amplified in a single 20 μl PCR reaction using the SequalPrep Long PCR Kit (Invitrogen). .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs). .. The sequencing was done on Illumina HiSequation 2000 or MiSeq instruments with paired ends of 101 or 150 bp, respectively.

    Article Title: Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
    Article Snippet: Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs). .. Genomic DNA was prepared using AllPrep DNA/RNA mini kit (QIAGEN), fragmented by sonication (Covaris) and ligated to methylated adapters (Illumina) with the NEBnext library preparation kit (New England BioLabs).

    Article Title: Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila
    Article Snippet: Briefly, total RNA from dissected ovaries was purified using Trizol, and ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (human/mouse/rat) (Epicenter) with additional probes. .. Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform.

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Amplified library was purified and size-selected as described above. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    Polymerase Chain Reaction:

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA). .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA).

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Both tags were amplified in a single 20 μl PCR reaction using the SequalPrep Long PCR Kit (Invitrogen). .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs). .. The sequencing was done on Illumina HiSequation 2000 or MiSeq instruments with paired ends of 101 or 150 bp, respectively.

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs). .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions. .. The adapter ligated library fragments were separated by gel electrophoresis followed by extraction of approximately 500 bp fragments from a 2% ( w / v ) E‐gel (Life Technologies).

    Agarose Gel Electrophoresis:

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs). .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

    Article Title: Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States
    Article Snippet: The quality and quantity of the genomic DNA were assessed by agarose gel electrophoresis and spectrophotometric analysis, respectively. .. A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: The quality and quantity of the genomic DNA were assessed by agarose gel electrophoresis and fluorometric analysis, respectively. .. A 450 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Chromatin Immunoprecipitation:

    Article Title: Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States
    Article Snippet: A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions. .. A 400 bp library was prepared from genomic DNA with the NEBNext Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs, Ipswich, NE, USA) following the manufacturer's instructions.

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: Paragraph title: Chromatin immunoprecipitation ... ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Plasmid Preparation:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland). .. The resulting SFF files were split into separate files of each BAC clone based on MID by using the sffile program in SFF Tools (Roche, Basel, Switzerland).

    SYBR Green Assay:

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: Relative fold enrichment of SRF was determined by adding DNA to Brilliant II SYBR Green qPCR Master Mix Kit (Agilent Technologies). .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs).

    Multiplex Assay:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb. .. For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb.

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: BAC DNAs were prepared in a 96-deepwell plate, extracted using the alkaline lysis method and purified with the MultiScreen Filter plate (Millipore, Billerica, MA, USA). .. After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland). .. The tagged DNAs were subjected to size selection using agarose gel electrophoresis to obtain DNA fragments of the appropriate size (600–1200 bp) and then quantified using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Both tags were amplified in a single 20 μl PCR reaction using the SequalPrep Long PCR Kit (Invitrogen). .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs). .. The sequencing was done on Illumina HiSequation 2000 or MiSeq instruments with paired ends of 101 or 150 bp, respectively.

    Sample Prep:

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Both tags were amplified in a single 20 μl PCR reaction using the SequalPrep Long PCR Kit (Invitrogen). .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs). .. The sequencing was done on Illumina HiSequation 2000 or MiSeq instruments with paired ends of 101 or 150 bp, respectively.

    Article Title: Genome-Wide Binding Patterns of Thyroid Hormone Receptor Beta
    Article Snippet: Samples were used in ChIP analyses were analyzed in triplicate, and three pooled replicate samples were used for ChIP-Seq analysis. .. Solexa libraries were prepared using the NEBNext DNA Sample Preparation Kit (NEB) and Illumina PE adapters (Illumina) from three pooled replicates of control cell line and TRβ-expressing cells +/−T3. .. Libraries were sequenced on a Solexa GAIIx following standard procedures.

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Briefly, 10–15 ng DNA were fragmented to a 150–600 bp size range using the E210 Covaris instrument. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs). .. After two consecutive 1x AMPure XP clean ups, the ligated product was amplified by 12 cycles PCR using Platinium Pfx DNA polymerase followed by 0.6x AMPure XP purification.

    Next-Generation Sequencing:

    Article Title: Genome-wide methylation analysis in Silver-Russell syndrome patients
    Article Snippet: Each sample was sonicated for 6 cycles of 10 mins (30s on/off) cycle at +4°C. .. Next generation sequencing libraries were prepared from sonicated DNA samples using the NEBNEXT DNA library preparation kit (NEB, USA). .. MeDIP was performed using 4μg of each library, using a previously described method ( ).

    Article Title: Viral to metazoan marine plankton nucleotide sequences from theTara Oceans expedition
    Article Snippet: Library amplification was performed using Kapa Hifi HotStart NGS library Amplification kit (Kapa Biosystems, Wilmington, MA) (98 °C for 45 s, 12 cycles of 15 s at 98 °C, 30 s at 60 °C, 30 s at 72 °C and 72 °C for 1 min) instead of Platinum Pfx Taq Polymerase. .. End repair, A-tailing and ligation with adjusted concentrations of homemade adaptors were performed using the NEBNext DNA Sample Preparation Reagent Set 1 (New England Biolabs).

    Ancient DNA Assay:

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
    Article Snippet: Paragraph title: Ancient DNA library preparation ... For BE libraries, we used the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, reference nb.

    Produced:

    Article Title: Holo-Seq: single-cell sequencing of holo-transcriptome
    Article Snippet: cDNA from 1 ng of total mESC RNA or single cells was produced following the manufacturer’s protocol using the Smart-Seq2® v4 Ultra® Low Input RNA kit (Clontech) for single cells. .. Then, 2 ng of cDNA was sheared into 150- to 350-bp fragments by sonication, and a NEBNext DNA library preparation kit (E7645) was used to construct the sequencing library.

    Concentration Assay:

    Article Title: Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species. Mitochondrial DNA of pre‐last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species
    Article Snippet: 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070). .. 2.5 DNA libraries were built using the NEBNext DNA Library Prep Master Mix Set for 454 (New England BioLabs, ref: E6070).

    Article Title: The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target) The role of apolipoprotein N‐acyl transferase, Lnt, in the lipidation of factor H binding protein of Neisseria meningitidis strain MC58 and its potential as a drug target
    Article Snippet: The sequencing library was prepared using 0.5 μg of genomic DNA and the ‘fragmentation and library preparation kit’ (New England Biolabs), according to the manufacturer's instructions. .. The gel extracted DNA fragments were PCR amplified using 6 cycles as described in the ‘fragmentation and library preparation kit’.

    Alkaline Lysis:

    Article Title: A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
    Article Snippet: BAC DNAs were prepared in a 96-deepwell plate, extracted using the alkaline lysis method and purified with the MultiScreen Filter plate (Millipore, Billerica, MA, USA). .. After fragmentation with the Covaris Acoustic Solubilizer LE220 (Covaris, Woburn, MA, USA), the sequencing libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for 454 (New England Biolabs, Ipswich, MA, USA) and tagged with Multiplex Identifier (MID) Adaptors (Roche, Basel, Switzerland).

    ChIP-sequencing:

    Article Title: Non-canonical hedgehog pathway activation by MKL1/SRF promotes drug-resistance in basal cell carcinomas
    Article Snippet: ChIP with non-specific IgG control antibody incubated with ASZ001 extract was used as a control to calculate fold enrichment. .. ChIP-seq libraries were generated using the standard protocol for the NEB-Illumina library preparation kit (New England BioLabs). .. ChIP libraries were sequenced using the Illumina HiSeq 4000 platform.

    DNA Purification:

    Article Title: Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae
    Article Snippet: Genomic DNA purification was done using 10 μl of the hygromycin-resistant cells. .. The PCR products were then purified and used for library preparation and multiplex sequencing ( ) using the NEBNext DNA Sample Preparation kit (New England BioLabs).

    High Throughput Screening Assay:

    Article Title: Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila
    Article Snippet: Paragraph title: RNA-seq library preparation and high-throughput data analyses ... Libraries were generated using the NEBNext library preparation kit (New England Biolabs) for Illumina HiSeq 2500 (50-base-pair [bp] reads) platform.

    Lysis:

    Article Title: Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish
    Article Snippet: The cell pellet was treated with cell lysis solution (20 mg/ml lysozyme, 20 mM Tris-HCl [pH 8.0], 2 mM EDTA, 1.2% Triton X-100) for 30 min at 37°C. .. A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: Cross-linked material was resuspended in 7 mL of nuclear lysis buffer supplemented with protease inhibitor cocktail and Superase-In and then solubilized and sheared by sonication using a Covaris E-series focused ultrasonicator (850 µL per tube, 4°C water bath, 5% duty cycle, 140 PIP, 60 min total). .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

    Fluorescence In Situ Hybridization:

    Article Title: Rapid evolutionary turnover underlies conserved lncRNA–genome interactions
    Article Snippet: ChIRP oligos were designed against roX1 and roX2 RNAs from each species using the Stellaris single-molecule FISH oligo designer (Biosearch Technologies). .. The DNA fraction from each ChIRP experiment and inputs were purified, and libraries were constructed using the NEBNext DNA library preparation kit (New England Biolabs).

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