e6040  (New England Biolabs)


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  • 99
    Name:
    NEBNext DNA Library Prep Master Mix Set for Illumina
    Description:
    NEBNext DNA Library Prep Master Mix Set for Illumina 60 rxns
    Catalog Number:
    E6040L
    Price:
    1428
    Size:
    60 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs e6040
    NEBNext DNA Library Prep Master Mix Set for Illumina
    NEBNext DNA Library Prep Master Mix Set for Illumina 60 rxns
    https://www.bioz.com/result/e6040/product/New England Biolabs
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    e6040 - by Bioz Stars, 2019-07
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Hybridisation probes of 0.5 to 1.6 kilobase pairs (kb) were generated for these genes from either cDNA clones of the genes or by polymerase chain reaction (PCR) amplification from targeted gDNA regions. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Amplification:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Hybridisation probes of 0.5 to 1.6 kilobase pairs (kb) were generated for these genes from either cDNA clones of the genes or by polymerase chain reaction (PCR) amplification from targeted gDNA regions. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies. .. Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Article Title: Targeted resequencing and variant validation using pxlence PCR assays
    Article Snippet: To assess assay performance and end-point equimolarity, quantitative PCR was used for sample 1, while classical PCR was performed for sample 2. .. Following amplification using a universal protocol (KAPA 2G Robust–spiked with LCGreen Plus for sample 1), products were pooled per sample and prepped for sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs). .. Both samples were sequenced on a single Illumina MiSeq run (2 × 150 cycles) generating 3,819,421 and 3,747,843 reads, respectively.

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor. .. Both oligos were custom ordered from Sigma Aldrich (St Louis). (2) After each consecutive library preparation step the library was purified with Agencourt AMPure XP -beads (Beckman Coulter, cat. no A63881). (3) For each library 15 ng of ligated library was used for pre-capture PCR in five parallel reactions.

    Article Title: The spectrum of somatic mutations in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape than that in multiple myeloma
    Article Snippet: A total of 200 ng DNA from peripheral blood and 3 μg whole-genome amplified tumor DNA were fragmented by the Covaris E-Series. .. Fragmented DNA was end-repaired, A-tailed and adaptors ligated by the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA, USA).

    Article Title: Molecular mechanisms of fission in echinoderms: Transcriptome analysis
    Article Snippet: The amplified dsDNA was prepared using the SMART method. .. Samples of cDNA were prepared for sequencing using NEBNext dsDNA Fragmentase (NEB) and a NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB).

    Construct:

    Article Title: Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome
    Article Snippet: Total genomic DNA was extracted using a mini-scale CTAB protocol [ ]. .. 5 μg of total DNA were fragmented using a Covaris S-series sonicator, and short-insert (300 bp) libraries were constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs Inc., Ipswich, MA) following the manufacturer’s protocol. .. To verify the expected size profile, library products were run against a size standard on a 1% low-melt agarose gel at 120 V for 30 min. DNA library concentration was determined using the Kapa Library Quantification Kit (Kapa Biosystems Inc., Wilmington, MA) on an Applied Biosystems 7500 Real-Time PCR System.

    Article Title: Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam
    Article Snippet: Whole blood was collected from these birds, and genomic DNA was extracted by a combination of standard phenol/chloroform methods [ ] and DNeasy Blood Kit (Qiagen, Valencia, CA, USA). .. Samples of genomic DNA (1μg) were fragmented to a median fragment size of 200 bp using a Covaris S2 Sample Preparation System (Covaris Inc., Woburn, MA, USA) and used to construct DNA libraries using NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA). .. Library quality and quantity were evaluated using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and a KAPA Library Quantification Kit (Kapabiosystems, Inc., Woburn, MA, USA).

    Article Title: Concurrent Mutations in ATM and Genes Associated with Common γ Chain Signaling in Peripheral T Cell Lymphoma
    Article Snippet: Sequencing library construction, exome capture, sequencing, and analyses were carried out by the Genomics Resource Center (GRC) within the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. .. Genomic DNA libraries with 7bp molecular barcode indexes were constructed for sequencing on the Illumina platform using the NEBNext® DNA Sample Prep Master Mix Set 1 (New England Biolabs, Ipswich, MA). .. DNA was fragmented with the Covaris E210 focused ultrasonicator (Covaris Woburn, MA), targeting a size of 200bp, and libraries were prepared using a modified version of manufacturer’s protocol.

    Article Title: A mutagenesis-derived Lrp5 mouse mutant with abnormal retinal vasculature and low bone mineral density
    Article Snippet: Genomic DNA (1 µg) was fragmented using a E220 Focused-ultrasonicator (Covaris, Woburn, MA) E220 to a range of sizes centered on 300 bp. .. The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR. .. The precapture library was hybridized to the Roche (Madison, WI) NimbleGen SeqCap EZ Mouse Exome Design (Ref #9999042611) capture probe set according to the manufacturer’s instructions.

    Article Title: Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)
    Article Snippet: For that, we extracted the genomic DNA from fresh leaf material dried in silica gel from a single individual of S. riparium (voucher: Nogueira 170 ; ) collected in Manaus (Amazonas State, Brazil) using the Invisorb Spin Plant Mini Kit (Invitek, Berlin, Germany) and following the manufacturer’s instructions. .. Approximately 5 μg of total DNA was fragmented using a Covaris S-Series Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA) and a short-insert (300 bp) library was constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocol. .. The library concentration was diluted to 10 mM and sequenced (single end) on an Ilumina HiSeq 2000 system (Illumina, San Diego, California, USA) at the University of São Paulo (Escola Superior de Agricultura Luiz de Queiroz da Universidade de São Paulo [ESALq]) in Piracicaba, Brazil.

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: After the DNA was de-crosslinked and extracted, ChIP-seq and qPCR were conducted as previously described , , , . .. The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol. .. The primers’ sequences for ChIP-qPCR are listed in Supplementary Table .

    Real-time Polymerase Chain Reaction:

    Article Title: Targeted resequencing and variant validation using pxlence PCR assays
    Article Snippet: To assess assay performance and end-point equimolarity, quantitative PCR was used for sample 1, while classical PCR was performed for sample 2. .. Following amplification using a universal protocol (KAPA 2G Robust–spiked with LCGreen Plus for sample 1), products were pooled per sample and prepped for sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs).

    Article Title: A mutagenesis-derived Lrp5 mouse mutant with abnormal retinal vasculature and low bone mineral density
    Article Snippet: The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR. .. The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR.

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Products from each step of the library preparation were purified with either Agencourt AMPure XP SPRI beads using the same protocol or the QIAquick 96 PCR purification kit (Qiagen, Hilden, Germany).

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: After the DNA was de-crosslinked and extracted, ChIP-seq and qPCR were conducted as previously described , , , . .. The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol.

    Incubation:

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: To obtain fragments of interest, samples were incubated with anti-H3K4me3 antibody (Abcam, ab8580) or anti-Flag (Sigma, F1804) antibody overnight. .. The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol.

    Article Title: Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
    Article Snippet: The overnight broth was used to seed a fresh TPG broth and incubated for 8 h. Cultures were then centrifuged at 14,000 rpm for 30 min and the supernatant was discarded. .. Sequencing libraries were prepared for Roche/454 sequencing using the NEBNext Quick DNA Library Prep Reagent Set (New England Biolabs) and for Illumina MiSeq using the Nextera XT DNA Library Preparation Kit (Illumina).

    Article Title: Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
    Article Snippet: Approximately 100 ng of DNA was built into each Illumina shotgun library at the LMAMR, Norman, Oklahoma using NEBNext DNA Library Prep Master Set (E6076) and blunt-end modified Illumina adapters. .. Approximately 100 ng of DNA was built into each Illumina shotgun library at the LMAMR, Norman, Oklahoma using NEBNext DNA Library Prep Master Set (E6076) and blunt-end modified Illumina adapters.

    Modification:

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: DNA from pooled and individual flies was extracted following a modified high-salt protocol ( ) and fragmented using a Covaris (Woburn, MA) S2 device. .. Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies. .. Size selection and final library purification were performed using AMPureXP beads (Beckman Coulter, Fullerton, CA) with an additional gel-based size selection for the pooled South African sample and the individually sequenced Viennese flies.

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: Preparation of libraries for Illumina whole-genome sequencing was based upon a previously published method ( ) but was modified as sequencing technology evolved during the course of the project. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA).

    Article Title: Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
    Article Snippet: The extracts were quantified using a Qubit High Sensitivity fluorometer (Life Technologies) (Supplementary Table ). .. Approximately 100 ng of DNA was built into each Illumina shotgun library at the LMAMR, Norman, Oklahoma using NEBNext DNA Library Prep Master Set (E6076) and blunt-end modified Illumina adapters. .. Blunt-end repair was performed using 50 μl reactions with 30 μl of DNA extract for each sample which was then incubated for 20 min at 12 °C and 15 min at 37 °C and purified using Qiagen MinElute silica spin columns following the manufacturer’s instructions.

    Gel Purification:

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Flow Cytometry:

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies. .. Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Ligation:

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: Two different DNA library preparation kits were used in this study: NEBNext (New England BioLabs, cat. no E6040L) and ThruPLEX DNA-seq (Rubicon Genomics, cat. no R400407). .. For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor. .. Illumina Index PE adaptor oligo mix (from primers 5′-GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) was used in ligation.

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: The shearing protocol was as follows: 75 s at 0°C prechill, followed by 20 cycles of sonication for 10.0 s at full power, 75 s at 0°C lid chill, 10 s at 0°C plate chill, and 75 s at 0°C postchill. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Cell Culture:

    Article Title: Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
    Article Snippet: Strains were cultured from -80 °C glycerol stocks on fresh Tryptone-Sulphite-Cycloserine (TSC) plates (Oxoid). .. Sequencing libraries were prepared for Roche/454 sequencing using the NEBNext Quick DNA Library Prep Reagent Set (New England Biolabs) and for Illumina MiSeq using the Nextera XT DNA Library Preparation Kit (Illumina).

    Generated:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: To ensure reliable capture of shorter exons, we specifically generated longer hybridisation probes from gDNA for those exons that were shorter than 50 bp by including approximately 100 bp genomic DNA flanking the exons on both sides. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Article Title: Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936
    Article Snippet: Genomic DNA was isolated from a 50-mL yeast extract-peptone-dextrose culture, after spheroplast osmotic lysis and glass-rod purification of ethanol-precipitated nucleic acids. .. The DNA library was prepared from 1 μg according to the NEBNext DNA library prep master mix set for the Illumina (E6040) protocol with an insert size of 368 ± 122 nucleotides generated with a Covaris ultrasonicator. .. The library was sequenced on the Illumina MiSeq version 1.18.54 platform, producing approximately 1.5 million paired-end reads, representing a 28× coverage.

    DNA Sequencing:

    Article Title: Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome
    Article Snippet: Paragraph title: Collecting material and DNA sequencing ... 5 μg of total DNA were fragmented using a Covaris S-series sonicator, and short-insert (300 bp) libraries were constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs Inc., Ipswich, MA) following the manufacturer’s protocol.

    Article Title: Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam
    Article Snippet: Paragraph title: Library preparation and DNA sequencing ... Samples of genomic DNA (1μg) were fragmented to a median fragment size of 200 bp using a Covaris S2 Sample Preparation System (Covaris Inc., Woburn, MA, USA) and used to construct DNA libraries using NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA).

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: Two different DNA library preparation kits were used in this study: NEBNext (New England BioLabs, cat. no E6040L) and ThruPLEX DNA-seq (Rubicon Genomics, cat. no R400407). .. For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor.

    Sequencing:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Further details of the capture probe validation and preparation can be found in a previous report [ ]. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA). .. End repair of DNA fragments, addition of a 3′ adenine (A), adaptor ligation, and reaction clean-up were performed according to the manufacturer’s protocol.

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paragraph title: DNA extraction, library preparation, and sequencing ... Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Article Title: Targeted resequencing and variant validation using pxlence PCR assays
    Article Snippet: To assess assay performance and end-point equimolarity, quantitative PCR was used for sample 1, while classical PCR was performed for sample 2. .. Following amplification using a universal protocol (KAPA 2G Robust–spiked with LCGreen Plus for sample 1), products were pooled per sample and prepped for sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs). .. Both samples were sequenced on a single Illumina MiSeq run (2 × 150 cycles) generating 3,819,421 and 3,747,843 reads, respectively.

    Article Title: Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam
    Article Snippet: Samples of genomic DNA (1μg) were fragmented to a median fragment size of 200 bp using a Covaris S2 Sample Preparation System (Covaris Inc., Woburn, MA, USA) and used to construct DNA libraries using NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA). .. Samples of genomic DNA (1μg) were fragmented to a median fragment size of 200 bp using a Covaris S2 Sample Preparation System (Covaris Inc., Woburn, MA, USA) and used to construct DNA libraries using NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA).

    Article Title: Concurrent Mutations in ATM and Genes Associated with Common γ Chain Signaling in Peripheral T Cell Lymphoma
    Article Snippet: Sequencing library construction, exome capture, sequencing, and analyses were carried out by the Genomics Resource Center (GRC) within the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. .. Genomic DNA libraries with 7bp molecular barcode indexes were constructed for sequencing on the Illumina platform using the NEBNext® DNA Sample Prep Master Mix Set 1 (New England Biolabs, Ipswich, MA). .. DNA was fragmented with the Covaris E210 focused ultrasonicator (Covaris Woburn, MA), targeting a size of 200bp, and libraries were prepared using a modified version of manufacturer’s protocol.

    Article Title: Development of microsatellite markers for Sargentodoxa cuneata (Lardizabalaceae) using next-generation sequencing technology
    Article Snippet: Genomic DNA was extracted from silica gel–dried leaves of S. cuneata using the cetyltrimethylammonium bromide (CTAB) method , and microsatellites were isolated using Illumina MiSeq sequencing technology (Illumina, San Diego, California, USA). .. Approximately 1 μg of genomic DNA was used as template for a library preparation with a NEBNext DNA Prep Master Mix Set for Illumina (New England Biolabs, Ipswich, Massachusetts, USA).

    Article Title: A novel FGD1 mutation in a family with Aarskog–Scott syndrome and predominant features of congenital joint contractures
    Article Snippet: Paragraph title: Sample Collection and Whole-Exome Sequencing ... The libraries were prepared using the NEBNext DNA Library Prep Master Mix kit and gel size selected for 450-bp fragments.

    Article Title: Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes
    Article Snippet: Size selection and further purification was performed on pooled PCR products using a 2% E-Gel EX with SYBR Gold II, ran on an E-Gel iBase (Life Technologies, Carlsbad, CA, USA), with products of approximately 340 bp selected for. .. In order to convert samples into Illumina sequencing libraries, a NEBNext DNA Library Prep Master Mix Set for 454 (#E6070, NEB, Ipswich, MA, USA) was used. .. This was performed as per manufacturers guidelines; however, blunt-end p5/p7 Illumina adapters (Meyer and Kircher, ) were substituted in the place of the Roche FLX adapters.

    Article Title: A mutagenesis-derived Lrp5 mouse mutant with abnormal retinal vasculature and low bone mineral density
    Article Snippet: Paragraph title: Whole-exome sequencing ... The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR.

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: Paragraph title: Immunopanel sequencing ... For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor.

    Article Title: Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936
    Article Snippet: We report here the genome sequencing and assembly of the C. lusitaniae type strain CBS 6936 , isolated from citrus peel juice. .. The DNA library was prepared from 1 μg according to the NEBNext DNA library prep master mix set for the Illumina (E6040) protocol with an insert size of 368 ± 122 nucleotides generated with a Covaris ultrasonicator.

    Article Title: Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)
    Article Snippet: We first obtained the chloroplast genome sequence of S. riparium using an Illumina platform. .. Approximately 5 μg of total DNA was fragmented using a Covaris S-Series Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA) and a short-insert (300 bp) library was constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocol.

    Article Title: The spectrum of somatic mutations in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape than that in multiple myeloma
    Article Snippet: Paragraph title: Exome sequencing ... Fragmented DNA was end-repaired, A-tailed and adaptors ligated by the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA, USA).

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: The shearing protocol was as follows: 75 s at 0°C prechill, followed by 20 cycles of sonication for 10.0 s at full power, 75 s at 0°C lid chill, 10 s at 0°C plate chill, and 75 s at 0°C postchill. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: After the DNA was de-crosslinked and extracted, ChIP-seq and qPCR were conducted as previously described , , , . .. The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol. .. The primers’ sequences for ChIP-qPCR are listed in Supplementary Table .

    Article Title: Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
    Article Snippet: The pellets were then subjected to a phenol/chloroform DNA extraction. .. Sequencing libraries were prepared for Roche/454 sequencing using the NEBNext Quick DNA Library Prep Reagent Set (New England Biolabs) and for Illumina MiSeq using the Nextera XT DNA Library Preparation Kit (Illumina). .. Genomes were sequenced using Roche/454 (Titanium chemistry) and Illumina MiSeq (2 × 300 bp paired-end reads) methods.

    Article Title: Molecular mechanisms of fission in echinoderms: Transcriptome analysis
    Article Snippet: To obtain the most complete transcriptome, the in vitro DSN-normalization method was used [ ]. .. Samples of cDNA were prepared for sequencing using NEBNext dsDNA Fragmentase (NEB) and a NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB). .. The quality control of a sample ready for sequencing (pool of libraries) included determination of concentration using Qubit, qPCR, and testing for Agilent DNA7500 chip.

    Article Title: Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
    Article Snippet: We used the NEB Next Ultimate Library Preparation Kit for Illumina and the Ribo-Zero Magnetic Gold Kit. .. We used the NEB Next Ultimate Library Preparation Kit for Illumina and the Ribo-Zero Magnetic Gold Kit.

    Sonication:

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: The shearing protocol was as follows: 75 s at 0°C prechill, followed by 20 cycles of sonication for 10.0 s at full power, 75 s at 0°C lid chill, 10 s at 0°C plate chill, and 75 s at 0°C postchill. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA).

    Hybridization:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: To ensure reliable capture of shorter exons, we specifically generated longer hybridisation probes from gDNA for those exons that were shorter than 50 bp by including approximately 100 bp genomic DNA flanking the exons on both sides. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    ChIP-sequencing:

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: Paragraph title: ChIP-seq and ChIP-qPCR ... The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol.

    DNA Extraction:

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paragraph title: DNA extraction, library preparation, and sequencing ... Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Article Title: Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens
    Article Snippet: Paragraph title: DNA extraction and genome sequencing ... Sequencing libraries were prepared for Roche/454 sequencing using the NEBNext Quick DNA Library Prep Reagent Set (New England Biolabs) and for Illumina MiSeq using the Nextera XT DNA Library Preparation Kit (Illumina).

    RNA Sequencing Assay:

    Article Title: Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
    Article Snippet: Paragraph title: Bulk RNA Sequencing ... We used the NEB Next Ultimate Library Preparation Kit for Illumina and the Ribo-Zero Magnetic Gold Kit.

    Magnetic Beads:

    Article Title: Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes
    Article Snippet: In order to convert samples into Illumina sequencing libraries, a NEBNext DNA Library Prep Master Mix Set for 454 (#E6070, NEB, Ipswich, MA, USA) was used. .. Samples were equilibrated to 25 μM using molecular grade water and PCR reactions contained: 5 μL of blunt-end products with 0.2 μL of AmpliTaq Gold (Applied Biosystems, Forster City, CA), 2.5 μL of x10 buffer, 2.5 μL of 25 mM MgCl2 , 0.2 μL of 25 mM dNTPs (Invitrogen) and 1 μM of BSA (NEB), 1 μL of primer paired end 1 μL of 10 mM (InPE1.0) forward primer and 1 μM of 10 mM tagged reverse index primer.

    Isolation:

    Article Title: Development of microsatellite markers for Sargentodoxa cuneata (Lardizabalaceae) using next-generation sequencing technology
    Article Snippet: Genomic DNA was extracted from silica gel–dried leaves of S. cuneata using the cetyltrimethylammonium bromide (CTAB) method , and microsatellites were isolated using Illumina MiSeq sequencing technology (Illumina, San Diego, California, USA). .. Approximately 1 μg of genomic DNA was used as template for a library preparation with a NEBNext DNA Prep Master Mix Set for Illumina (New England Biolabs, Ipswich, Massachusetts, USA).

    Article Title: Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936
    Article Snippet: Genomic DNA was isolated from a 50-mL yeast extract-peptone-dextrose culture, after spheroplast osmotic lysis and glass-rod purification of ethanol-precipitated nucleic acids. .. The DNA library was prepared from 1 μg according to the NEBNext DNA library prep master mix set for the Illumina (E6040) protocol with an insert size of 368 ± 122 nucleotides generated with a Covaris ultrasonicator.

    Article Title: Molecular mechanisms of fission in echinoderms: Transcriptome analysis
    Article Snippet: Total RNA was isolated by extraction in phenol-chloroform with TRIreagent (MRC) by the standard method. .. Samples of cDNA were prepared for sequencing using NEBNext dsDNA Fragmentase (NEB) and a NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB).

    Purification:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: All PCR products (10 ng each) were purified using the QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA) before use. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Article Title: Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes
    Article Snippet: Size selection and further purification was performed on pooled PCR products using a 2% E-Gel EX with SYBR Gold II, ran on an E-Gel iBase (Life Technologies, Carlsbad, CA, USA), with products of approximately 340 bp selected for. .. In order to convert samples into Illumina sequencing libraries, a NEBNext DNA Library Prep Master Mix Set for 454 (#E6070, NEB, Ipswich, MA, USA) was used.

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor. .. Illumina Index PE adaptor oligo mix (from primers 5′-GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) was used in ligation.

    Article Title: Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936
    Article Snippet: Genomic DNA was isolated from a 50-mL yeast extract-peptone-dextrose culture, after spheroplast osmotic lysis and glass-rod purification of ethanol-precipitated nucleic acids. .. The DNA library was prepared from 1 μg according to the NEBNext DNA library prep master mix set for the Illumina (E6040) protocol with an insert size of 368 ± 122 nucleotides generated with a Covaris ultrasonicator.

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: Genomic DNA was extracted from P. destructans by a variety of methods, including the OmniPrep for Fungi kit (G-Biosciences, St. Louis, MO), the DNeasy blood and tissue kit (Qiagen, Hilden, Germany) using the supplementary protocol from the manufacturer “Purification of total DNA from yeast using the DNeasy Blood and Tissue kit (DIY13 Aug-06)” as described previously , or a phenol-chloroform extraction. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA).

    Article Title: Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
    Article Snippet: Approximately 100 ng of DNA was built into each Illumina shotgun library at the LMAMR, Norman, Oklahoma using NEBNext DNA Library Prep Master Set (E6076) and blunt-end modified Illumina adapters. .. Approximately 100 ng of DNA was built into each Illumina shotgun library at the LMAMR, Norman, Oklahoma using NEBNext DNA Library Prep Master Set (E6076) and blunt-end modified Illumina adapters.

    Polymerase Chain Reaction:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: All PCR products (10 ng each) were purified using the QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA) before use. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies. .. Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Article Title: Targeted resequencing and variant validation using pxlence PCR assays
    Article Snippet: To assess assay performance and end-point equimolarity, quantitative PCR was used for sample 1, while classical PCR was performed for sample 2. .. Following amplification using a universal protocol (KAPA 2G Robust–spiked with LCGreen Plus for sample 1), products were pooled per sample and prepped for sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs).

    Article Title: Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes
    Article Snippet: Size selection and further purification was performed on pooled PCR products using a 2% E-Gel EX with SYBR Gold II, ran on an E-Gel iBase (Life Technologies, Carlsbad, CA, USA), with products of approximately 340 bp selected for. .. In order to convert samples into Illumina sequencing libraries, a NEBNext DNA Library Prep Master Mix Set for 454 (#E6070, NEB, Ipswich, MA, USA) was used.

    Article Title: A mutagenesis-derived Lrp5 mouse mutant with abnormal retinal vasculature and low bone mineral density
    Article Snippet: Genomic DNA (1 µg) was fragmented using a E220 Focused-ultrasonicator (Covaris, Woburn, MA) E220 to a range of sizes centered on 300 bp. .. The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR. .. The precapture library was hybridized to the Roche (Madison, WI) NimbleGen SeqCap EZ Mouse Exome Design (Ref #9999042611) capture probe set according to the manufacturer’s instructions.

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor. .. For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor.

    Article Title: The spectrum of somatic mutations in monoclonal gammopathy of undetermined significance indicates a less complex genomic landscape than that in multiple myeloma
    Article Snippet: Fragmented DNA was end-repaired, A-tailed and adaptors ligated by the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA, USA). .. Fragmented DNA was end-repaired, A-tailed and adaptors ligated by the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA, USA).

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Size selection of 600-bp fragments was accomplished by excision from 2% agarose gels followed by purification with a QIAquick gel purification kit (Qiagen, Hilden, Germany), E-Gel SizeSelect gel (Life Technologies, Inc., Grand Island, NY), or Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Indianapolis, IN) using the Kapa Biosystems “High-throughput NGS library preparation technical guide, Illumina platforms” ( ).

    Chromatin Immunoprecipitation:

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: Paragraph title: ChIP-seq and ChIP-qPCR ... The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol.

    Software:

    Article Title: Concurrent Mutations in ATM and Genes Associated with Common γ Chain Signaling in Peripheral T Cell Lymphoma
    Article Snippet: Genomic DNA libraries with 7bp molecular barcode indexes were constructed for sequencing on the Illumina platform using the NEBNext® DNA Sample Prep Master Mix Set 1 (New England Biolabs, Ipswich, MA). .. Libraries were pooled so that each received ¼ or ½ a lane of sequencing, and were sequenced with an Illumina HiSeq2000 sequencer 100PE run, generating an average of 86.8 million passed-filter reads per sample.

    Article Title: Molecular mechanisms of fission in echinoderms: Transcriptome analysis
    Article Snippet: Samples of cDNA were prepared for sequencing using NEBNext dsDNA Fragmentase (NEB) and a NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB). .. The library pool was sequenced in one run of Illumina HiSeq 2000, 101 cycles, paired-end reads with the use of TruSeq SBS sequencing kit version 3 (Illumina).

    Multiplex Assay:

    Article Title: Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome
    Article Snippet: Total genomic DNA was extracted using a mini-scale CTAB protocol [ ]. .. 5 μg of total DNA were fragmented using a Covaris S-series sonicator, and short-insert (300 bp) libraries were constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs Inc., Ipswich, MA) following the manufacturer’s protocol. .. To verify the expected size profile, library products were run against a size standard on a 1% low-melt agarose gel at 120 V for 30 min. DNA library concentration was determined using the Kapa Library Quantification Kit (Kapa Biosystems Inc., Wilmington, MA) on an Applied Biosystems 7500 Real-Time PCR System.

    Article Title: Using genomic data to develop chloroplast DNA SSRs for the Neotropical liana Stizophyllum riparium (Bignonieae, Bignoniaceae)
    Article Snippet: For that, we extracted the genomic DNA from fresh leaf material dried in silica gel from a single individual of S. riparium (voucher: Nogueira 170 ; ) collected in Manaus (Amazonas State, Brazil) using the Invisorb Spin Plant Mini Kit (Invitek, Berlin, Germany) and following the manufacturer’s instructions. .. Approximately 5 μg of total DNA was fragmented using a Covaris S-Series Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA) and a short-insert (300 bp) library was constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocol. .. The library concentration was diluted to 10 mM and sequenced (single end) on an Ilumina HiSeq 2000 system (Illumina, San Diego, California, USA) at the University of São Paulo (Escola Superior de Agricultura Luiz de Queiroz da Universidade de São Paulo [ESALq]) in Piracicaba, Brazil.

    Selection:

    Article Title: Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes
    Article Snippet: Size selection and further purification was performed on pooled PCR products using a 2% E-Gel EX with SYBR Gold II, ran on an E-Gel iBase (Life Technologies, Carlsbad, CA, USA), with products of approximately 340 bp selected for. .. In order to convert samples into Illumina sequencing libraries, a NEBNext DNA Library Prep Master Mix Set for 454 (#E6070, NEB, Ipswich, MA, USA) was used.

    Article Title: A mutagenesis-derived Lrp5 mouse mutant with abnormal retinal vasculature and low bone mineral density
    Article Snippet: Genomic DNA (1 µg) was fragmented using a E220 Focused-ultrasonicator (Covaris, Woburn, MA) E220 to a range of sizes centered on 300 bp. .. The precapture paired-end library was constructed using the NEBNext DNA Library Prep Master Mix set for Illumina (New England BioLabs, Ipswich, MA) including a bead-based size selection to select for inserts with an average size of 300 bp followed by 18 cycles of PCR. .. The precapture library was hybridized to the Roche (Madison, WI) NimbleGen SeqCap EZ Mouse Exome Design (Ref #9999042611) capture probe set according to the manufacturer’s instructions.

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Sample Prep:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Further details of the capture probe validation and preparation can be found in a previous report [ ]. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA). .. End repair of DNA fragments, addition of a 3′ adenine (A), adaptor ligation, and reaction clean-up were performed according to the manufacturer’s protocol.

    Article Title: Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster
    Article Snippet: Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies. .. Paired-end library preparation was based on the NEBNext DNA Library Prep Master Mix Set (E6040L; New England Biolabs, Ipswich, MA) for the pooled South African sample and the individually sequenced Viennese flies, whereas a modified protocol of the NEBNext Ultra DNA Library Prep Kit (E7370L) was used for the individually sequenced South African flies.

    Article Title: Genetic features of red and green junglefowls and relationship with Indonesian native chickens Sumatera and Kedu Hitam
    Article Snippet: Whole blood was collected from these birds, and genomic DNA was extracted by a combination of standard phenol/chloroform methods [ ] and DNeasy Blood Kit (Qiagen, Valencia, CA, USA). .. Samples of genomic DNA (1μg) were fragmented to a median fragment size of 200 bp using a Covaris S2 Sample Preparation System (Covaris Inc., Woburn, MA, USA) and used to construct DNA libraries using NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA). .. Library quality and quantity were evaluated using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and a KAPA Library Quantification Kit (Kapabiosystems, Inc., Woburn, MA, USA).

    Article Title: Concurrent Mutations in ATM and Genes Associated with Common γ Chain Signaling in Peripheral T Cell Lymphoma
    Article Snippet: Sequencing library construction, exome capture, sequencing, and analyses were carried out by the Genomics Resource Center (GRC) within the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine. .. Genomic DNA libraries with 7bp molecular barcode indexes were constructed for sequencing on the Illumina platform using the NEBNext® DNA Sample Prep Master Mix Set 1 (New England Biolabs, Ipswich, MA). .. DNA was fragmented with the Covaris E210 focused ultrasonicator (Covaris Woburn, MA), targeting a size of 200bp, and libraries were prepared using a modified version of manufacturer’s protocol.

    Article Title: Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis
    Article Snippet: Two different DNA library preparation kits were used in this study: NEBNext (New England BioLabs, cat. no E6040L) and ThruPLEX DNA-seq (Rubicon Genomics, cat. no R400407). .. For the NEBNext kit, the DNA libraries were prepared from 1–3 μg DNA according to NEBNext DNA Sample Prep Master Mix Set 1 (New England BioLabs) manual with minor modifications: (1) 1 μl of the 25 μM adaptor was used in ligation instead of 10 μl of 15 μM adaptor. .. Illumina Index PE adaptor oligo mix (from primers 5′-GATCGGAAGAGCACACGTCT-3′ and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) was used in ligation.

    Article Title: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
    Article Snippet: After the DNA was de-crosslinked and extracted, ChIP-seq and qPCR were conducted as previously described , , , . .. The sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) following the manufacturer’s protocol. .. The primers’ sequences for ChIP-qPCR are listed in Supplementary Table .

    In Vitro:

    Article Title: Molecular mechanisms of fission in echinoderms: Transcriptome analysis
    Article Snippet: To obtain the most complete transcriptome, the in vitro DSN-normalization method was used [ ]. .. Samples of cDNA were prepared for sequencing using NEBNext dsDNA Fragmentase (NEB) and a NEBNext® DNA Library Prep Master Mix Set for Illumina (NEB).

    Next-Generation Sequencing:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Exons and their flanking 50 bp from 129 known human deafness genes were selected for capture and NGS sequencing using an Illumina HiSeq2000. .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA).

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Concentration Assay:

    Article Title: Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome
    Article Snippet: 5 μg of total DNA were fragmented using a Covaris S-series sonicator, and short-insert (300 bp) libraries were constructed with NEBNext DNA Library Prep Master Mix Set and NEBNext Multiplex oligos for Illumina (New England BioLabs Inc., Ipswich, MA) following the manufacturer’s protocol. .. To verify the expected size profile, library products were run against a size standard on a 1% low-melt agarose gel at 120 V for 30 min. DNA library concentration was determined using the Kapa Library Quantification Kit (Kapa Biosystems Inc., Wilmington, MA) on an Applied Biosystems 7500 Real-Time PCR System.

    DNA Purification:

    Article Title: Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation
    Article Snippet: Fragmented gDNA libraries for Illumina GAII sequencing were prepared using the NEBNextTM DNA Sample Prep Master Mix set (E6040; NEB Biolab, Ipswich, MA, USA). .. End repair of DNA fragments, addition of a 3′ adenine (A), adaptor ligation, and reaction clean-up were performed according to the manufacturer’s protocol.

    Article Title: A novel FGD1 mutation in a family with Aarskog–Scott syndrome and predominant features of congenital joint contractures
    Article Snippet: DNA was extracted from whole blood using the Wizard Genomic DNA Purification Kit per the manufacturer's instructions (Promega). .. The libraries were prepared using the NEBNext DNA Library Prep Master Mix kit and gel size selected for 450-bp fragments.

    High Throughput Screening Assay:

    Article Title: Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
    Article Snippet: The shearing protocol was as follows: 75 s at 0°C prechill, followed by 20 cycles of sonication for 10.0 s at full power, 75 s at 0°C lid chill, 10 s at 0°C plate chill, and 75 s at 0°C postchill. .. End repair, dA-tailing, adapter ligation, and indexing followed the standard Illumina protocol “Preparing samples for multiplexed paired-end sequencing” (part no. 1005361) using reagents from the NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA) or the KAPA high-throughput library preparation kit “with bead” (Kapa Biosystems, Wilmington, MA). .. Libraries were indexed with the Illumina multiplexing sample preparation oligonucleotide kit 6-bp indices (Illumina, San Diego, CA) or custom 8-bp indices for higher index read discrimination ( ).

    Lysis:

    Article Title: Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936
    Article Snippet: Genomic DNA was isolated from a 50-mL yeast extract-peptone-dextrose culture, after spheroplast osmotic lysis and glass-rod purification of ethanol-precipitated nucleic acids. .. The DNA library was prepared from 1 μg according to the NEBNext DNA library prep master mix set for the Illumina (E6040) protocol with an insert size of 368 ± 122 nucleotides generated with a Covaris ultrasonicator.

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