ultra ii ligation mix  (New England Biolabs)


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    Name:
    NEBNext Ultra II DNA Library Prep with Sample Purification Beads
    Description:
    NEBNext Ultra II DNA Library Prep with Sample Purification Beads 96 rxns
    Catalog Number:
    e7103l
    Price:
    2465
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs ultra ii ligation mix
    NEBNext Ultra II DNA Library Prep with Sample Purification Beads
    NEBNext Ultra II DNA Library Prep with Sample Purification Beads 96 rxns
    https://www.bioz.com/result/ultra ii ligation mix/product/New England Biolabs
    Average 94 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    ultra ii ligation mix - by Bioz Stars, 2020-02
    94/100 stars

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    Amplification:

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples. .. These test amplifications were cleaned with 9 μl AMPure beads, eluted with 1.5 μl 0.1x TE and 1 μl run on a Bioanalyzer to determine the optimal cycle number for the final amplification.

    Picogreen Assay:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA). .. Before pooling the barcoded sequencing library, we assessed its quality using a Bio-Rad (Hercules, CA) Experion DNA analysis kit and quantified it using the PicoGreen dsDNA assay.

    Construct:

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany). .. For PacBio SMRT sequencing, a PacBio SMRTbell library was constructed according to the manufacturer’s instructions and the library was sequenced on the PacBio RSII platform.

    Real-time Polymerase Chain Reaction:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Following ChIP, immunoprecipitated DNA was quantified by qPCR using Power SYBR (Life Technologies) on ViiA 7 real-time PCR (Life Technologies). .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Quantitation Assay:

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: .. Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany). .. For PacBio SMRT sequencing, a PacBio SMRTbell library was constructed according to the manufacturer’s instructions and the library was sequenced on the PacBio RSII platform.

    Modification:

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: Chromatin immunoprecipitation sequencing (ChIPseq) ChIP analysis was done essentially as described before [ ], with the modification that chromatin was sheared in a Covaris S200 set to yield a DNA average size of approximately 100–300 bp. .. For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs).

    Flow Cytometry:

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: Genomic DNA of E. coli TolC was extracted by gravity flow using the Genomic-tip 20/G kit (Qiagen, Germany). .. Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany).

    Ligation:

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: .. After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. Samples were cleaned with 44 μl AMPure beads, eluted with 30 μl 0.1x TE, then cleaned again with 27 μl AMPure beads and eluted with 22.5 μl 0.1x TE.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples.

    Protease Inhibitor:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Briefly, chromatin was suspended in lysis buffer 3 (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× inhibitors [protease inhibitor, sodium butyrate, and phosphatase inhibitors] added fresh) and sheared with a Covaris Sonicator (S220). .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Sequencing:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: Paragraph title: Genome extraction and sequencing of C. gilardii W2-2. ... Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA).

    Article Title: Wiskott–Aldrich syndrome protein (WASP) is a tumor suppressor in T cell lymphoma
    Article Snippet: Paragraph title: Library Preparation and Sequencing ... Library preparation of ChIP-seq DNA was performed using the Ultra II Library Prep Kit (NEB E7103L) and Multiplex Oligos for Illumina (NEB E7335L) and sequenced on an Illuminia Nextseq 500 (75bp single end).

    Article Title: A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
    Article Snippet: Multiplexed ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Preparation kit (E7103S) with 25 ng of input or IP DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina [Set 1, E7335] & [Set 2, E7500]). .. Paired-end sequencing (50-nt reads) was performed on an Illumina NextSeq 500.

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: Paragraph title: Extraction of genomic DNA and PacBio/Illumina sequencing. ... Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany).

    Article Title: Acute Inhibition of MEK Suppresses Congenital Melanocytic Nevus Syndrome in a Murine Model Driven by Activated NRAS and Wnt Signaling
    Article Snippet: Paragraph title: Whole-exome sequencing ... For the first batch, a total of 3 μg of DNA was used to prepare a DNA library using Covaris DNA sonication and NEB NEBNext DNA Sample Prep Reagent Set 1 (E6000S, New England Biolabs, Ipswich, MA).

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs). .. Libraries were sequenced on a HiSeq4000 instrument (Illumina Inc) using the HiSeq 3000/4000 SR Cluster Kit for cluster generation and the HiSeq 3000/4000 SBS Kit (50 cycles) for sequencing in the single-end mode, running 1x 50 cycles.

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: .. Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S). .. Libraries were quantified using the Agilent DNA 7500 Kit, and samples were mixed together at equimolar concentration.

    Sonication:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction—H3K27ac (Abcam, ab4729), IgG (Cell Signaling Technology, 2729S), and histone H3 (Abcam, ab1791)—overnight at 4°C. .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Article Title: Acute Inhibition of MEK Suppresses Congenital Melanocytic Nevus Syndrome in a Murine Model Driven by Activated NRAS and Wnt Signaling
    Article Snippet: .. For the first batch, a total of 3 μg of DNA was used to prepare a DNA library using Covaris DNA sonication and NEB NEBNext DNA Sample Prep Reagent Set 1 (E6000S, New England Biolabs, Ipswich, MA). .. DNA fragments containing adaptors were enriched by PCR (four cycles).

    ChIP-sequencing:

    Article Title: Wiskott–Aldrich syndrome protein (WASP) is a tumor suppressor in T cell lymphoma
    Article Snippet: .. Library preparation of ChIP-seq DNA was performed using the Ultra II Library Prep Kit (NEB E7103L) and Multiplex Oligos for Illumina (NEB E7335L) and sequenced on an Illuminia Nextseq 500 (75bp single end). .. ChIP-seq samples were sequenced with the Illumina NextSeq technology, and output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.

    Article Title: A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
    Article Snippet: .. Multiplexed ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Preparation kit (E7103S) with 25 ng of input or IP DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina [Set 1, E7335] & [Set 2, E7500]). .. Paired-end sequencing (50-nt reads) was performed on an Illumina NextSeq 500.

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: Paragraph title: Chromatin immunoprecipitation sequencing (ChIPseq) ... For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs).

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: Paragraph title: ChIP-Sequencing ... Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S).

    Article Title: H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    Article Snippet: Paragraph title: ChIP-seq ... Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with sample purification beads using 100 ng of input DNA.

    Nucleic Acid Electrophoresis:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: We then assessed the DNA quality using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Canoga Park, CA), the DNA size via gel electrophoresis, and finally, the DNA concentration with a Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Life Technologies, Carlsbad, CA). .. Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA).

    Magnetic Beads:

    Article Title: H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    Article Snippet: Antibody-bound chromatin was captured with magnetic beads for 1 h at 4 °C (50 µl 1:1 mixture of Dynabeads Protein A and Dynabeads Protein G, Invitrogen). .. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with sample purification beads using 100 ng of input DNA.

    Purification:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: .. Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA). .. DNA was barcoded using NEBNext multiplex oligonucleotides for Illumina (96 index primers; NEB).

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: The beads were then washed, and DNA was reverse-cross-linked and purified. .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: Exonuclease treated and total DNA samples were incubated at 37°C for 45 minutes with 2 μl NEBNext DNA fragmentase (M0348) and 2 μl fragmentase buffer; then 5 μl 0.5 M EDTA was added followed by 25 μl water, and samples were purified using 50 μl AMPure beads (A63881 Beckman Coulter, UK) and eluted with 25.5 μl 0.1x TE. .. After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C.

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: Purified genomic DNA of E. coli TolC was processed for PacBio SMRT sequencing and Illumina MiSeq paired-end sequencing (2 × 250 bp) with a target genome coverage of 150-fold. .. Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany).

    Article Title: Acute Inhibition of MEK Suppresses Congenital Melanocytic Nevus Syndrome in a Murine Model Driven by Activated NRAS and Wnt Signaling
    Article Snippet: For the first batch, a total of 3 μg of DNA was used to prepare a DNA library using Covaris DNA sonication and NEB NEBNext DNA Sample Prep Reagent Set 1 (E6000S, New England Biolabs, Ipswich, MA). .. Purified libraries were checked for quality throughout the process and quantified using an Agilent (Santa Clara, CA) 2,100 Bioanalyser.

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: DNA was recovered by column purification (PCR Purification Kit, Qiagen) and subjected to library preparation. .. For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs).

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: The samples were extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and with chloroform-isoamyl alcohol (24:1) and then purified using Qiagen PCR cleanup columns. .. Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S).

    Article Title: H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    Article Snippet: .. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with sample purification beads using 100 ng of input DNA. .. Libraries were sequenced using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.

    Polymerase Chain Reaction:

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples. .. These test amplifications were cleaned with 9 μl AMPure beads, eluted with 1.5 μl 0.1x TE and 1 μl run on a Bioanalyzer to determine the optimal cycle number for the final amplification.

    Article Title: Acute Inhibition of MEK Suppresses Congenital Melanocytic Nevus Syndrome in a Murine Model Driven by Activated NRAS and Wnt Signaling
    Article Snippet: For the first batch, a total of 3 μg of DNA was used to prepare a DNA library using Covaris DNA sonication and NEB NEBNext DNA Sample Prep Reagent Set 1 (E6000S, New England Biolabs, Ipswich, MA). .. DNA fragments containing adaptors were enriched by PCR (four cycles).

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: DNA was recovered by column purification (PCR Purification Kit, Qiagen) and subjected to library preparation. .. For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs).

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: The samples were extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and with chloroform-isoamyl alcohol (24:1) and then purified using Qiagen PCR cleanup columns. .. Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S).

    Immunoprecipitation:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Following ChIP, immunoprecipitated DNA was quantified by qPCR using Power SYBR (Life Technologies) on ViiA 7 real-time PCR (Life Technologies). .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Chromatin Immunoprecipitation:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Paragraph title: ChIP library preparation ... Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: Chromatin immunoprecipitation sequencing (ChIPseq) ChIP analysis was done essentially as described before [ ], with the modification that chromatin was sheared in a Covaris S200 set to yield a DNA average size of approximately 100–300 bp. .. For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs).

    Article Title: H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    Article Snippet: DNA from both input and ChIP samples was then extracted using phenol/chloroform. .. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with sample purification beads using 100 ng of input DNA.

    Multiplex Assay:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA). .. DNA was barcoded using NEBNext multiplex oligonucleotides for Illumina (96 index primers; NEB).

    Article Title: Wiskott–Aldrich syndrome protein (WASP) is a tumor suppressor in T cell lymphoma
    Article Snippet: .. Library preparation of ChIP-seq DNA was performed using the Ultra II Library Prep Kit (NEB E7103L) and Multiplex Oligos for Illumina (NEB E7335L) and sequenced on an Illuminia Nextseq 500 (75bp single end). .. ChIP-seq samples were sequenced with the Illumina NextSeq technology, and output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.

    Article Title: A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
    Article Snippet: .. Multiplexed ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Preparation kit (E7103S) with 25 ng of input or IP DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina [Set 1, E7335] & [Set 2, E7500]). .. Paired-end sequencing (50-nt reads) was performed on an Illumina NextSeq 500.

    Sample Prep:

    Article Title: Acute Inhibition of MEK Suppresses Congenital Melanocytic Nevus Syndrome in a Murine Model Driven by Activated NRAS and Wnt Signaling
    Article Snippet: .. For the first batch, a total of 3 μg of DNA was used to prepare a DNA library using Covaris DNA sonication and NEB NEBNext DNA Sample Prep Reagent Set 1 (E6000S, New England Biolabs, Ipswich, MA). .. DNA fragments containing adaptors were enriched by PCR (four cycles).

    Next-Generation Sequencing:

    Article Title: A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II
    Article Snippet: Multiplexed ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Preparation kit (E7103S) with 25 ng of input or IP DNA and barcode adaptors (NEBNext Multiplex Oligos for Illumina [Set 1, E7335] & [Set 2, E7500]). .. Quality control and adapter trimming of FASTQ (raw sequencing) files were done in Galaxy using FastQC Read Quality reports (Galaxy Version 0.69) and trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.3), respectively.

    dsDNA Assay:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: We then assessed the DNA quality using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Canoga Park, CA), the DNA size via gel electrophoresis, and finally, the DNA concentration with a Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Life Technologies, Carlsbad, CA). .. Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA).

    Incubation:

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: .. After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. Samples were cleaned with 44 μl AMPure beads, eluted with 30 μl 0.1x TE, then cleaned again with 27 μl AMPure beads and eluted with 22.5 μl 0.1x TE.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: After addition of 1.25 μl 1:25 diluted NEBNext adaptor (E7335), 0.5 μl ligation enhancer and 15 μl NEBNext Ultra II ligation mix (E7103) samples were incubated 15 minutes at 20°C, then 1.5 μl USER enzyme (E7335) was added and incubated 15 minutes at 37°C. .. A total of 1.25 μl library was amplified with 0.4 μl each NEBNext index and universal primers (E7335) and 5μl NEBNext Ultra II PCR mix (E7103) in 10 μl total volume using recommended cycling conditions with 8 cycles for total samples, 16 cycles for 48 hour aged samples and 18 cycles for 24 hour samples.

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: Beads were resuspended in IP elution buffer [1% SDS, 0.1M NaHCO3 ] and incubated at 65°C for 2 hr 900 rpm. .. Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S).

    Article Title: H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans
    Article Snippet: The soluble chromatin fraction was incubated with primary antibodies against H3K27me2/me3 (Active Motif 39535), OLLAS (Novus Biologicals NBP1-06713B) or H3K36me3 (Abcam ab9050) overnight at 4 °C. .. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep with sample purification beads using 100 ng of input DNA.

    Spectrophotometry:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: We then assessed the DNA quality using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Canoga Park, CA), the DNA size via gel electrophoresis, and finally, the DNA concentration with a Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Life Technologies, Carlsbad, CA). .. Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA).

    Concentration Assay:

    Article Title: Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
    Article Snippet: We then assessed the DNA quality using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Canoga Park, CA), the DNA size via gel electrophoresis, and finally, the DNA concentration with a Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Life Technologies, Carlsbad, CA). .. Next, we prepared a DNA library using a NEBNext Ultra II DNA library preparation kit for Illumina with sample purification beads from New England Biolabs (NEB; Ipswich, MA).

    Article Title: Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
    Article Snippet: For ChIPseq experiments the libraries were prepared from 1 ng of enriched DNA or input DNA using the NEBNext Ultra II DNA Library Prep with Beads as recommended by the manufacturer (New England BioLabs). .. Concentration of the libraries was determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH).

    Article Title: Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
    Article Snippet: Each sample was quantified using a Qubit 2.0 fluorometer (Invitrogen) and 2–20 ng was used to create sequencing libraries using the NEBNext Ultra II DNA Library preparation kit (NEB #E7103S). .. Libraries were quantified using the Agilent DNA 7500 Kit, and samples were mixed together at equimolar concentration.

    Lysis:

    Article Title: Acetyl-CoA promotes glioblastoma cell adhesion and migration through Ca2+–NFAT signaling
    Article Snippet: Briefly, chromatin was suspended in lysis buffer 3 (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× inhibitors [protease inhibitor, sodium butyrate, and phosphatase inhibitors] added fresh) and sheared with a Covaris Sonicator (S220). .. Libraries were prepared using the New England Biolabs Next Ultra II DNA library kit with 25 nM starting material.

    Variant Assay:

    Article Title: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli
    Article Snippet: Quality controls of NEBNext Ultra DNA libraries were conducted by fluorometric quantitation using the Qubit 3.0 fluorometer (Thermo, Fisher Scientific, Germany). .. The genome was error corrected against indel errors by a mapping of Illumina reads onto finished genomes, using BWA ( ) with subsequent variant and consensus calling using VarScan ( ); automated sequence annotation was performed with Prokka (v.1.8) ( ).

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    New England Biolabs ultra ii ligation mix
    Ultra Ii Ligation Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ultra ii ligation mix/product/New England Biolabs
    Average 94 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    ultra ii ligation mix - by Bioz Stars, 2020-02
    94/100 stars
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