ultra ii dna library prep library preparation  (New England Biolabs)


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    Name:
    NEBNext Ultra II Ligation Module
    Description:
    NEBNext Ultra II Ligation Module 96 rxns
    Catalog Number:
    e7595l
    Price:
    1270
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs ultra ii dna library prep library preparation
    NEBNext Ultra II Ligation Module
    NEBNext Ultra II Ligation Module 96 rxns
    https://www.bioz.com/result/ultra ii dna library prep library preparation/product/New England Biolabs
    Average 95 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    ultra ii dna library prep library preparation - by Bioz Stars, 2020-02
    95/100 stars

    Images

    1) Product Images from "Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue"

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

    Journal: Genome Medicine

    doi: 10.1186/s13073-016-0375-z

    CN profiles of unamplified (UA) and WGA samples. a CN profile of MCC sample MCT4, which is unamplified and untreated, with 100 ng input of DNA. b CN profile of the same sample, which is unamplified and untreated, down-sampled to the similar coverage as the matched WGA sample. c CN profile of the same sample, which is WGA and untreated. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]
    Figure Legend Snippet: CN profiles of unamplified (UA) and WGA samples. a CN profile of MCC sample MCT4, which is unamplified and untreated, with 100 ng input of DNA. b CN profile of the same sample, which is unamplified and untreated, down-sampled to the similar coverage as the matched WGA sample. c CN profile of the same sample, which is WGA and untreated. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Techniques Used: Whole Genome Amplification

    Experimental design testing a low-input method (NEBNext Ultra II) on copy number detection of two FFPE MCC samples by LC WGS as well as the effect of WGA with or without NEB DNA repair treatment
    Figure Legend Snippet: Experimental design testing a low-input method (NEBNext Ultra II) on copy number detection of two FFPE MCC samples by LC WGS as well as the effect of WGA with or without NEB DNA repair treatment

    Techniques Used: Formalin-fixed Paraffin-Embedded, Whole Genome Amplification

    Copy number profiles of MCC sample MCT4 with DNA input of ( a ) 100 ng, ( b ) 20 ng, and ( c ) 5 ng. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]
    Figure Legend Snippet: Copy number profiles of MCC sample MCT4 with DNA input of ( a ) 100 ng, ( b ) 20 ng, and ( c ) 5 ng. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Techniques Used:

    Related Articles

    Centrifugation:

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 × g for 1 h at 4 °C, washed once with 1.5 ml 70% ethanol, and re-pelleted by centrifugation. .. It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Amplification:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The panel was split into 2 primer pools and amplified with 5× Ion AmpliSeq HiFi Master Mix, followed by FuPa treatment (Ion AmpliSeq DNA Library Kit 2.0; Thermo Fisher Scientific). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ). .. 1μL amplified DNA was electrophoresed using a DNA 12,000 chip on the 2100 Bioanalyser system (Agilent, US) to determine the concentration.

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: Paragraph title: Sequence-Independent, Single-Primer Amplification (SISPA) library preparation and sequencing ... For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl NEBNext Ultra II end prep enzyme (E7103) were mixed in and samples incubated 30 minutes at 20°C, then 30 minutes at 65°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.

    DNA Synthesis:

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: A Klenow fragment DNA polymerase was used for second strand DNA synthesis (New England Biolabs, Ipswich, MA). .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used.

    Synthesized:

    Article Title: A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
    Article Snippet: .. NEBNext ultra II library preparation 1 ng of purified cfDNA or 5 ng of synthesized oligos, as measured by the Quant-iT, was taken through library preparation (end-polishing, adapter ligation, index PCR) as outlined in the NEBNext Ultra II manual using the supplied reagents, recommended AMPure cleanup ratios, and recommended index PCR cycles. .. Sequencing All cfDNA libraries were sequenced on an Illumina® HiSeqX at a 2 × 151 read length by Fulgent Genetics.

    Construct:

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: DNA repair and large insert library preparation Large insert libraries were constructed using an adaptation of NEBNext® UltraTM II DNA Library Prep protocol (New England Biolabs, US) with preliminary steps of single strand DNA elimination using Exonuclease VII treatment and DNA damage repair using PreCR® repair mix (New England Biolabs, US) (Fig. ). .. Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ).

    Real-time Polymerase Chain Reaction:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Library concentration was determined with Kapa Biosystems Library qPCR quantification kit on the Lightcycler 480 Real-Time PCR System (Roche).

    Incubation:

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: DNA end repair and adapter ligation Eluted products were pooled to 500 µL in TES and incubated with 1 mg/ml Proteinase K (Sigma) for 30 min at 60 °C, prior to overnight ethanol precipitation at −80 °C with 1.41 ml ethanol, 0.2 mg/ml glycogen and 200 mM NaOAc. .. It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. After adding resuspended AMPure XP Beads to the PCR products, the mixture was incubated at room temperature for at least 20 min instead of 5 min.

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: The sheared DNA was end repaired and A-tailed by addition of 3 μL of NEBNext® UltraTM II End Prep Enzyme Mix and incubated for 5 minutes at 25 °C and then 30 minutes at 65 °C. .. Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ).

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: The recommended SQK-LSK109 protocol for library preparation for PromethION (ONT) sequencing was followed with slight increases in all enzymatic incubation times and during elution. .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: .. 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl NEBNext Ultra II end prep enzyme (E7103) were mixed in and samples incubated 30 minutes at 20°C, then 30 minutes at 65°C. .. 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.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Activity Assay:

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded. .. It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Modification:

    Article Title: Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
    Article Snippet: Library preparation and sequencing Eight sequencing library preparation kits were used in this study: XT, KAPA HyperPlus (NIPPON Genetics Co. Ltd, Tokyo, Japan) with PCR or PCR-free workflow (referred to as KP and KPF, respectively), NEBNext Ultra II (referred to as NN; New England Biolabs Japan, Tokyo, Japan), QIAseq FX (QS; QIAGEN), TruSeq nano (TS; Illumina), TruSeq DNA PCR-Free (TSF; Illumina), and Nextera DNA Flex (FL; Illumina) ( ). .. These parameters were set according to the XT protocol, for which the amount of input DNA and the number of PCR cycles were essentially unable to be modified.

    Flow Cytometry:

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007) to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)***. .. Another round of AMPure XP purification was then performed before the DNA library was eluted and loaded onto a running buffer-primed flow cell for sequencing.

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007)*** to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)****. .. Another round of AMPure XP purification was then performed before the DNA library was eluted and loaded onto a running buffer-primed flow cell for sequencing.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Ligation:

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: .. Next, adaptor ligation was performed as described in the NEBNext Ultra II DNA Library Prep protocol, following the instructions for 1 μg of input DNA. .. After ligation of Illumina adaptors on the beads, the beads were washed twice with 1× Binding and Wash buffer and twice with 0.1× TE.

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: .. Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007) to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)***. .. Another round of AMPure XP purification was then performed before the DNA library was eluted and loaded onto a running buffer-primed flow cell for sequencing.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Ligation products were purified and size selected using 0.8× Agencourt AMPure XP beads.

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: Paragraph title: DNA end repair and adapter ligation ... It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: .. Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007)*** to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)****. .. Another round of AMPure XP purification was then performed before the DNA library was eluted and loaded onto a running buffer-primed flow cell for sequencing.

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. In brief, DNA fragmented using the Covaris S2 in 50 μL was used for NEBNext End Prep, followed by an immediate adaptor ligation step with a 1.5 μM diluted adaptor.

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: .. Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ). .. A 96 μL reaction volume contained 60 μL of the end repaired reaction mixture (previous step), 30 μL NEBNext® UltraTM II Ligation Master Mix, 1μL NEBNext® Ligation Enhancer and 4 μL SeqCap® Adapter A (10 μM stock).

    Article Title: A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
    Article Snippet: .. NEBNext ultra II library preparation 1 ng of purified cfDNA or 5 ng of synthesized oligos, as measured by the Quant-iT, was taken through library preparation (end-polishing, adapter ligation, index PCR) as outlined in the NEBNext Ultra II manual using the supplied reagents, recommended AMPure cleanup ratios, and recommended index PCR cycles. .. Sequencing All cfDNA libraries were sequenced on an Illumina® HiSeqX at a 2 × 151 read length by Fulgent Genetics.

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: Next, adaptor ligation was performed as described in the NEBNext Ultra II DNA Library Prep protocol, following the instructions for 1 μg of input DNA. .. The PCR was carried out as outlined in the NEBNext Ultra II protocol, NEBNext Multiplex oligos for Illumina (NEB #E7335S and #E7500S) were used for the individual barcodes and the enrichment was performed using ten cycles.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used. ..

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl NEBNext Ultra II end prep enzyme (E7103) were mixed in and samples incubated 30 minutes at 20°C, then 30 minutes at 65°C. .. 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.

    DNA Sequencing:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Polymerase Chain Reaction:

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: Next, adaptor ligation was performed as described in the NEBNext Ultra II DNA Library Prep protocol, following the instructions for 1 μg of input DNA. .. Fifteen microliters of the beads containing adaptor-ligated DNA was transferred to a new tube and we continued on to PCR enrichment of adaptor-ligated DNA on the beads.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: DNA (10 ng) was amplified for 18 cycles of PCR with the Ion AmpliSeq custom DNA panel (Thermo Fisher Scientific), enriching the 195 target amplicons. .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
    Article Snippet: .. Library preparation and sequencing Eight sequencing library preparation kits were used in this study: XT, KAPA HyperPlus (NIPPON Genetics Co. Ltd, Tokyo, Japan) with PCR or PCR-free workflow (referred to as KP and KPF, respectively), NEBNext Ultra II (referred to as NN; New England Biolabs Japan, Tokyo, Japan), QIAseq FX (QS; QIAGEN), TruSeq nano (TS; Illumina), TruSeq DNA PCR-Free (TSF; Illumina), and Nextera DNA Flex (FL; Illumina) ( ). .. For XT, KP, NN, QS, and FL, 1 ng of DNA, measured by Agilent TapeStation (Agilent Technologies, CA, USA), was used for input DNA, and the number of PCR cycles was fixed at 12.

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Article Title: A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
    Article Snippet: .. NEBNext ultra II library preparation 1 ng of purified cfDNA or 5 ng of synthesized oligos, as measured by the Quant-iT, was taken through library preparation (end-polishing, adapter ligation, index PCR) as outlined in the NEBNext Ultra II manual using the supplied reagents, recommended AMPure cleanup ratios, and recommended index PCR cycles. .. Sequencing All cfDNA libraries were sequenced on an Illumina® HiSeqX at a 2 × 151 read length by Fulgent Genetics.

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: .. The PCR was carried out as outlined in the NEBNext Ultra II protocol, NEBNext Multiplex oligos for Illumina (NEB #E7335S and #E7500S) were used for the individual barcodes and the enrichment was performed using ten cycles. .. Forty-five microliters of the supernatant containing the PCR products was transferred to a new tube and were cleaned using a 0.8× bead cleanup of the PCR reaction with Agencourt AMPure XP beads (Beckman Coulter #A63881).

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: Amplified PCR products were treated with an RNAse cocktail and column purified (Qiagen Valencia, CA). .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used.

    Article Title: Transcription-induced formation of extrachromosomal DNA during yeast ageing
    Article Snippet: 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl NEBNext Ultra II end prep enzyme (E7103) were mixed in and samples incubated 30 minutes at 20°C, then 30 minutes at 65°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.

    Binding Assay:

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: Next, adaptor ligation was performed as described in the NEBNext Ultra II DNA Library Prep protocol, following the instructions for 1 μg of input DNA. .. After ligation of Illumina adaptors on the beads, the beads were washed twice with 1× Binding and Wash buffer and twice with 0.1× TE.

    Magnetic Beads:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The 2 primer pools for each sample were then pooled and purified with 1.8× Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Isolation:

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded. .. After ligation of the P7 adapter, DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90) and eluted in 50 µL 10 mM Tris-HCl.

    Purification:

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: Damage to DNA was then repaired using the preCR repair mix (NEB)**, according to manufacturer recommendations and DNA subsequently purified using AMPureXP beads (Beckman Coulter). .. Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007) to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)***.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The 2 primer pools for each sample were then pooled and purified with 1.8× Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: Damage to DNA was then repaired using the preCR repair mix (NEB)**, according to manufacturer recommendations and DNA subsequently purified using AMPureXP beads (Beckman Coulter). .. Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007)*** to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)****.

    Article Title: A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
    Article Snippet: .. NEBNext ultra II library preparation 1 ng of purified cfDNA or 5 ng of synthesized oligos, as measured by the Quant-iT, was taken through library preparation (end-polishing, adapter ligation, index PCR) as outlined in the NEBNext Ultra II manual using the supplied reagents, recommended AMPure cleanup ratios, and recommended index PCR cycles. .. Sequencing All cfDNA libraries were sequenced on an Illumina® HiSeqX at a 2 × 151 read length by Fulgent Genetics.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: Amplified PCR products were treated with an RNAse cocktail and column purified (Qiagen Valencia, CA). .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used.

    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. .. 3.5 μl NEBNext Ultra II end prep buffer and 1.5 μl NEBNext Ultra II end prep enzyme (E7103) were mixed in and samples incubated 30 minutes at 20°C, then 30 minutes at 65°C.

    Sequencing:

    Article Title: Robust long-read native DNA sequencing using the ONT CsgG Nanopore system
    Article Snippet: Paragraph title: Library preparation and sequencing ... Ligation of ‘E7’ motor protein-complexed AMX adapter (ONT, NSK007) to genomic DNA ends was next carried out using the NEBNext Ultra II Ligation Module (NEB)***.

    Article Title: Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
    Article Snippet: .. Library preparation and sequencing Eight sequencing library preparation kits were used in this study: XT, KAPA HyperPlus (NIPPON Genetics Co. Ltd, Tokyo, Japan) with PCR or PCR-free workflow (referred to as KP and KPF, respectively), NEBNext Ultra II (referred to as NN; New England Biolabs Japan, Tokyo, Japan), QIAseq FX (QS; QIAGEN), TruSeq nano (TS; Illumina), TruSeq DNA PCR-Free (TSF; Illumina), and Nextera DNA Flex (FL; Illumina) ( ). .. For XT, KP, NN, QS, and FL, 1 ng of DNA, measured by Agilent TapeStation (Agilent Technologies, CA, USA), was used for input DNA, and the number of PCR cycles was fixed at 12.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Paragraph title: Whole genome sequencing (WGS) ... In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used. ..

    Chromatin Immunoprecipitation:

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ). .. 1μL amplified DNA was electrophoresed using a DNA 12,000 chip on the 2100 Bioanalyser system (Agilent, US) to determine the concentration.

    Software:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Additionally, the public genome data repository of Complete Genomics Inc. containing freely accessible WGS data of 69 individuals, 52 unrelated individuals (software version 1.10.0; http://www.completegenomics.com/public-data/ ) [ ], as well as WGS data from 427 individuals (157 unrelated) sequenced by Complete Genomics Inc. (software version 2.2.0) and distributed by the 1000 genome project [ ] were used for comparative purposes. .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Multiplex Assay:

    Article Title: Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance
    Article Snippet: .. The PCR was carried out as outlined in the NEBNext Ultra II protocol, NEBNext Multiplex oligos for Illumina (NEB #E7335S and #E7500S) were used for the individual barcodes and the enrichment was performed using ten cycles. .. Forty-five microliters of the supernatant containing the PCR products was transferred to a new tube and were cleaned using a 0.8× bead cleanup of the PCR reaction with Agencourt AMPure XP beads (Beckman Coulter #A63881).

    Selection:

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Agarose Gel Electrophoresis:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Prior to library preparation, the DNA was sheared to 35 kb using the Megaruptor (Diagenode, BE) and size selected to a minimal length of 6 kb on the BluePippin (Sage Science, MA, USA) using a High-pass protocol and the S1 external marker on a 0.75% agarose gel (Sage Science, USA). .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Ethanol Precipitation:

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: DNA end repair and adapter ligation Eluted products were pooled to 500 µL in TES and incubated with 1 mg/ml Proteinase K (Sigma) for 30 min at 60 °C, prior to overnight ethanol precipitation at −80 °C with 1.41 ml ethanol, 0.2 mg/ml glycogen and 200 mM NaOAc. .. It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Random Hexamer Labeling:

    Article Title: Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
    Article Snippet: Briefly, random hexamer oligonucleotides coupled with unique barcodes were used for first strand cDNA synthesis (Life Technologies, Carlsbad, CA). .. For Illumina Miseq sequencing, the New England Biolabs (NEB) end prep and ligation modules (E7546S, E7595S) and Bio Scientific barcoded adapters (514113) were used.

    Concentration Assay:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Library concentration was determined with Kapa Biosystems Library qPCR quantification kit on the Lightcycler 480 Real-Time PCR System (Roche).

    Article Title: A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
    Article Snippet: The remaining 50 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except for the use of a custom P7 adapter (Supplementary Table ). .. It is our understanding that NEBNext Ultra II contains a polymerase capable of blunting ends by either extending the complementary strand towards a ssDNA 5′ extension, or exonucleolytically trimming a ssDNA 3′ extension, but that ssDNA 5′ extensions are not degraded.

    Article Title: Large Enriched Fragment Targeted Sequencing (LEFT-SEQ) Applied to Capture of Wolbachia Genomes
    Article Snippet: Following this, SeqCap® adaptors (Roche, NimbleGen) were ligated to both ends of DNA using the NEBNext® UltraTM II Ligation Module (New England Biolabs) (Fig. ). .. 1μL amplified DNA was electrophoresed using a DNA 12,000 chip on the 2100 Bioanalyser system (Agilent, US) to determine the concentration.

    Marker:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Prior to library preparation, the DNA was sheared to 35 kb using the Megaruptor (Diagenode, BE) and size selected to a minimal length of 6 kb on the BluePippin (Sage Science, MA, USA) using a High-pass protocol and the S1 external marker on a 0.75% agarose gel (Sage Science, USA). .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

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    New England Biolabs ultra ii dna library prep library preparation
    CN profiles of unamplified (UA) and WGA samples. a CN profile of <t>MCC</t> sample MCT4, which is unamplified and untreated, with 100 ng input of <t>DNA.</t> b CN profile of the same sample, which is unamplified and untreated, down-sampled to the similar coverage as the matched WGA sample. c CN profile of the same sample, which is WGA and untreated. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]
    Ultra Ii Dna Library Prep Library Preparation, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    CN profiles of unamplified (UA) and WGA samples. a CN profile of MCC sample MCT4, which is unamplified and untreated, with 100 ng input of DNA. b CN profile of the same sample, which is unamplified and untreated, down-sampled to the similar coverage as the matched WGA sample. c CN profile of the same sample, which is WGA and untreated. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Journal: Genome Medicine

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

    doi: 10.1186/s13073-016-0375-z

    Figure Lengend Snippet: CN profiles of unamplified (UA) and WGA samples. a CN profile of MCC sample MCT4, which is unamplified and untreated, with 100 ng input of DNA. b CN profile of the same sample, which is unamplified and untreated, down-sampled to the similar coverage as the matched WGA sample. c CN profile of the same sample, which is WGA and untreated. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications.

    Techniques: Whole Genome Amplification

    Experimental design testing a low-input method (NEBNext Ultra II) on copy number detection of two FFPE MCC samples by LC WGS as well as the effect of WGA with or without NEB DNA repair treatment

    Journal: Genome Medicine

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

    doi: 10.1186/s13073-016-0375-z

    Figure Lengend Snippet: Experimental design testing a low-input method (NEBNext Ultra II) on copy number detection of two FFPE MCC samples by LC WGS as well as the effect of WGA with or without NEB DNA repair treatment

    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications.

    Techniques: Formalin-fixed Paraffin-Embedded, Whole Genome Amplification

    Copy number profiles of MCC sample MCT4 with DNA input of ( a ) 100 ng, ( b ) 20 ng, and ( c ) 5 ng. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Journal: Genome Medicine

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

    doi: 10.1186/s13073-016-0375-z

    Figure Lengend Snippet: Copy number profiles of MCC sample MCT4 with DNA input of ( a ) 100 ng, ( b ) 20 ng, and ( c ) 5 ng. Each point represents the normalized read count ratio of a 50 kb sized bin. Separate chromosomes from 1 to 22 as well as X and Y are shown and a log 2 (copy number/2) equal to zero corresponds to a copy number of 2. Segments were removed from highly repetitive or problematic regions [ 8 ]

    Article Snippet: NEBNext® Ultra ™ II DNA Library Prep Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications.

    Techniques: