rna library prep kit  (New England Biolabs)


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    Name:
    NEBNext Ultra II RNA Library Prep Kit for Illumina
    Description:
    NEBNext Ultra II RNA Library Prep Kit for Illumina 96 rxns
    Catalog Number:
    E7770L
    Price:
    3025
    Size:
    96 rxns
    Category:
    mRNA Template Preparation for PCR
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    Structured Review

    New England Biolabs rna library prep kit
    NEBNext Ultra II RNA Library Prep Kit for Illumina
    NEBNext Ultra II RNA Library Prep Kit for Illumina 96 rxns
    https://www.bioz.com/result/rna library prep kit/product/New England Biolabs
    Average 99 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    rna library prep kit - by Bioz Stars, 2019-08
    99/100 stars

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    Amplification:

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction. .. The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction.

    Construct:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: After two 200μL washes beads were resuspended in 10μL Tris pH 7.5, heated at 75°C for 2 min and eluate was immediately subjected to a second round of purification using 10μL beads per sample and eluting in 20μL – resulting in 30-100ng RNA. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles. .. Library concentrations were estimated using Bioanalyzer (Agilent) and Qubit (ThermoFisher) assays, pooled and sequenced on a Next-seq instrument (Illumina) using 1.8pM, 75bp paired-end.

    Real-time Polymerase Chain Reaction:

    Article Title: Destabilization of B2 RNA by EZH2 activates the stress response
    Article Snippet: Subsequently we used the NEBnext small RNA library construction kit (NEB) with the following modifications: Incubation of the 3′adaptor was performed for 2 hours, and the libraries at the end were not subjected to double size selection with the Ampure beads but with 1.2X size selection. .. For sequencing of the in vitro B2 fragments no ribosomal depletion was applied For the longer RNAs we used the NEBNext Ultra directional RNA library kit (NEB) with an RNA fragmentation of 10 min at 95C and with the following modifications: First strand synthesis at 42C was done for 50 min and the End Prep of cDNA library was followed by an Ampure Beads selection of 1.8x and ligation of the adapters using the 5x quick ligation buffer and Quick T4 DNA ligase (NEB) for 30 min. Incubation with the USER enzyme was done before the PCR amplification for 30 min, followed by a double size selection of 0.5x–1x, while the final library was size selected using Ampure beads at a 1x sample-beads ratio.

    Incubation:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: To purify polyA+ species 10μg DNAse treated RNA was heated at 65°C 5 min, transferred on ice, mixed with 20μL oligodT(25) magnetic beads (ThermoFisher) prewashed and resuspended in 45μL binding buffer and incubated 15min at room temperature. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles.

    Article Title: Destabilization of B2 RNA by EZH2 activates the stress response
    Article Snippet: For short RNA library construction, ribo-depleted short RNAs were subjected to PNK 3′-phosphoryl removal for 1 hour at 37C. .. Subsequently we used the NEBnext small RNA library construction kit (NEB) with the following modifications: Incubation of the 3′adaptor was performed for 2 hours, and the libraries at the end were not subjected to double size selection with the Ampure beads but with 1.2X size selection. .. For sequencing of the in vitro B2 fragments no ribosomal depletion was applied For the longer RNAs we used the NEBNext Ultra directional RNA library kit (NEB) with an RNA fragmentation of 10 min at 95C and with the following modifications: First strand synthesis at 42C was done for 50 min and the End Prep of cDNA library was followed by an Ampure Beads selection of 1.8x and ligation of the adapters using the 5x quick ligation buffer and Quick T4 DNA ligase (NEB) for 30 min. Incubation with the USER enzyme was done before the PCR amplification for 30 min, followed by a double size selection of 0.5x–1x, while the final library was size selected using Ampure beads at a 1x sample-beads ratio.

    Expressing:

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs). .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs).

    Article Title: PDE4D regulates Spine Plasticity and Memory in the Retrosplenial Cortex
    Article Snippet: RNA-Seq libraries prepared with non-stranded NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) using random hexamers. .. 3–20 pM of each library underwent paired end (2 × 50) sequencing on a HighSeq 2000 (Illumina) with 8 libraries multiplexed per lane.

    Modification:

    Article Title: MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice
    Article Snippet: The mRNA was purified from 2 μg of total RNA using the Dynabeads mRNA Purification Kit (Invitrogen) and then submitted to library construction for the transcriptome experiments using the Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. .. The mRNA was purified from 2 μg of total RNA using the Dynabeads mRNA Purification Kit (Invitrogen) and then submitted to library construction for the transcriptome experiments using the Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol.

    Flow Cytometry:

    Article Title: Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
    Article Snippet: The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA. .. The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA.

    Article Title: Destabilization of B2 RNA by EZH2 activates the stress response
    Article Snippet: The flow through was collected and 100% EtOH at 2/3 of the flow through volume was added and passed through a new filter column to bind short RNAs. .. Subsequently we used the NEBnext small RNA library construction kit (NEB) with the following modifications: Incubation of the 3′adaptor was performed for 2 hours, and the libraries at the end were not subjected to double size selection with the Ampure beads but with 1.2X size selection.

    Sequencing:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: Paragraph title: Library preparation and sequencing ... Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes.

    Article Title: MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice
    Article Snippet: The mRNA was purified from 2 μg of total RNA using the Dynabeads mRNA Purification Kit (Invitrogen) and then submitted to library construction for the transcriptome experiments using the Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. .. After removing adaptor and low-quality reads, clean reads were mapped to the rice genome MSU7.0 using TopHat and analyzed using Cufflinks according to with a little modification, which includes the Poisson dispersion model of fragments being used to conduct statistical analysis (false discovery rate < 0.05) and ethylene-responsive genes being identified by fragments per kilobase per million reads requiring more than 1.5-fold change between two samples.

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: RNA isolation and sequencing were done at the RNA Sequencing Core at Cornell University. .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs).

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: Paragraph title: Library preparations and sequencing. ... The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction.

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S). .. RNA-Seq data were generated with Illumina HiSeq3000 for 50 cycles (single-end reads).

    Article Title: Tet1 and Tet2 maintain mesenchymal stem cell homeostasis via demethylation of the P2rX7 promoter
    Article Snippet: Three RNA samples from each group were used for RNA-seq analysis. .. For each sample, we used NEBNext Ultra RNA library Pre Kit to prepare a sequencing library from 1 μg of total RNA, and 2 × 100 paired-end sequencing in fat run mode was performed using the HiSeq 2500 and Illumina TruSeq SBS-Kit v2 (200 cycles). .. Illunina’s bcl bcl2fastq v1.8.4 software (Illumina,San Diego, CA) was used to convert the resulting base calling (.bcl) to FASTQ files.

    Article Title: PDE4D regulates Spine Plasticity and Memory in the Retrosplenial Cortex
    Article Snippet: RNA-Seq libraries prepared with non-stranded NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) using random hexamers. .. RNA-Seq libraries prepared with non-stranded NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) using random hexamers.

    Article Title: LincRNA H19 protects from dietary obesity by constraining expression of monoallelic genes in brown fat
    Article Snippet: All libraries were sequenced in parallel on a HiSeq2500 instrument (Illumina) in 2 × 100 bp sequencing mode. (2) For siH19 and siCtrl transfected 1° BAT and 1° vWAT samples: library preparation and sequencing was carried out by the Core facility Genomics, Medical University of Vienna, Vienna, Austria. .. Briefly, sequencing libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer’s instructions and sequenced on Illumina NextSeq550 platforms. .. The resulting 75 bp single-end reads were quality-checked with FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), and low quality reads were removed using the fastq_quality_trimmer (“-t 20 -l 25” parameters) from the FASTX-Toolkit.

    Ligation:

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction. .. The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction.

    Genomic Sequencing:

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: We detected virus titers of ≈105 50% tissue culture infectious dose (TCID50 )/g or TCID50 /mL in the salivary gland and oral swab samples, respectively; however, virus was not detected in the nasal and rectal swab samples ( , panel B). .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB). .. De novo assembly on CLC Genomics Workbench (QIAGEN, Hilden, Germany) determined virtually full-length sequences of all 3 RNA segments of 2 SFTSV isolates.

    Infection:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: N. benthamiana and P. palmivora messenger RNAs (mRNAs) were purified using Poly(A) selection from the total RNA sample and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. cDNA sequencing of the 13 samples (MZ, infected N. benthamiana root samples and uninfected N. benthamiana plants) was performed in four lanes of Illumina NextSeq 2500 in a 100 paired-end mode. .. Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes.

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: To assess the potential for virus shedding into the secretions of infected animals, infectious SFTSV of the salivary gland, oral, nasal, and rectal swabs from cheetah 2 were titrated using Huh-7 cells. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    Generated:

    Article Title: Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
    Article Snippet: RNA sequencing was conducted at the Genomics Core Facility of the EMBL, Heidelberg, Germany ( RRID:SCR_004473 ). .. The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA. .. For library enrichment, 13–14 PCR cycles were performed.

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: All RNA samples (three biological replicates in each group) passed quality control analysis on a Fragment Analyzer (Advanced Analytical). .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs). .. Libraries were sequenced on a NextSeq500 (Illumina) for a mean of 41 million reads per sample.

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S). .. The fragmentation of the libraries was assessed with Agilent Technologies’ D1000 ScreenTape and concentration quantified with picogreen (Agilent Technologies).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: Conditions of the plasma and serum samples may result in negative RT-PCR results in the plasma and negative RT-PCR results and virus isolation in the serum because both samples were collected from animals supposed to cause viremia. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    Recombinant:

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: Infected cells were clearly stained in an immunofluorescence assay with a monoclonal antibody YG1-7-3-3-4 raised against the recombinant SFTSV nucleoprotein of the Japanese prototype strain YG1. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    Immunofluorescence:

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: Infected cells were clearly stained in an immunofluorescence assay with a monoclonal antibody YG1-7-3-3-4 raised against the recombinant SFTSV nucleoprotein of the Japanese prototype strain YG1. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    FACS:

    Article Title: Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation
    Article Snippet: Total RNA was extracted from FACS-sorted lineage-labeled AT2CTRL and AT2CAB cells using Direct-zol RNA MiniPrep Kit (Zymo Research) and mRNA was enriched from 200 ng of each total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). .. Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: Briefly, total RNA was extracted from FACS-purified lung macrophages using Trizol according to the commercial protocol, with the addition of a chloroform back-extraction step, addition of GlycoBlue (Thermo Fisher) as a carrier at the precipitation step, and a second 70% ethanol wash of the RNA pellet. .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs).

    RNA Sequencing Assay:

    Article Title: Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation
    Article Snippet: Paragraph title: RNA sequencing and analysis ... Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

    Article Title: Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
    Article Snippet: Paragraph title: RNA sequencing ... The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA.

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: All RNA samples (three biological replicates in each group) passed quality control analysis on a Fragment Analyzer (Advanced Analytical). .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs). .. Libraries were sequenced on a NextSeq500 (Illumina) for a mean of 41 million reads per sample.

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: Total RNA (1.0 μg) was poly(A)+ selected and fragmented using divalent cations and heat (94°C, 8 min). .. The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction. .. Fragmented poly(A)+ RNA samples were converted to cDNA by random primed synthesis using ProtoScript II reverse transcriptase (New England Biolabs).

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S). .. RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S).

    Article Title: Tet1 and Tet2 maintain mesenchymal stem cell homeostasis via demethylation of the P2rX7 promoter
    Article Snippet: Paragraph title: RNA-sequencing ... For each sample, we used NEBNext Ultra RNA library Pre Kit to prepare a sequencing library from 1 μg of total RNA, and 2 × 100 paired-end sequencing in fat run mode was performed using the HiSeq 2500 and Illumina TruSeq SBS-Kit v2 (200 cycles).

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: After two 200μL washes beads were resuspended in 10μL Tris pH 7.5, heated at 75°C for 2 min and eluate was immediately subjected to a second round of purification using 10μL beads per sample and eluting in 20μL – resulting in 30-100ng RNA. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles. .. Library concentrations were estimated using Bioanalyzer (Agilent) and Qubit (ThermoFisher) assays, pooled and sequenced on a Next-seq instrument (Illumina) using 1.8pM, 75bp paired-end.

    Article Title: PDE4D regulates Spine Plasticity and Memory in the Retrosplenial Cortex
    Article Snippet: RNA was sampled as above and concentration and quality were determined using a NanoDrop 8000 (ThermoFisher Scientific) and Bioanalyzer (Agilent), respectively. .. RNA-Seq libraries prepared with non-stranded NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) using random hexamers. .. Illumina-compatible adaptors and unique indexes were added and DNA fragments were amplified with 12 rounds of PCR.

    Article Title: LincRNA H19 protects from dietary obesity by constraining expression of monoallelic genes in brown fat
    Article Snippet: Paragraph title: Deep RNA-sequencing procedure ... Briefly, sequencing libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer’s instructions and sequenced on Illumina NextSeq550 platforms.

    Fluorescence:

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: All samples were quantified using a Qubit fluorescence assay (Thermo Scientific). .. The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction.

    Magnetic Beads:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: To purify polyA+ species 10μg DNAse treated RNA was heated at 65°C 5 min, transferred on ice, mixed with 20μL oligodT(25) magnetic beads (ThermoFisher) prewashed and resuspended in 45μL binding buffer and incubated 15min at room temperature. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles.

    Isolation:

    Article Title: MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice
    Article Snippet: Two-day-old etiolated seedlings of the wild type, mhz7-2/osein2 , mhz6-1 , and OsEIL2 -RNAi-19 were treated with or without 10 µL L−1 ethylene for 8 h, and the RNA was isolated. .. The mRNA was purified from 2 μg of total RNA using the Dynabeads mRNA Purification Kit (Invitrogen) and then submitted to library construction for the transcriptome experiments using the Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol.

    Article Title: Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation
    Article Snippet: Total RNA was extracted from FACS-sorted lineage-labeled AT2CTRL and AT2CAB cells using Direct-zol RNA MiniPrep Kit (Zymo Research) and mRNA was enriched from 200 ng of each total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). .. Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

    Article Title: Growth of Mycobacterium tuberculosis in vivo segregates with host macrophage metabolism and ontogeny
    Article Snippet: RNA isolation and sequencing were done at the RNA Sequencing Core at Cornell University. .. Directional poly-A+ RNA-sequencing libraries were generated with the NEBNext Ultra II RNA library prep kit (New England BioLabs).

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: Inguinal lymph nodes and spleens were collected from imiquimod-treated mice at euthanasia and frozen at –80°C in Tri-Reagent (MilliporeSigma). .. RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S). .. The fragmentation of the libraries was assessed with Agilent Technologies’ D1000 ScreenTape and concentration quantified with picogreen (Agilent Technologies).

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: We isolated infectious viruses using Huh-7 cells and Vero E6 cells from the plasma and popliteal lymph node of cheetah 1 and the spleen, lymph nodes, and brain of cheetah 2 but not from the serum of cheetah 2. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    Transfection:

    Article Title: LincRNA H19 protects from dietary obesity by constraining expression of monoallelic genes in brown fat
    Article Snippet: All libraries were sequenced in parallel on a HiSeq2500 instrument (Illumina) in 2 × 100 bp sequencing mode. (2) For siH19 and siCtrl transfected 1° BAT and 1° vWAT samples: library preparation and sequencing was carried out by the Core facility Genomics, Medical University of Vienna, Vienna, Austria. .. Briefly, sequencing libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit according to manufacturer’s instructions and sequenced on Illumina NextSeq550 platforms.

    Purification:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: N. benthamiana and P. palmivora messenger RNAs (mRNAs) were purified using Poly(A) selection from the total RNA sample and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. cDNA sequencing of the 13 samples (MZ, infected N. benthamiana root samples and uninfected N. benthamiana plants) was performed in four lanes of Illumina NextSeq 2500 in a 100 paired-end mode. .. Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes. .. Reads obtained from these three samples were used for P. palmivora de novo transcriptome assembly only.

    Article Title: MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice
    Article Snippet: Two-day-old etiolated seedlings of the wild type, mhz7-2/osein2 , mhz6-1 , and OsEIL2 -RNAi-19 were treated with or without 10 µL L−1 ethylene for 8 h, and the RNA was isolated. .. The mRNA was purified from 2 μg of total RNA using the Dynabeads mRNA Purification Kit (Invitrogen) and then submitted to library construction for the transcriptome experiments using the Ultra RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. .. Multiplex paired-end adapters (New England Biolabs) were used to multiplex libraries.

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: After two 200μL washes beads were resuspended in 10μL Tris pH 7.5, heated at 75°C for 2 min and eluate was immediately subjected to a second round of purification using 10μL beads per sample and eluting in 20μL – resulting in 30-100ng RNA. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles.

    Polymerase Chain Reaction:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: After two 200μL washes beads were resuspended in 10μL Tris pH 7.5, heated at 75°C for 2 min and eluate was immediately subjected to a second round of purification using 10μL beads per sample and eluting in 20μL – resulting in 30-100ng RNA. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles. .. Library concentrations were estimated using Bioanalyzer (Agilent) and Qubit (ThermoFisher) assays, pooled and sequenced on a Next-seq instrument (Illumina) using 1.8pM, 75bp paired-end.

    Selection:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: N. benthamiana and P. palmivora messenger RNAs (mRNAs) were purified using Poly(A) selection from the total RNA sample and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. cDNA sequencing of the 13 samples (MZ, infected N. benthamiana root samples and uninfected N. benthamiana plants) was performed in four lanes of Illumina NextSeq 2500 in a 100 paired-end mode. .. Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes. .. Reads obtained from these three samples were used for P. palmivora de novo transcriptome assembly only.

    Article Title: Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
    Article Snippet: RNA sequencing was conducted at the Genomics Core Facility of the EMBL, Heidelberg, Germany ( RRID:SCR_004473 ). .. The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA. .. For library enrichment, 13–14 PCR cycles were performed.

    Article Title: Destabilization of B2 RNA by EZH2 activates the stress response
    Article Snippet: For short RNA library construction, ribo-depleted short RNAs were subjected to PNK 3′-phosphoryl removal for 1 hour at 37C. .. Subsequently we used the NEBnext small RNA library construction kit (NEB) with the following modifications: Incubation of the 3′adaptor was performed for 2 hours, and the libraries at the end were not subjected to double size selection with the Ampure beads but with 1.2X size selection. .. For sequencing of the in vitro B2 fragments no ribosomal depletion was applied For the longer RNAs we used the NEBNext Ultra directional RNA library kit (NEB) with an RNA fragmentation of 10 min at 95C and with the following modifications: First strand synthesis at 42C was done for 50 min and the End Prep of cDNA library was followed by an Ampure Beads selection of 1.8x and ligation of the adapters using the 5x quick ligation buffer and Quick T4 DNA ligase (NEB) for 30 min. Incubation with the USER enzyme was done before the PCR amplification for 30 min, followed by a double size selection of 0.5x–1x, while the final library was size selected using Ampure beads at a 1x sample-beads ratio.

    Staining:

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: Cells were stained for CD4, CD62L, CD44, IFN-γ, and IL-17A. .. RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S).

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: Infected cells were clearly stained in an immunofluorescence assay with a monoclonal antibody YG1-7-3-3-4 raised against the recombinant SFTSV nucleoprotein of the Japanese prototype strain YG1. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    cDNA Library Assay:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: N. benthamiana and P. palmivora messenger RNAs (mRNAs) were purified using Poly(A) selection from the total RNA sample and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. cDNA sequencing of the 13 samples (MZ, infected N. benthamiana root samples and uninfected N. benthamiana plants) was performed in four lanes of Illumina NextSeq 2500 in a 100 paired-end mode. .. Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes.

    Article Title: Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation
    Article Snippet: RNA sequencing was conducted at the Genomics Core Facility of the EMBL, Heidelberg, Germany ( RRID:SCR_004473 ). .. The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (NEB: Ipswich, Massachusetts, United States, catalogue #E7530), which includes oligo-dT bead selection of mRNA. .. For library enrichment, 13–14 PCR cycles were performed.

    Mouse Assay:

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: Inguinal lymph nodes and spleens were collected from imiquimod-treated mice at euthanasia and frozen at –80°C in Tri-Reagent (MilliporeSigma). .. RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S).

    Chromatin Immunoprecipitation:

    Article Title: Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection
    Article Snippet: Total RNA quality was assessed using an RNA 6000 chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). .. The NEBNext Ultra II RNA library kit (New England Biolabs) was used for RNA-Seq library construction.

    Binding Assay:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: To purify polyA+ species 10μg DNAse treated RNA was heated at 65°C 5 min, transferred on ice, mixed with 20μL oligodT(25) magnetic beads (ThermoFisher) prewashed and resuspended in 45μL binding buffer and incubated 15min at room temperature. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles.

    Sample Prep:

    Article Title: Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
    Article Snippet: N. benthamiana and P. palmivora messenger RNAs (mRNAs) were purified using Poly(A) selection from the total RNA sample and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. cDNA sequencing of the 13 samples (MZ, infected N. benthamiana root samples and uninfected N. benthamiana plants) was performed in four lanes of Illumina NextSeq 2500 in a 100 paired-end mode. .. Samples were de-multiplexed and analysed further. mRNAs from additional samples of a short leaf time course (P. palmivora mycelium, N. benthamiana leaves 2 days after inoculation (dai) and N. benthamiana leaves 3 dai) were purified using Poly(A) selection from the total RNA sample. cDNA libraries were prepared using the NEBNext® RNA library preparation kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s protocol and sequenced on an Illumina GAII Genome Analyzer in a 76 paired-end mode in three separate lanes.

    Ethanol Precipitation:

    Article Title: Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
    Article Snippet: Total RNA was prepared by Ethanol precipitation as described in Jay & Ciaudo 2013. .. RNA-seq library were constructed using the NEBNext ultra (non-directional) RNA library kit for Illumina using 10ng polyA+ RNA as input and 12-15 PCR cycles.

    Activation Assay:

    Article Title: Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7–dependent lupus
    Article Snippet: Paragraph title: Mouse T cell activation and polarization assays. ... RNA was isolated with Direct-zol RNA MiniPrep (Genesee El Cajon) and cDNA libraries prepared with poly (A) tail enrichment using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s instructions (New England Biolabs; E7770S and E7490S).

    Concentration Assay:

    Article Title: PDE4D regulates Spine Plasticity and Memory in the Retrosplenial Cortex
    Article Snippet: RNA was sampled as above and concentration and quality were determined using a NanoDrop 8000 (ThermoFisher Scientific) and Bioanalyzer (Agilent), respectively. .. RNA-Seq libraries prepared with non-stranded NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) using random hexamers.

    Virus Isolation Assay:

    Article Title: Fatal Tickborne Phlebovirus Infection in Captive Cheetahs, Japan
    Article Snippet: Conditions of the plasma and serum samples may result in negative RT-PCR results in the plasma and negative RT-PCR results and virus isolation in the serum because both samples were collected from animals supposed to cause viremia. .. We determined genomic sequences of 2 isolates (SkrP/2017 from the plasma of cheetah 1 and ArtSp/2017 from the spleen of cheetah 2) using MiSeq (Illumina, San Diego, CA, USA) with NEBNext-Ultra RNA Library Prep kit (NEB).

    Lysis:

    Article Title: Destabilization of B2 RNA by EZH2 activates the stress response
    Article Snippet: Incubation of the RNA with the probe was done for 40 min instead of 20 min. RNA depleted RNA was separated into two fractions of short ( < 200) and longer RNAs using the mirVana separation kit (Life technologies) with the following modifications: After addition of the lysis/binding buffer and the miRNA homogenate additive solution, 100% EtOH at 1/3 of the volume was added and the mix was passed through the filter to bind long RNAs. .. Subsequently we used the NEBnext small RNA library construction kit (NEB) with the following modifications: Incubation of the 3′adaptor was performed for 2 hours, and the libraries at the end were not subjected to double size selection with the Ampure beads but with 1.2X size selection.

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    New England Biolabs ultra directional rna library prep kit
    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: <t>NEBNext®</t> Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of <t>RNA;</t> Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients
    Ultra Directional Rna Library Prep Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 367 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering of expression levels, based on the rank of the count of exon per million mapped reads (CPM). Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples.. Color scale: Spearman correlation coefficients

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques: Expressing

    Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Hierarchical clustering based on the rank of IP/input value. Dendrogram represents Spearman correlation coefficients between pairs of samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques:

    Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristic of enrichment or depletion profiles as generated by the different library preparation kits. Genes which have at least 20 raw reads in the input samples and a ratio of IP/Input ≥2 or Input/IP ≥2 were used to generate the plots. a Total number of transcripts enriched or depleted. b Percentage of enriched or depleted transcripts grouped into different bins. X-axis: log2(IP/input), Y-axis: percentage of genes in each bin over whole population. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques: Generated

    Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Enrichment profiles and top 50 enriched transcripts. a Enrichment factor of transcripts are sorted in decreasing order based on log2 (IP/input). X-axis:transcripts, Y-axis:log2 value of enrichment (IP/Input). b Boxplot of top 50 enriched transcripts. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuGEN samples; Green and grey: TruSeq samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques:

    Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Descriptive characteristics of raw and mapped reads. a Total number of raw reads and number of reads mapped to the mouse genome (mm10, GRCm38.84). b Percentage of reads mapped to exonic, intronic and intergenic regions. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques:

    Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Distribution of normalized mean expression of the first (last) 100 bases of transcripts (in 5′- > 3′-orientation). X axis represents the 5′-3′ normalized position; Y axis represents normalized coverage. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA. Yellow and orange: SMTseq samples; Red: SMTer samples; Black: NEB samples; Blue: NuG samples; Green and grey: TruSeq samples. Solid: Input samples. Dotted: Ribo-IP samples

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques: Expressing

    Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Journal: BMC Genomics

    Article Title: A comparative analysis of library prep approaches for sequencing low input translatome samples

    doi: 10.1186/s12864-018-5066-2

    Figure Lengend Snippet: Venn diagrams of identified features in the different libraries. The features with CPM ≥ 1 in at least one out of 3 replicates were used to generate these plots. a and c represent input samples and b and d represent IP samples. Most transcripts were detected by all kits tested. However, a higher rate of agreement is seen between the NEB, TruSeq and SMART-Seq prepared samples. NEB: NEBNext® Ultra™, NuG: NuGEN Ovation®, SMTer: SMARTer® Stranded; Tru4: TruSeq using 4 ng of RNA; Tru70: TruSeq using 70 ng of RNA. SMTseq4: SMART-Seq® v4 using 4 ng of RNA; SMTseq0.25: SMART-Seq® v4 using 250 pg of RNA

    Article Snippet: NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina with 4 ng of RNA

    Techniques: