e7420  (New England Biolabs)


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  • 99
    Name:
    NEBNext Ultra Directional RNA Library Prep Kit for Illumina
    Description:
    NEBNext Ultra Directional RNA Library Prep Kit for Illumina 96 rxns
    Catalog Number:
    E7420L
    Price:
    3801
    Size:
    96 rxns
    Category:
    mRNA Template Preparation for PCR
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    Structured Review

    New England Biolabs e7420
    NEBNext Ultra Directional RNA Library Prep Kit for Illumina
    NEBNext Ultra Directional RNA Library Prep Kit for Illumina 96 rxns
    https://www.bioz.com/result/e7420/product/New England Biolabs
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    e7420 - by Bioz Stars, 2019-07
    99/100 stars

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    Related Articles

    Centrifugation:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information. .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information.

    Amplification:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: The kit has, however, given low recoveries of viruses from sediment ( ). .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information. .. Instead, we increased the number of cycles of random PCR during library preparation from 12 to 15 to counteract the low input quantity of RNA ( < 1 ng).

    Filtration:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information. .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information.

    Synthesized:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions. .. The short fragments of mRNA were then used for the first strand strands with random hexamer primers.

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    Construct:

    Article Title: Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement
    Article Snippet: The transcriptome library of Lepidodinium chlorophorum (Roscoff collection no. RCC1488) was generated using the NEBNext Ultra Directional RNA Library kit (New England Biolabs, Ipswitch, MA, USA) according to the manufacturer`s instructions. .. The transcriptome library of Lepidodinium chlorophorum (Roscoff collection no. RCC1488) was generated using the NEBNext Ultra Directional RNA Library kit (New England Biolabs, Ipswitch, MA, USA) according to the manufacturer`s instructions.

    Article Title: Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling
    Article Snippet: RNA (3 μg per sample) was used as the input material for the RNA sample preparations. .. Sequencing libraries were constructed according to the manufacturer’s instructions using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). .. After clustering of the index-coded samples, we performed RNA sequencing of each library on an Illumina HiSequation 2500 platform to generate 100-bp single-end (SE) reads.

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The same total RNA extraction method for 454 sequencing was also used to prepare for the RNA samples for Illumina Sequencing performed at North Carolina State University Genomic Sciences Laboratory. .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.). .. All procedures for library construction followed the protocol provided by the vendor.

    Article Title: upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks
    Article Snippet: Nascent-RNA was ethanol precipitated overnight except without the addition of glycogen. .. Illumina sequencing libraries were constructed using the NEBNext Ultra Directional RNA Library kit (NEB 7420). .. The tag density profiles were generated using get.smoothed.tag.density function of SPP R package, with a Gaussian kernel of 100 bp, and a step size of 10 bp after library size normalization.

    Electrophoresis:

    Article Title: Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling
    Article Snippet: RNA quality was examined by electrophoresis through 1.2% agarose gels to check for possible degradation and contamination. .. Sequencing libraries were constructed according to the manufacturer’s instructions using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

    Microarray:

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: The mixed library was sequenced with PE-150 bp run using 64% of a single Illumina lane on HiSeq 2500 at UT Southwestern Medical Center Genomics and Microarray Core Facility. .. RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA USA) for Illumina following manufacturer’s protocol.

    Random Hexamer Labeling:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions. .. Fragmentation buffer was added to the purified mRNA to break them into a suitable size (about 200 bp).

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    HAT Assay:

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: Samples of fresh shoot tissue were collected from treated and untreated plants at 24 HAT ( Figure ), immediately frozen in liquid nitrogen and stored at -80°C. .. Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions.

    Expressing:

    Article Title: The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation
    Article Snippet: RNA libraries were prepared from 1 μg of total RNA using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on a HiSeq2500 (Illumina) system at the Max Planck‐Genome‐centre Cologne ( http://mpgc.mpipz.mpg.de/home/ ). .. Reads were mapped to the Arabidopsis genome (tair10) using the splice‐aware read aligner TopHat and transformed into a count per gene per library by using HTSeq (Anders et al , ).

    Article Title: Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
    Article Snippet: 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S). .. 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S).

    Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
    Article Snippet: RNA samples were then subjected to rRNA depletion using RiboZero (Epicentre) followed by the construction of next-generation sequencing libraries using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. Subsequent to alignment using BWA , read counts for individual transcripts were produced with HTSEQ , based on UCBPP-PA14 transcriptome annotation (NC_002516).

    Article Title: Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis
    Article Snippet: RNA-seq libraries were prepared according to NEBNext Ultra Directional RNA Library Prep Kit for Illumina and ran on Hiseq2000 sequencer platform. .. RNA-seq libraries were prepared according to NEBNext Ultra Directional RNA Library Prep Kit for Illumina and ran on Hiseq2000 sequencer platform.

    Article Title: Ablation of the epithelial‐specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number
    Article Snippet: The pooled 200‐ng samples were used for poly A selected RNA‐Seq library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (mRNA) (New England Biolabs) [products: NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420S)]. .. RNA‐Seq reads were mapped to the mouse genome (mm10) and a data set of all possible exon‐exon junction reads as previously described (Bebee et al., ).

    Article Title: Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    Article Snippet: Paragraph title: RNA-seq and differential expression (DE) analysis ... Among the obtained 1 µg enriched mRNAs, 100 ng was subjected to cDNA library preparation using the NEBNext Ultra Directional RNA library prep kit (New England Biolabs).

    Article Title: Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
    Article Snippet: After ribosomal RNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), libraries were prepared by the dUTP-based method using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) (NEB). .. After ribosomal RNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), libraries were prepared by the dUTP-based method using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) (NEB).

    Flow Cytometry:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: Samples were first concentrated from volumes of 1 liter (wastewater) or 50 liters (surface water) down to 50 ml, using tangential flow filtration (TFF) at a molecular-mass cutoff of 100 kDa, followed by polyethylene glycol (PEG) 6000 precipitation. .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information.

    Generated:

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: Quality and quantity of samples was assessed on an Agilent bioanalyzer using an RNA Nano chip (Agilent). .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. During library preparation, barcode sequences were introduced for identifying sequences from each biological replicate and 6–7 libraries were pooled and run per lane on an Illumina HiSeq 2500 using a 100-cycle single-end program.

    Article Title: Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement
    Article Snippet: GSA-AT of Karenia brevis ( ) were automatically annotated using the InterProScan feature of Geneious 8.1 [ ]. .. The transcriptome library of Lepidodinium chlorophorum (Roscoff collection no. RCC1488) was generated using the NEBNext Ultra Directional RNA Library kit (New England Biolabs, Ipswitch, MA, USA) according to the manufacturer`s instructions. .. Quality assessment and sequencing were performed in a specialized facility, using the Illumina MiSeq (2×250 bp) platform.

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. .. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: RNA was quantified using a NanoDrop (ND-1000) spectrophotometer (Thermo Scientific, Wilmington, DE, United States) and RNA integrity and quality were assessed with a 2100 Bioanalyzer (Agilent Technologies Inc., Germany). .. Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions. .. After verifying their quality, libraries were indexed with six-nucleotide barcodes and sequencing was performed on the Illumina HiSeq2000 machine using multiplexing for generating 50 base-paired (bp) end reads.

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA. .. Thirdly, double-stranded cDNA was synthesized replacing dTTPs with dUTPs in the reaction buffer used in second strand cDNA synthesis after RNA fragmenting.

    Sequencing:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information. .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information.

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: Paragraph title: RNA-Seq library preparation and sequencing ... The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions.

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: Paragraph title: Deep sequencing and analysis of C/C transcriptome ... 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. .. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X).

    Article Title: Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
    Article Snippet: 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S). .. 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S).

    Article Title: Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling
    Article Snippet: RNA (3 μg per sample) was used as the input material for the RNA sample preparations. .. Sequencing libraries were constructed according to the manufacturer’s instructions using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). .. After clustering of the index-coded samples, we performed RNA sequencing of each library on an Illumina HiSequation 2500 platform to generate 100-bp single-end (SE) reads.

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: Paragraph title: Illumina sequencing ... The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.).

    Article Title: Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis
    Article Snippet: RNA-seq libraries were prepared according to NEBNext Ultra Directional RNA Library Prep Kit for Illumina and ran on Hiseq2000 sequencer platform. .. RNA-seq libraries were prepared according to NEBNext Ultra Directional RNA Library Prep Kit for Illumina and ran on Hiseq2000 sequencer platform.

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: Paragraph title: Library preparation and sequencing ... RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA USA) for Illumina following manufacturer’s protocol.

    Article Title: upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks
    Article Snippet: Nascent-RNA was ethanol precipitated overnight except without the addition of glycogen. .. Illumina sequencing libraries were constructed using the NEBNext Ultra Directional RNA Library kit (NEB 7420). .. The tag density profiles were generated using get.smoothed.tag.density function of SPP R package, with a Gaussian kernel of 100 bp, and a step size of 10 bp after library size normalization.

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions. .. After verifying their quality, libraries were indexed with six-nucleotide barcodes and sequencing was performed on the Illumina HiSeq2000 machine using multiplexing for generating 50 base-paired (bp) end reads.

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA. .. Thirdly, double-stranded cDNA was synthesized replacing dTTPs with dUTPs in the reaction buffer used in second strand cDNA synthesis after RNA fragmenting.

    Article Title: Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees
    Article Snippet: Paragraph title: RNA extraction and library preparation for sequencing ... LncRNA and mRNA library preparation was carried out using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following manufacturer’s recommendations.

    RNA Sequencing Assay:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: Paragraph title: RNA-Seq library preparation and sequencing ... The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions.

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: Quality and quantity of samples was assessed on an Agilent bioanalyzer using an RNA Nano chip (Agilent). .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. During library preparation, barcode sequences were introduced for identifying sequences from each biological replicate and 6–7 libraries were pooled and run per lane on an Illumina HiSeq 2500 using a 100-cycle single-end program.

    Article Title: The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation
    Article Snippet: Paragraph title: RNA‐seq analysis and quantitative RT–PCR ... RNA libraries were prepared from 1 μg of total RNA using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on a HiSeq2500 (Illumina) system at the Max Planck‐Genome‐centre Cologne ( http://mpgc.mpipz.mpg.de/home/ ).

    Article Title: Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
    Article Snippet: Paragraph title: RNA-seq ... 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S).

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The same total RNA extraction method for 454 sequencing was also used to prepare for the RNA samples for Illumina Sequencing performed at North Carolina State University Genomic Sciences Laboratory. .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.). .. All procedures for library construction followed the protocol provided by the vendor.

    Article Title: Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis
    Article Snippet: 4.4 Total RNAs from adipocytes were extracted according to Qiagen miRNeasy kit. .. RNA-seq libraries were prepared according to NEBNext Ultra Directional RNA Library Prep Kit for Illumina and ran on Hiseq2000 sequencer platform. .. The 100 bp paired-end reads were first quality checked with FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), subsequently aligned to mm9, using Tophat (version tophat-2.0.11).

    Article Title: Ablation of the epithelial‐specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number
    Article Snippet: Each pooled biological replicate was made using 66.6 ng of total RNA, for a total of 200 ng. .. The pooled 200‐ng samples were used for poly A selected RNA‐Seq library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (mRNA) (New England Biolabs) [products: NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420S)]. .. Biological replicates (n = 2 per genetic group) were individually bar‐coded, pooled, and sequenced in a single lane of a HiSeq 2000 for 100 × 2 bp paired‐end RNA‐Seq at the Penn Next Generation Sequencing Core (NGSC) Facility.

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: We further isolated mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, MA USA). .. RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA USA) for Illumina following manufacturer’s protocol. .. The RNA-seq library was sequenced with PE-150 bp run using 9% of an Illumina lane.

    Article Title: Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    Article Snippet: Paragraph title: RNA-seq and differential expression (DE) analysis ... Among the obtained 1 µg enriched mRNAs, 100 ng was subjected to cDNA library preparation using the NEBNext Ultra Directional RNA library prep kit (New England Biolabs).

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: Paragraph title: Sample Preparation and RNA Sequencing ... Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions.

    Article Title: Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
    Article Snippet: Paragraph title: RNA-seq ... After ribosomal RNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), libraries were prepared by the dUTP-based method using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) (NEB).

    Mutagenesis:

    Article Title: Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    Article Snippet: For each growth condition (anaerobic, aerobic, heat stress, vancomycin stress), total RNA was isolated from n =3 independent cultures each for the wild-type and lrgAB mutant. .. Among the obtained 1 µg enriched mRNAs, 100 ng was subjected to cDNA library preparation using the NEBNext Ultra Directional RNA library prep kit (New England Biolabs).

    Isolation:

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: Quality and quantity of samples was assessed on an Agilent bioanalyzer using an RNA Nano chip (Agilent). .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. During library preparation, barcode sequences were introduced for identifying sequences from each biological replicate and 6–7 libraries were pooled and run per lane on an Illumina HiSeq 2500 using a 100-cycle single-end program.

    Article Title: The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation
    Article Snippet: Total RNA was isolated from 8‐day‐old seedlings harvested at 3 h after treatment with mock or chitin using TRIzol reagent (Invitrogen) and treated with DNase I (Roche). .. RNA libraries were prepared from 1 μg of total RNA using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on a HiSeq2500 (Illumina) system at the Max Planck‐Genome‐centre Cologne ( http://mpgc.mpipz.mpg.de/home/ ).

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Paragraph title: RNA isolation, library construction and sequencing ... Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    Article Title: Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
    Article Snippet: RNA was extracted using the Qiagen RNeasy kit with on-column DNase I treatment. .. 1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420S). .. RNA libraries were then sequenced on an Illumina MiSeq (75bp paired-end).

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The same total RNA extraction method for 454 sequencing was also used to prepare for the RNA samples for Illumina Sequencing performed at North Carolina State University Genomic Sciences Laboratory. .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.). .. All procedures for library construction followed the protocol provided by the vendor.

    Article Title: Ablation of the epithelial‐specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number
    Article Snippet: Each pooled biological replicate was made using 66.6 ng of total RNA, for a total of 200 ng. .. The pooled 200‐ng samples were used for poly A selected RNA‐Seq library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (mRNA) (New England Biolabs) [products: NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420S)]. .. Biological replicates (n = 2 per genetic group) were individually bar‐coded, pooled, and sequenced in a single lane of a HiSeq 2000 for 100 × 2 bp paired‐end RNA‐Seq at the Penn Next Generation Sequencing Core (NGSC) Facility.

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: We further isolated mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, MA USA). .. RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA USA) for Illumina following manufacturer’s protocol.

    Article Title: Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    Article Snippet: For each growth condition (anaerobic, aerobic, heat stress, vancomycin stress), total RNA was isolated from n =3 independent cultures each for the wild-type and lrgAB mutant. .. Among the obtained 1 µg enriched mRNAs, 100 ng was subjected to cDNA library preparation using the NEBNext Ultra Directional RNA library prep kit (New England Biolabs).

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Paragraph title: RNA isolated, library preparation and sequencing ... Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA.

    Article Title: Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
    Article Snippet: Total RNA was isolated from hybrid female clonal cell line of MEFs (EY.T4) prepared from the cross of female mice of Mus musculus (129S1) and male mice of Mus castaneus (CAST/EiJ) origins [ ]. .. After ribosomal RNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), libraries were prepared by the dUTP-based method using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) (NEB).

    Purification:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions. .. Briefly, poly-A mRNA was purified from total RNA samples with Magnetic Oligo (dT) Beads.

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: Total RNA was extracted using a Plant/Fungi Total RNA Purification Kit (Norgen Biotek Corp., Canada). .. Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions.

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA. .. Thirdly, double-stranded cDNA was synthesized replacing dTTPs with dUTPs in the reaction buffer used in second strand cDNA synthesis after RNA fragmenting.

    Polymerase Chain Reaction:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information. .. The random amplification during library construction led to a trade-off in which genome strand information was gained for a loss of quantitative power, making it difficult to compare abundances of viral types within and across libraries.

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA. .. Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA.

    Quantitative RT-PCR:

    Article Title: The Arabidopsis CERK1‐associated kinase PBL27 connects chitin perception to MAPK activation
    Article Snippet: Paragraph title: RNA‐seq analysis and quantitative RT–PCR ... RNA libraries were prepared from 1 μg of total RNA using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on a HiSeq2500 (Illumina) system at the Max Planck‐Genome‐centre Cologne ( http://mpgc.mpipz.mpg.de/home/ ).

    cDNA Library Assay:

    Article Title: Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    Article Snippet: RNA processing (including 16S/23S removal and cDNA library creation) was performed on 5 µg of high-quality total RNA (A 260/280 > 2.0) as described previously [ ]. .. Among the obtained 1 µg enriched mRNAs, 100 ng was subjected to cDNA library preparation using the NEBNext Ultra Directional RNA library prep kit (New England Biolabs). .. The final concentration and quality of each cDNA library was analysed on an Agilent TapeStation (Agilent Technologies) prior to Illumina NextSeq500 sequencing (single-read format) by the NextGen DNA Sequencing Core Laboratory, ICBR, at the University of Florida (Gainesville, FL, USA).

    Agarose Gel Electrophoresis:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: Total RNA was extracted from gonads using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and examined on a 1% agarose gel. .. The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions.

    Mouse Assay:

    Article Title: Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
    Article Snippet: Total RNA was isolated from hybrid female clonal cell line of MEFs (EY.T4) prepared from the cross of female mice of Mus musculus (129S1) and male mice of Mus castaneus (CAST/EiJ) origins [ ]. .. After ribosomal RNA depletion with RiboMinus Eukaryote System v2 (Thermo Fisher Scientific), libraries were prepared by the dUTP-based method using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) (NEB).

    Chromatin Immunoprecipitation:

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: Quality and quantity of samples was assessed on an Agilent bioanalyzer using an RNA Nano chip (Agilent). .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.). .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.).

    Software:

    Article Title: Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement
    Article Snippet: The transcriptome library of Lepidodinium chlorophorum (Roscoff collection no. RCC1488) was generated using the NEBNext Ultra Directional RNA Library kit (New England Biolabs, Ipswitch, MA, USA) according to the manufacturer`s instructions. .. The generated reads were quality-trimmed using the FASTQ Toolkit (v1.0) of the Illumina BaseSpace platform and then assembled using Trinity v2.1.1 [ ] and SOAPdenovo2 v2.0 r240 [ ] and clustered using CAP3 [ ].

    RNA Extraction:

    Article Title: Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
    Article Snippet: After implementing these steps, we performed viral RNA extraction using the Mo Bio PowerViral environmental DNA/RNA extraction kit, which has previously been shown to perform best overall in spiking experiments with murine norovirus, in terms of extraction efficiency and removal of inhibitors ( ). .. We did not perform an amplification step before library construction with the NEBNext Ultra directional RNA library preparation kit for Illumina, to retain the genome sense and strand information.

    Article Title: Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling
    Article Snippet: Paragraph title: RNA extraction, library preparation, and Hi-sequation 2500 sequencing ... Sequencing libraries were constructed according to the manufacturer’s instructions using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The same total RNA extraction method for 454 sequencing was also used to prepare for the RNA samples for Illumina Sequencing performed at North Carolina State University Genomic Sciences Laboratory. .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.).

    Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
    Article Snippet: Duplicates of each culture were processed for RNA extraction using the RNeasy kit (QIAGEN) and DNAse treatment was performed with the TURBO DNA-free kit (Thermo-Fisher). .. RNA samples were then subjected to rRNA depletion using RiboZero (Epicentre) followed by the construction of next-generation sequencing libraries using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Article Title: Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees
    Article Snippet: Paragraph title: RNA extraction and library preparation for sequencing ... LncRNA and mRNA library preparation was carried out using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following manufacturer’s recommendations.

    Sample Prep:

    Article Title: Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum
    Article Snippet: The same total RNA extraction method for 454 sequencing was also used to prepare for the RNA samples for Illumina Sequencing performed at North Carolina State University Genomic Sciences Laboratory. .. The MG and MW RNA-Seq library constructions were carried out using the Illumina TruSeq RNA sample preparation kit while the VG and HG RNA-Seq libraries were constructed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs Inc.), NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L, New England Biolabs Inc.), and indexed with the NEBNext Mulitplex Oligos for Illumina (E7335S, New England Biolabs Inc.). .. All procedures for library construction followed the protocol provided by the vendor.

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: Paragraph title: Sample Preparation and RNA Sequencing ... Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions.

    Ethanol Precipitation:

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: After DNase treatment, the RNA was repurified using phenol:chloroform extraction followed by ethanol precipitation. .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. .. Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA.

    Next-Generation Sequencing:

    Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
    Article Snippet: Duplicates of each culture were processed for RNA extraction using the RNeasy kit (QIAGEN) and DNAse treatment was performed with the TURBO DNA-free kit (Thermo-Fisher). .. RNA samples were then subjected to rRNA depletion using RiboZero (Epicentre) followed by the construction of next-generation sequencing libraries using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. These libraries were sequenced on Illumina HiSeq 2500 instrument resulting in approximately 8.8 million reads per sample on average.

    Spectrophotometry:

    Article Title: Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes
    Article Snippet: RNA was quality-controlled by using a NanoPhotometer® spectrophotometer (Implen, Westlake Village, CA, USA) and quantified using a Qubit® RNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). .. The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (Neb, Beverly, MA, USA) was used for library construction according to manufacturer’s instructions.

    Article Title: Severe impairment of male reproductive organ development in a low SMN expressing mouse model of spinal muscular atrophy
    Article Snippet: The isolated RNA was quantified using a UV spectrophotometer and 10 μg of total RNA was subjected to digestion with RQ1 RNase-free DNase (Promega). .. 300 ng of RNA was used as input for poly(A) + RNA enrichment using the NEBNext poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and RNA-Seq libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: RNA degradation and contamination was monitored on 1% agarose gels and RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    Article Title: Unraveling the Transcriptional Basis of Temperature-Dependent Pinoxaden Resistance in Brachypodium hybridum
    Article Snippet: RNA was quantified using a NanoDrop (ND-1000) spectrophotometer (Thermo Scientific, Wilmington, DE, United States) and RNA integrity and quality were assessed with a 2100 Bioanalyzer (Agilent Technologies Inc., Germany). .. Additional data concerning sample quality and other parameters are presented in Supplementary Table . cDNA libraries were generated using a NEBNext Ultra Directional RNA Prep Kit (New England Biolabs, Ipswich, MA, United States), following the manufacturer’s instructions.

    Article Title: Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees
    Article Snippet: The purity of RNA was checked using the NanoPhotometer spectrophotometer (Implen, Westlake Village, CA, USA), and the concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, Carlsbad, CA, USA). .. LncRNA and mRNA library preparation was carried out using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following manufacturer’s recommendations.

    Sampling:

    Article Title: Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement
    Article Snippet: Bayesian inferences were calculated with the following parameters: 2 chains, 15,000 generations under the C20 model with Poisson exchange rate, sampling every 100 generations, and a maximum divergence of 0.1. .. The transcriptome library of Lepidodinium chlorophorum (Roscoff collection no. RCC1488) was generated using the NEBNext Ultra Directional RNA Library kit (New England Biolabs, Ipswitch, MA, USA) according to the manufacturer`s instructions.

    Produced:

    Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
    Article Snippet: RNA samples were then subjected to rRNA depletion using RiboZero (Epicentre) followed by the construction of next-generation sequencing libraries using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). .. RNA samples were then subjected to rRNA depletion using RiboZero (Epicentre) followed by the construction of next-generation sequencing libraries using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

    Concentration Assay:

    Article Title: Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)
    Article Snippet: RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). .. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

    Article Title: Transcriptomic Analysis of Differentially Expressed Genes During Larval Development of Rapana venosa by Digital Gene Expression Profiling
    Article Snippet: Integrity and concentration and of RNA was measured using a Qubit RNA Assay Kit in a Qubit 2.0 Flurometer (Life Technologies, CA), and the RNA 6000 Nano Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA), respectively. .. Sequencing libraries were constructed according to the manufacturer’s instructions using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

    Article Title: Downregulated long noncoding RNA ALDBGALG0000005049 induces inflammation in chicken muscle suffered from selenium deficiency by regulating stearoyl-CoA desaturase
    Article Snippet: Total RNA purity, concentration and integrity were checked, respectively. .. Secondly, sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) using the rRNA-depleted RNA.

    Article Title: Integration of lncRNA–miRNA–mRNA reveals novel insights into oviposition regulation in honey bees
    Article Snippet: The purity of RNA was checked using the NanoPhotometer spectrophotometer (Implen, Westlake Village, CA, USA), and the concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, Carlsbad, CA, USA). .. LncRNA and mRNA library preparation was carried out using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following manufacturer’s recommendations.

    FACS:

    Article Title: Ablation of the epithelial‐specific splicing factor Esrp1 results in ureteric branching defects and reduced nephron number
    Article Snippet: Total RNA from FACS‐sorted DBA + from control E18.5 control and DKO UE in TRIzol was isolated according to the manufacturer's protocol and resuspended in 10mM Tris‐Cl pH 8.0. .. The pooled 200‐ng samples were used for poly A selected RNA‐Seq library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (mRNA) (New England Biolabs) [products: NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (E7420S)].

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  • 99
    New England Biolabs ultra directional rna library prep kit
    CircRNA-protein complexes in human platelets. Sedimentation profiles of circRNPs. Platelet extract and corresponding free <t>RNA</t> (prepared from the same extract) were fractionated by glycerol gradient centrifugation (fractions #1–12 from top to bottom), followed by RT-PCR analysis across the gradient for five abundant circRNAs ( RAP1B, GSE1, CORO1C, PCMTD1 and Plt-circR4 ) and for one linear mRNA control ( RAP1B ). The positions of ribosomal RNAs are marked by arrowheads (5S, 18S and 28S). M , markers (300, 200, 100 bp); lane I, 10% platelet extract input. The right panel shows quantification of the gradient fractionation of extract vs. RNA.
    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
    https://www.bioz.com/result/ultra directional rna library prep kit/product/New England Biolabs
    Average 99 stars, based on 367 article reviews
    Price from $9.99 to $1999.99
    ultra directional rna library prep kit - by Bioz Stars, 2019-07
    99/100 stars
      Buy from Supplier

    87
    New England Biolabs ultra directional mrnaseq kit
    Dynamics of H3K4me3 and expression in subsets of genes. ( A ) Genomic regions subject to age-linked CNV detected by comparison between input samples; these were excluded from ChIP analysis. ( B ) Scatter plot of log 2 -transformed <t>mRNAseq</t> read counts from protein coding genes defined in Figure 4A normalised for ORF length comparing log phase cells to 48-hr-aged cells. Data averaged across five replicates per condition. ( C ) Average profile of H3K4me3 ChIP signal for 1 kb either side of the TSS performed as in Figure 4C , for 300 genes least induced with age. ( D ) As ( C ) for 300 most induced genes. ( E ) Hierarchical clustering analysis of log 2 -transformed mRNA levels across age for the 4806 unambiguous genes defined in Figure 4A .
    Ultra Directional Mrnaseq Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ultra directional mrnaseq kit/product/New England Biolabs
    Average 87 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ultra directional mrnaseq kit - by Bioz Stars, 2019-07
    87/100 stars
      Buy from Supplier

    Image Search Results


    CircRNA-protein complexes in human platelets. Sedimentation profiles of circRNPs. Platelet extract and corresponding free RNA (prepared from the same extract) were fractionated by glycerol gradient centrifugation (fractions #1–12 from top to bottom), followed by RT-PCR analysis across the gradient for five abundant circRNAs ( RAP1B, GSE1, CORO1C, PCMTD1 and Plt-circR4 ) and for one linear mRNA control ( RAP1B ). The positions of ribosomal RNAs are marked by arrowheads (5S, 18S and 28S). M , markers (300, 200, 100 bp); lane I, 10% platelet extract input. The right panel shows quantification of the gradient fractionation of extract vs. RNA.

    Journal: Journal of Extracellular Vesicles

    Article Title: Selective release of circRNAs in platelet-derived extracellular vesicles

    doi: 10.1080/20013078.2018.1424473

    Figure Lengend Snippet: CircRNA-protein complexes in human platelets. Sedimentation profiles of circRNPs. Platelet extract and corresponding free RNA (prepared from the same extract) were fractionated by glycerol gradient centrifugation (fractions #1–12 from top to bottom), followed by RT-PCR analysis across the gradient for five abundant circRNAs ( RAP1B, GSE1, CORO1C, PCMTD1 and Plt-circR4 ) and for one linear mRNA control ( RAP1B ). The positions of ribosomal RNAs are marked by arrowheads (5S, 18S and 28S). M , markers (300, 200, 100 bp); lane I, 10% platelet extract input. The right panel shows quantification of the gradient fractionation of extract vs. RNA.

    Article Snippet: For high-throughput sequencing, total RNA from platelets and microvesicles was depleted of ribosomal RNA, using the Ribo-Zero Gold rRNA Removal Kit (Epicenter, MRZG126), followed by library preparation (NEBNext Ultra Directional RNA Library Prep Kit, NEB, E7420, according to the manufacturer’s instructions).

    Techniques: Sedimentation, Gradient Centrifugation, Reverse Transcription Polymerase Chain Reaction, Fractionation

    Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Article Snippet: Strand-specific RNA-Seq libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, catalogue number: E7420) with the following adjustments to the manufacturer’s instructions: fragmentation was performed for 1 min at 94°C given the size range of our exosomal RNA was typically smaller than 1000 bp (data not shown), and PCR was set to 15 cycles.

    Techniques: Flow Cytometry, Transmission Assay, Electron Microscopy, Transmission Electron Microscopy, RNA Extraction, RNA Sequencing Assay, Centrifugation, Quantitative RT-PCR

    Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Article Snippet: Strand-specific RNA-Seq libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit (NEB, catalogue number: E7420) with the following adjustments to the manufacturer’s instructions: fragmentation was performed for 1 min at 94°C given the size range of our exosomal RNA was typically smaller than 1000 bp (data not shown), and PCR was set to 15 cycles.

    Techniques: Flow Cytometry, Transmission Assay, Electron Microscopy, Transmission Electron Microscopy, RNA Extraction, RNA Sequencing Assay, Centrifugation, Quantitative RT-PCR

    Dynamics of H3K4me3 and expression in subsets of genes. ( A ) Genomic regions subject to age-linked CNV detected by comparison between input samples; these were excluded from ChIP analysis. ( B ) Scatter plot of log 2 -transformed mRNAseq read counts from protein coding genes defined in Figure 4A normalised for ORF length comparing log phase cells to 48-hr-aged cells. Data averaged across five replicates per condition. ( C ) Average profile of H3K4me3 ChIP signal for 1 kb either side of the TSS performed as in Figure 4C , for 300 genes least induced with age. ( D ) As ( C ) for 300 most induced genes. ( E ) Hierarchical clustering analysis of log 2 -transformed mRNA levels across age for the 4806 unambiguous genes defined in Figure 4A .

    Journal: eLife

    Article Title: Tri-methylation of histone H3 lysine 4 facilitates gene expression in ageing cells

    doi: 10.7554/eLife.34081

    Figure Lengend Snippet: Dynamics of H3K4me3 and expression in subsets of genes. ( A ) Genomic regions subject to age-linked CNV detected by comparison between input samples; these were excluded from ChIP analysis. ( B ) Scatter plot of log 2 -transformed mRNAseq read counts from protein coding genes defined in Figure 4A normalised for ORF length comparing log phase cells to 48-hr-aged cells. Data averaged across five replicates per condition. ( C ) Average profile of H3K4me3 ChIP signal for 1 kb either side of the TSS performed as in Figure 4C , for 300 genes least induced with age. ( D ) As ( C ) for 300 most induced genes. ( E ) Hierarchical clustering analysis of log 2 -transformed mRNA levels across age for the 4806 unambiguous genes defined in Figure 4A .

    Article Snippet: 500 ng RNA was used to prepare libraries using the NEBNext Ultra Directional mRNAseq kit (NEB E7420, E7490, E7335, E7500, E7710) as described with modifications: Reagent volumes for RT, second strand synthesis, tailing and ligation were reduced by 50%, while libraries were amplified for 12 cycles using 2 µl each primer per reaction before two rounds of AMPure bead purification as described in the kit at 0.9x ratio prior to quality control using a Bioanalyzer and quantification usinng KAPA Biosystems kit KK4824.

    Techniques: Expressing, Chromatin Immunoprecipitation, Transformation Assay