nebnext ultra directional rna library prep kit for illumina  (New England Biolabs)


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    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:
    3877
    Size:
    96 rxns
    Category:
    mRNA Template Preparation for PCR
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    Structured Review

    New England Biolabs nebnext ultra directional rna library prep kit for illumina
    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/nebnext ultra directional rna library prep kit for illumina/product/New England Biolabs
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    nebnext ultra directional rna library prep kit for illumina - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs"

    Article Title: Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs

    Journal: Genes & Development

    doi: 10.1101/gad.241950.114

    RNA-seq analysis of BioTAP-XL pull-downs. ( A ) Enrichment of repeat-derived RNA in HP1a-BioTAP cross-linked complexes from S2 cells compared with MSL3-BioTAP complexes from S2 cells detected using a random-priming approach for cDNA synthesis and Illumina
    Figure Legend Snippet: RNA-seq analysis of BioTAP-XL pull-downs. ( A ) Enrichment of repeat-derived RNA in HP1a-BioTAP cross-linked complexes from S2 cells compared with MSL3-BioTAP complexes from S2 cells detected using a random-priming approach for cDNA synthesis and Illumina

    Techniques Used: RNA Sequencing Assay, Derivative Assay

    2) Product Images from "Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia"

    Article Title: Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-16091-0

    Comparison of mRNAs half-lives in S. maltophilia strains D457 and ALB001. Messenger RNA half-lives determined by RNA-Seq Illumina 1.9 in S. maltophilia strains D457 and ALB001 were correlated between them. Half-lives are shown at log scale.
    Figure Legend Snippet: Comparison of mRNAs half-lives in S. maltophilia strains D457 and ALB001. Messenger RNA half-lives determined by RNA-Seq Illumina 1.9 in S. maltophilia strains D457 and ALB001 were correlated between them. Half-lives are shown at log scale.

    Techniques Used: RNA Sequencing Assay

    Distribution of global mRNA half-lives for S. maltophilia D457 and ALB001 determined by RNA-Seq using Illumina 1.9 technology and depicted by a boxplot at log scale. Each box comprises the 25 to 75 percentile of measured mRNA half-lives for the indicated strain (the 50% of the calculated half-life values). Whisker top bar corresponds to maximum half-life except from outlier values (over Q3 + 1,5(IQR)) and whisker bottom bar corresponds to minimum half-life except from outlier values (under Q1 − 1,5(IQR)). The bar inside each box marks the median mRNA half-life in each of the two bacterial strains. Q1: Quartile 1; Q3: Quartile 3; IQR: Interquartile Range.
    Figure Legend Snippet: Distribution of global mRNA half-lives for S. maltophilia D457 and ALB001 determined by RNA-Seq using Illumina 1.9 technology and depicted by a boxplot at log scale. Each box comprises the 25 to 75 percentile of measured mRNA half-lives for the indicated strain (the 50% of the calculated half-life values). Whisker top bar corresponds to maximum half-life except from outlier values (over Q3 + 1,5(IQR)) and whisker bottom bar corresponds to minimum half-life except from outlier values (under Q1 − 1,5(IQR)). The bar inside each box marks the median mRNA half-life in each of the two bacterial strains. Q1: Quartile 1; Q3: Quartile 3; IQR: Interquartile Range.

    Techniques Used: RNA Sequencing Assay, Whisker Assay

    Related Articles

    Amplification:

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335). .. After adaptor ligation, the libraries were amplified by qPCR using the KAPA Real-time amplification kit (KAPA Biosystems).

    Construct:

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: .. One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. Briefly, poly(A)+ RNA was purified with oligo-d(T) beads, and fragmented to ~200 nucleotide lengths prior to cDNA synthesis using random primers.

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions. .. High-throughput sequencing and quality control (QC) cDNA libraries were sequenced on an Illumina HiSeq 2000 platform.

    Article Title: Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation
    Article Snippet: .. A total of 24 RNA-seq libraries (three biological replicates at four stages for both BLO and KID) were constructed as described previously ( ) using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). .. These libraries were multiplexed in an equal amount for single end 101-base sequencing in two lanes of HiSeq 2000 (Illumina, San Diego, CA) at the Cornell University Biotechnology Resource Center (Ithaca, NY).

    Real-time Polymerase Chain Reaction:

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335). .. After adaptor ligation, the libraries were amplified by qPCR using the KAPA Real-time amplification kit (KAPA Biosystems).

    Incubation:

    Article Title: NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated
    Article Snippet: The beads with bound NAD-RNAs were suspended with the RT mixture and incubated at 94 °C for 6 min to ( i ) elute the RNAs from beads, ( ii ) fragment the RNAs, and ( iii ) denature the RNAs. .. The same batch of RNAs was also used for RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs).

    Expressing:

    Article Title: NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated
    Article Snippet: The same batch of RNAs was also used for RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs). .. The sequences were deposited at the National Center for Biotechnology Information Gene Expression Omnibus database under the accession number .

    Ligation:

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. Double-stranded cDNA was purified with AMPure XP beads and subjected to end-repair, adapter ligation, and PCR enrichment.

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: Both the TEX-treated and untreated RNA samples were then subject to a treatment of tobacco acid pyrophosphatase (TAP, Epicentre) to generate 5′ P-transcripts for linker ligation. .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions.

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335). .. After adaptor ligation, the libraries were amplified by qPCR using the KAPA Real-time amplification kit (KAPA Biosystems).

    Cell Culture:

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: Overnight cultures of wild-type strain U112 and the Δ greA mutant were diluted 100-fold with fresh TSB and cultured in triplicate to mid-log phase on a shaker. .. The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).

    Generated:

    Article Title: A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species
    Article Snippet: .. RNAseq libraries were generated with polyA enrichment and rRNA depletion using NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, Ipswich, USA, http://www.neb.com ) for Illumina® and were sequenced on an Illumina® HiSeq 2500 at the Max Planck Genome Centre, Cologne, Germany. .. RNAseq analysis Illumina 100 bp paired-end reads from four biological replicates of the four internode zones were imported into CLC genomics workbench 8 (CLCbio, Aarhus, Denmark, http://www.clcbio.com ) for adapter removal, trimming, mapping, and read counting.

    Polymerase Chain Reaction:

    Article Title: Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs
    Article Snippet: An NEBNext ultradirectional RNA library kit (New England Biolabs, catalog no. E7420S) was used to make cDNA and RNA-seq libraries. .. Several minor modifications to the standard kit protocol were made based on (1) size (RNA fragmentation time was decreased from 15 to 5 min) and (2) the small amount of RNA (the number of PCR cycles were adjusted to 20 cycles in the USER excision and PCR library step).

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. Double-stranded cDNA was purified with AMPure XP beads and subjected to end-repair, adapter ligation, and PCR enrichment.

    Article Title: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
    Article Snippet: We prepared sequence library DNA with 1 μg of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit. .. In addition, we used SuperScript III instead of ProtoScript in the RT step and KAPA HiFi DNA polymerase instead of NEBNext High-Fidelity PCR DNA polymerase in the PCR step.

    Article Title: Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
    Article Snippet: After the final PCR step, all libraries were pooled together, purified using Agencourt Ampure XP magnetic beads (Beckman Coulter) and eluted in nuclease-free water. .. Input sample libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina HiSeq2000 at the Tayside Centre for Genomics Analysis, University of Dundee, with a pair-end read length of 75 bp.

    Nucleic Acid Electrophoresis:

    Article Title: Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
    Article Snippet: After reverse transcription, cDNA fraction corresponding to 70–200 nt was gel purified after 6% TBE-urea gel electrophoresis (Thermo Fisher Scientific). .. Input sample libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina HiSeq2000 at the Tayside Centre for Genomics Analysis, University of Dundee, with a pair-end read length of 75 bp.

    RNA Sequencing Assay:

    Article Title: Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs
    Article Snippet: .. An NEBNext ultradirectional RNA library kit (New England Biolabs, catalog no. E7420S) was used to make cDNA and RNA-seq libraries. .. Several minor modifications to the standard kit protocol were made based on (1) size (RNA fragmentation time was decreased from 15 to 5 min) and (2) the small amount of RNA (the number of PCR cycles were adjusted to 20 cycles in the USER excision and PCR library step).

    Article Title: Genetic modification of primary human B cells to model high-grade lymphoma
    Article Snippet: .. RNA-seq library was prepared using the NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions. .. NEBNext Multiplex Oligos for Illumina (E7500) was used for indexing and sequenced on a HiSeq4000 by 50-bp single-end sequencing.

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were utilized to construct small RNA sequencing libraries (miRNA-Seq) using the Illumina TruSeq Small RNA Sample Prep Kit (#RS-200-0012). .. One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S).

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: Next, using an RNA-Seq Library Preparation Kit for Transcriptome Discovery (Gnomegen), dRNA-seq cDNA libraries were constructed in accordance with the manufacturer's recommendations. .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions.

    Article Title: Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation
    Article Snippet: .. A total of 24 RNA-seq libraries (three biological replicates at four stages for both BLO and KID) were constructed as described previously ( ) using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). .. These libraries were multiplexed in an equal amount for single end 101-base sequencing in two lanes of HiSeq 2000 (Illumina, San Diego, CA) at the Cornell University Biotechnology Resource Center (Ithaca, NY).

    Article Title: Selective release of circRNAs in platelet-derived extracellular vesicles
    Article Snippet: .. RNA-seq and data analysis 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). .. For library preparation of RNA isolated from exosomes the SMARTer® Stranded RNA-Seq Kit (Takara-Clontech) was used, according to the manufacturer’s instructions.

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: Paragraph title: RNA-seq ... The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).

    Article Title: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
    Article Snippet: Paragraph title: Bulk RNA-seq methods for populations of cells ... We prepared sequence library DNA with 1 μg of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit.

    Article Title: NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated
    Article Snippet: .. The same batch of RNAs was also used for RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs). .. The libraries were sequenced with the 150-nucleotide paired-end mode with Illumina HiSeqX Ten.

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: Paragraph title: DNA and RNA sequencing ... After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335).

    Magnetic Beads:

    Article Title: NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated
    Article Snippet: For poly(A) mRNA NAD captureSeq, ∼4 μg of poly(A) RNAs were isolated from 500 μg of total RNAs using oligo (dT) magnetic beads (New England Biolabs). .. The same batch of RNAs was also used for RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs).

    Article Title: Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
    Article Snippet: After the final PCR step, all libraries were pooled together, purified using Agencourt Ampure XP magnetic beads (Beckman Coulter) and eluted in nuclease-free water. .. Input sample libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina HiSeq2000 at the Tayside Centre for Genomics Analysis, University of Dundee, with a pair-end read length of 75 bp.

    Mutagenesis:

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: Overnight cultures of wild-type strain U112 and the Δ greA mutant were diluted 100-fold with fresh TSB and cultured in triplicate to mid-log phase on a shaker. .. The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).

    Isolation:

    Article Title: Genetic modification of primary human B cells to model high-grade lymphoma
    Article Snippet: .. RNA-seq library was prepared using the NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions. .. NEBNext Multiplex Oligos for Illumina (E7500) was used for indexing and sequenced on a HiSeq4000 by 50-bp single-end sequencing.

    Article Title: Selective release of circRNAs in platelet-derived extracellular vesicles
    Article Snippet: RNA-seq and data analysis 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). .. For library preparation of RNA isolated from exosomes the SMARTer® Stranded RNA-Seq Kit (Takara-Clontech) was used, according to the manufacturer’s instructions.

    Article Title: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
    Article Snippet: .. We prepared sequence library DNA with 1 μg of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit. ..

    Article Title: NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated
    Article Snippet: For poly(A) mRNA NAD captureSeq, ∼4 μg of poly(A) RNAs were isolated from 500 μg of total RNAs using oligo (dT) magnetic beads (New England Biolabs). .. The same batch of RNAs was also used for RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420; New England Biolabs).

    Multiplex Assay:

    Article Title: Genetic modification of primary human B cells to model high-grade lymphoma
    Article Snippet: RNA-seq library was prepared using the NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions. .. NEBNext Multiplex Oligos for Illumina (E7500) was used for indexing and sequenced on a HiSeq4000 by 50-bp single-end sequencing.

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: .. After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335). .. After adaptor ligation, the libraries were amplified by qPCR using the KAPA Real-time amplification kit (KAPA Biosystems).

    Purification:

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. Briefly, poly(A)+ RNA was purified with oligo-d(T) beads, and fragmented to ~200 nucleotide lengths prior to cDNA synthesis using random primers.

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: The cDNAs were size-fractioned within the range of 300 to 600 nt on agarose gels and purified using a QIAquick Gel Extraction Kit (Qiagen). .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions.

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: The prepared RNAs were analyzed with a NanoDrop 2000 spectrophotometer (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent, San Diego, CA, USA), and purified with the RNeasy MinElute Cleanup Kit (Qiagen). .. The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).

    Article Title: Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
    Article Snippet: After the final PCR step, all libraries were pooled together, purified using Agencourt Ampure XP magnetic beads (Beckman Coulter) and eluted in nuclease-free water. .. Input sample libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina HiSeq2000 at the Tayside Centre for Genomics Analysis, University of Dundee, with a pair-end read length of 75 bp.

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335). .. Finally, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) as described in the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) protocol.

    Sequencing:

    Article Title: Genetic modification of primary human B cells to model high-grade lymphoma
    Article Snippet: RNA-seq library was prepared using the NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions. .. NEBNext Multiplex Oligos for Illumina (E7500) was used for indexing and sequenced on a HiSeq4000 by 50-bp single-end sequencing.

    Article Title: A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species
    Article Snippet: Paragraph title: RNA extraction, library preparation, and sequencing ... RNAseq libraries were generated with polyA enrichment and rRNA depletion using NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, Ipswich, USA, http://www.neb.com ) for Illumina® and were sequenced on an Illumina® HiSeq 2500 at the Max Planck Genome Centre, Cologne, Germany.

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: .. One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. Briefly, poly(A)+ RNA was purified with oligo-d(T) beads, and fragmented to ~200 nucleotide lengths prior to cDNA synthesis using random primers.

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions. .. High-throughput sequencing and quality control (QC) cDNA libraries were sequenced on an Illumina HiSeq 2000 platform.

    Article Title: Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation
    Article Snippet: A total of 24 RNA-seq libraries (three biological replicates at four stages for both BLO and KID) were constructed as described previously ( ) using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). .. These libraries were multiplexed in an equal amount for single end 101-base sequencing in two lanes of HiSeq 2000 (Illumina, San Diego, CA) at the Cornell University Biotechnology Resource Center (Ithaca, NY).

    Article Title: Selective release of circRNAs in platelet-derived extracellular vesicles
    Article Snippet: .. RNA-seq and data analysis 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). .. For library preparation of RNA isolated from exosomes the SMARTer® Stranded RNA-Seq Kit (Takara-Clontech) was used, according to the manufacturer’s instructions.

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB). .. The cDNA was sequenced with the Illumina sequencing technology (Illumina HiSeq™ 2500).

    Article Title: Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads
    Article Snippet: .. We prepared sequence library DNA with 1 μg of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit. ..

    Article Title: Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
    Article Snippet: Paired-end sequencing with a read length of 100 bp was carried out on an Illumina MiSeq v2 at Edinburgh Genomics, University of Edinburgh. .. Input sample libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina HiSeq2000 at the Tayside Centre for Genomics Analysis, University of Dundee, with a pair-end read length of 75 bp.

    Article Title: Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation
    Article Snippet: DNA libraries were sequenced on an Illumina HiSeq2500 Sequencing platform in two lanes as paired-end reads 100 cycle lanes. .. After rRNA depletion libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) and NEBNext Multiplex Oligos for Illumina Index Primers Set I (Illumina, E7335).

    Chromatin Immunoprecipitation:

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S). .. The products were purified with AMPure XP Beads, analyzed with the Agilent Bioanalyzer High Sensitivity DNA chip, pooled in equimolar amounts, and used for paired-end sequencing with the Illumina HiSeq 2000 instrument using 50 cycles.

    Software:

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB). .. The raw reads were processed with the Cutadapt (version 1.9.1) software.

    RNA Extraction:

    Article Title: A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species
    Article Snippet: Paragraph title: RNA extraction, library preparation, and sequencing ... RNAseq libraries were generated with polyA enrichment and rRNA depletion using NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, Ipswich, USA, http://www.neb.com ) for Illumina® and were sequenced on an Illumina® HiSeq 2500 at the Max Planck Genome Centre, Cologne, Germany.

    Sample Prep:

    Article Title: MicroRNAs Circulate in the Hemolymph of Drosophila and Accumulate Relative to Tissue microRNAs in an Age-Dependent Manner
    Article Snippet: One-microgram aliquots of total RNA were utilized to construct small RNA sequencing libraries (miRNA-Seq) using the Illumina TruSeq Small RNA Sample Prep Kit (#RS-200-0012). .. One-microgram aliquots of total RNA were used to construct mRNA sequencing libraries (mRNA-Seq) using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7420S).

    Spectrophotometry:

    Article Title: Transcription Elongation Factor GreA Plays a Key Role in Cellular Invasion and Virulence of Francisella tularensis subsp. novicida
    Article Snippet: The prepared RNAs were analyzed with a NanoDrop 2000 spectrophotometer (Thermo Scientific) and Agilent 2100 Bioanalyzer (Agilent, San Diego, CA, USA), and purified with the RNeasy MinElute Cleanup Kit (Qiagen). .. The Ribo-Zero™ Magnetic Kit (Epicentre, Madison, WI, USA) was used to remove the rRNA, and the rRNA-depleted RNA was used to generate cDNA libraries with the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB).

    High Throughput Screening Assay:

    Article Title: Selective release of circRNAs in platelet-derived extracellular vesicles
    Article Snippet: .. RNA-seq and data analysis 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). .. For library preparation of RNA isolated from exosomes the SMARTer® Stranded RNA-Seq Kit (Takara-Clontech) was used, according to the manufacturer’s instructions.

    Gel Extraction:

    Article Title: Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
    Article Snippet: The cDNAs were size-fractioned within the range of 300 to 600 nt on agarose gels and purified using a QIAquick Gel Extraction Kit (Qiagen). .. In addition, for TSS refinement and verificaion, standard strand-specific whole-transcript sequencing cDNA libraries (w library) were constructed for the total RNAs using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions.

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    New England Biolabs nebnext ultra directional rna library prep kit for illumina
    <t>RNA-seq</t> analysis of BioTAP-XL pull-downs. ( A ) Enrichment of repeat-derived RNA in HP1a-BioTAP cross-linked complexes from S2 cells compared with MSL3-BioTAP complexes from S2 cells detected using a random-priming approach for cDNA synthesis and <t>Illumina</t>
    Nebnext Ultra Directional Rna Library Prep Kit For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    RNA-seq analysis of BioTAP-XL pull-downs. ( A ) Enrichment of repeat-derived RNA in HP1a-BioTAP cross-linked complexes from S2 cells compared with MSL3-BioTAP complexes from S2 cells detected using a random-priming approach for cDNA synthesis and Illumina

    Journal: Genes & Development

    Article Title: Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs

    doi: 10.1101/gad.241950.114

    Figure Lengend Snippet: RNA-seq analysis of BioTAP-XL pull-downs. ( A ) Enrichment of repeat-derived RNA in HP1a-BioTAP cross-linked complexes from S2 cells compared with MSL3-BioTAP complexes from S2 cells detected using a random-priming approach for cDNA synthesis and Illumina

    Article Snippet: An NEBNext ultradirectional RNA library kit (New England Biolabs, catalog no. E7420S) was used to make cDNA and RNA-seq libraries.

    Techniques: RNA Sequencing Assay, Derivative Assay

    Comparison of mRNAs half-lives in S. maltophilia strains D457 and ALB001. Messenger RNA half-lives determined by RNA-Seq Illumina 1.9 in S. maltophilia strains D457 and ALB001 were correlated between them. Half-lives are shown at log scale.

    Journal: Scientific Reports

    Article Title: Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia

    doi: 10.1038/s41598-017-16091-0

    Figure Lengend Snippet: Comparison of mRNAs half-lives in S. maltophilia strains D457 and ALB001. Messenger RNA half-lives determined by RNA-Seq Illumina 1.9 in S. maltophilia strains D457 and ALB001 were correlated between them. Half-lives are shown at log scale.

    Article Snippet: RNA was then subjected to RNA library preparation using the Ultra Directional RNA Library Prep Kit (Cat no. E7420S, New England Biolabs) following manufacturer recommendations.

    Techniques: RNA Sequencing Assay

    Distribution of global mRNA half-lives for S. maltophilia D457 and ALB001 determined by RNA-Seq using Illumina 1.9 technology and depicted by a boxplot at log scale. Each box comprises the 25 to 75 percentile of measured mRNA half-lives for the indicated strain (the 50% of the calculated half-life values). Whisker top bar corresponds to maximum half-life except from outlier values (over Q3 + 1,5(IQR)) and whisker bottom bar corresponds to minimum half-life except from outlier values (under Q1 − 1,5(IQR)). The bar inside each box marks the median mRNA half-life in each of the two bacterial strains. Q1: Quartile 1; Q3: Quartile 3; IQR: Interquartile Range.

    Journal: Scientific Reports

    Article Title: Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia

    doi: 10.1038/s41598-017-16091-0

    Figure Lengend Snippet: Distribution of global mRNA half-lives for S. maltophilia D457 and ALB001 determined by RNA-Seq using Illumina 1.9 technology and depicted by a boxplot at log scale. Each box comprises the 25 to 75 percentile of measured mRNA half-lives for the indicated strain (the 50% of the calculated half-life values). Whisker top bar corresponds to maximum half-life except from outlier values (over Q3 + 1,5(IQR)) and whisker bottom bar corresponds to minimum half-life except from outlier values (under Q1 − 1,5(IQR)). The bar inside each box marks the median mRNA half-life in each of the two bacterial strains. Q1: Quartile 1; Q3: Quartile 3; IQR: Interquartile Range.

    Article Snippet: RNA was then subjected to RNA library preparation using the Ultra Directional RNA Library Prep Kit (Cat no. E7420S, New England Biolabs) following manufacturer recommendations.

    Techniques: RNA Sequencing Assay, Whisker Assay