next magnesium rna fragmentation module  (New England Biolabs)


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    Name:
    NEBNext Magnesium RNA Fragmentation Module
    Description:
    NEBNext Magnesium RNA Fragmentation Module 200 rxns
    Catalog Number:
    E6150S
    Price:
    45
    Size:
    200 rxns
    Category:
    mRNA Template Preparation for PCR
    Buy from Supplier


    Structured Review

    New England Biolabs next magnesium rna fragmentation module
    NEBNext Magnesium RNA Fragmentation Module
    NEBNext Magnesium RNA Fragmentation Module 200 rxns
    https://www.bioz.com/result/next magnesium rna fragmentation module/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    next magnesium rna fragmentation module - by Bioz Stars, 2019-07
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added. .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Article Title: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
    Article Snippet: CLIP-seq was performed with modifications according to ( , ). .. Briefly, RNAse I was used for RNA fragmentation, pre-adenylated 3′ linker and truncated RNA ligase 2 (NEB) was used for on-beads 3′ linker ligation and cDNA library was amplified by 25 PCR cycles (Detailed CLIP-seq procedure can be found in ). .. Cells expressing FLAG-tagged FTO were grown to 90% confluence, washed with ice cold PBS and lysed in lysis buffer (LB) containing 150 mM NaCl, 50 mM Tris pH 7.6, 1% Triton X-100, EDTA-free Complete Protease Inhibitor Cocktail (Roche), 1 mM DTT, RNase In (Promega).

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA).

    Synthesized:

    Article Title: Digital cell quantification identifies global immune cell dynamics during influenza infection
    Article Snippet: For the preparation of RNA‐Seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95°C) treatment for 4:30 min (NEBNext Magnesium RNA Fragmentation Module). .. The 3′ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen).

    Construct:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: Equal amounts of samples were used to construct the PARE libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Real-time Polymerase Chain Reaction:

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. The resulting product was PCR amplified with barcoded reverse primer for 15 cycles and subjected to polyacrylamide gel extraction to purify the cDNA (50 to 200 nt) devoid of library adapters and primers.

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: RNA isolation and qPCR analysis was done as described previously [ ]. .. 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).

    Article Title: The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis
    Article Snippet: Five micrograms of mRNA was used for each m6 A-IP sample. mRNA was fragmented into ∼200-nucleotide molecules with RNA fragmentation reagents (NEB) and incubated with 5 μg m6 A antibody (Synaptic Systems) for 4 h at 4°C. .. The m6 A-containing fragments were immunoprecipitated with preblocked Protein A Dynabeads (Thermo Scientific) and eluted with 7 mM m6 A nucleoside-containing solution.

    Article Title: Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    Article Snippet: A “degraded” RNA sample (used in qPCR analysis) was generated by incubating 1 AU260 of S. cerevisiae cytoplasmic lysate with 3 U of RNase 1 for 30 minutes at room temperature. .. A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs).

    Incubation:

    Article Title: A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing
    Article Snippet: RNA concentrations were determined by Qubit (Life Technologies), purity (A260 /A230 and A260 /A280 ) was determined by Nano Drop (Thermo), and the RNA integrity number for the total RNA was obtained by BioAnalyzer (Agilent). .. The RNA was next fragmented using the NEBNext Magnesium RNA Fragmentation Module [ ] with a 3 minute incubation at 94°C followed by a cleanup step using the RNA Clean & Concentrator-5 (Zymo Research). .. Double-stranded, tagged cDNA was generated from 50 ng of fragmented RNA by the Peregrine method as previously described [ , ].

    Article Title: Peregrine
    Article Snippet: E. coli RNA samples were separated into two aliquots, and one was depleted of rRNA via Ribo-Zero treatment using the “Gram-Negative Bacteria” kit (Epicentre); RNA samples from human PBMC or human cell line A549 were not treated with Ribo-Zero. .. In all cases, 200 ng aliquots of RNA (total or rRNA-depleted via Ribo-Zero) were subjected to random fragmentation in 20 μl reactions, through addition of 2 μl of 10X NEBNext RNA fragmentation buffer (New England BioLabs) and incubation at 94°C for 3 min, followed by immediate cooling on ice and addition of 2 μl of NEBNext RNA fragmentation stop solution (New England Biolabs). .. Fragmented RNA was purified using the Zymo RNA Clean and Concentrator-5 system (Zymo Research), following the manufacturer's general procedure (≥ 17 bp) and eluting in 6 μl of nuclease-free water.

    Article Title: The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis
    Article Snippet: Briefly, 14-d-old wild-type seedlings were used for the IP assays. .. Five micrograms of mRNA was used for each m6 A-IP sample. mRNA was fragmented into ∼200-nucleotide molecules with RNA fragmentation reagents (NEB) and incubated with 5 μg m6 A antibody (Synaptic Systems) for 4 h at 4°C. .. The m6 A-containing fragments were immunoprecipitated with preblocked Protein A Dynabeads (Thermo Scientific) and eluted with 7 mM m6 A nucleoside-containing solution.

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: Then, the RNA was washed and resuspended in 36 µl of RNase-free water. .. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity. .. The RNA-seq library was synthesized using a KAPA Hyper prep kit (KK8504), and a treatment with USER enzyme (NEB, M5505L) was added to digest the non-specific strand.

    Activity Assay:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The manufacturer's protocol was modified so that 5′ monophosphorylated ends that result from endonuclease cleavage or pyrophosphohydrolase activity were preferentially selected. .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Expressing:

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity. .. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity.

    Modification:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The manufacturer's protocol was modified so that 5′ monophosphorylated ends that result from endonuclease cleavage or pyrophosphohydrolase activity were preferentially selected. .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Hybridization:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: Briefly, after 3′ SR Adaptor ligation, reverse transcriptase (RT) primer hybridization and 5′ SR Adaptor ligation — performed as per the manufacturer's protocol — the reaction mixture volume was brought to 100 μl and samples were cleaned up with the RNeasy MinElute Cleanup Kit (Qiagen). .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Sequencing:

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome
    Article Snippet: Primary microRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina).

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: Bacterial rRNAs were removed using Life technologies MICROBExpress kit (Cat. No. AM1905, Grand Island, NY) and the extent of the removal of rRNA from the samples was analyzed on Agilent Bioanalyzer 2100. .. To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. Strand specific cDNA libraries were prepared by treating fragmented RNA sample to phosphatase followed by T4 RNA ligase (NEB, Ipswich, MA).

    Article Title: Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection
    Article Snippet: Paragraph title: DNA and RNA library preparation, emulsion PCR and sequencing ... About 100 ng mRNA was fragmented using NEB Next Magnesium RNA Fragmentation Module (E6150, NEB), purified with an RNA clean up kit (R6247, Omega, USA), end repaired with T4 Polynucleotide Kinase (T4 PNK) (M0201, NEB) and cleaned up again with a kit (R6247, Omega).

    Article Title: MicroRNA miR-23a cluster promotes osteocyte differentiation by regulating TGF-β signalling in osteoblasts
    Article Snippet: Primary miRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented by using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina).

    Article Title: Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    Article Snippet: A “degraded” RNA sample (used in qPCR analysis) was generated by incubating 1 AU260 of S. cerevisiae cytoplasmic lysate with 3 U of RNase 1 for 30 minutes at room temperature. .. A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs). .. A “RiboMinus™ spike-in” library (for assessing mRNA coverage and PCR duplication, was generated by mixing RiboMinus™-treated RNA (Life Technologies, generated as per manufacturer’s instructions) with total RNA in a 1:4 ratio and fragmenting for 6 minutes at 94°C.

    Article Title: Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species
    Article Snippet: RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (NEB) and ethanol Na-acetate precipitated with the addition of 2 μl of linear acrylamide (NEB). .. RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (NEB) and ethanol Na-acetate precipitated with the addition of 2 μl of linear acrylamide (NEB).

    Article Title: mTORC1 Signaling is a Critical Regulator of Postnatal Tendon Development
    Article Snippet: Primary mRNA was isolated using Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. The TruSeq RNA Library Preparation Kit (Illumina) was used to generate the RNA-seq library.

    Ligation:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: Briefly, after 3′ SR Adaptor ligation, reverse transcriptase (RT) primer hybridization and 5′ SR Adaptor ligation — performed as per the manufacturer's protocol — the reaction mixture volume was brought to 100 μl and samples were cleaned up with the RNeasy MinElute Cleanup Kit (Qiagen). .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Article Title: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
    Article Snippet: CLIP-seq was performed with modifications according to ( , ). .. Briefly, RNAse I was used for RNA fragmentation, pre-adenylated 3′ linker and truncated RNA ligase 2 (NEB) was used for on-beads 3′ linker ligation and cDNA library was amplified by 25 PCR cycles (Detailed CLIP-seq procedure can be found in ). .. Cells expressing FLAG-tagged FTO were grown to 90% confluence, washed with ice cold PBS and lysed in lysis buffer (LB) containing 150 mM NaCl, 50 mM Tris pH 7.6, 1% Triton X-100, EDTA-free Complete Protease Inhibitor Cocktail (Roche), 1 mM DTT, RNase In (Promega).

    Hemagglutination Assay:

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: Transgenic tissue-specific Cre recombinase mice (e.g., Tie2:Cre ( B6.Cg-Tg(Tek-cre)1Ywa/J ): The Jackson Laboratory, stock no. 008863) Transgenic CA > GFPstop > HA-UPRT mice (The Jackson Laboratory, stock no. 021469) !CAUTION All mouse procedures must be authorized by your institutional animal care and use committee in compliance with institutional and national animal care guidelines DMSO (Sigma, cat. no. D1435) Corn oil (Sigma, cat. no. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood.

    Generated:

    Article Title: Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome
    Article Snippet: Primary microRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNAs were synthesized with the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and used as the library template.

    Article Title: MicroRNA miR-23a cluster promotes osteocyte differentiation by regulating TGF-β signalling in osteoblasts
    Article Snippet: Primary miRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented by using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNAs were synthesized with the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and used as the library template.

    Article Title: Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    Article Snippet: A “degraded” RNA sample (used in qPCR analysis) was generated by incubating 1 AU260 of S. cerevisiae cytoplasmic lysate with 3 U of RNase 1 for 30 minutes at room temperature. .. A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs). .. A “RiboMinus™ spike-in” library (for assessing mRNA coverage and PCR duplication, was generated by mixing RiboMinus™-treated RNA (Life Technologies, generated as per manufacturer’s instructions) with total RNA in a 1:4 ratio and fragmenting for 6 minutes at 94°C.

    other:

    Article Title: Impact of RNA degradation on fusion detection by RNA-seq
    Article Snippet: Two micrograms of human universal reference RNA (UHR) (Agilent Technologies, Santa Clara, CA) and 1ug of RNA extracted from KU812 cell line (purchased from ATCC) were degraded at 74 °C for 1 to 11 min in 1 min intervals, using the NEBNext® Magnesium RNA Fragmentation Module Kit (NEB, Ipswich, MA).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added. .. Thus, after magnesium fragmentation only RNAs that retained their 5′ SR Adaptor (and original 5′ monophosphate) would undergo subsequent RT and PCR amplification.

    Binding Assay:

    Article Title: Global repositioning of transcription start sites in a plant-fermenting bacterium
    Article Snippet: RNA was fragmented for 30 s at 94 °C using NEBNext Magnesium-based RNA fragmentation buffer (NEB E6101) and purified by Zymo Concentrator-5 (total RNA capture) into 100 μl water. .. Streptavidin magnetic beads (NEB S1421S) were pre-washed twice with low-salt buffer (10 mM Tris, 50 mM NaCl, 1 mM EDTA), twice with binding buffer (10 mM Tris, 500 mM NaCl, 1 mM EDTA) and resuspended at 4 mg ml−1 beads in binding buffer.

    RNA Sequencing Assay:

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: Paragraph title: RNA-seq ... A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood.

    Article Title: Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome
    Article Snippet: Paragraph title: RNA Sequencing ... Primary microRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: Digital cell quantification identifies global immune cell dynamics during influenza infection
    Article Snippet: Primers used for DNA amplification in the PCR assays are presented in . .. For the preparation of RNA‐Seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95°C) treatment for 4:30 min (NEBNext Magnesium RNA Fragmentation Module). .. The 3′ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen).

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: Paragraph title: RNA isolation, RT-qPCR analysis and RNA-seq ... 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).

    Article Title: MicroRNA miR-23a cluster promotes osteocyte differentiation by regulating TGF-β signalling in osteoblasts
    Article Snippet: Paragraph title: RNA-Seq ... Primary miRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented by using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: Paragraph title: RNA sequencing ... RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity.

    Article Title: mTORC1 Signaling is a Critical Regulator of Postnatal Tendon Development
    Article Snippet: Paragraph title: RNA-seq ... Primary mRNA was isolated using Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Magnetic Beads:

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: For isolation of poly(A) RNA, total RNA was subjected to two rounds of purification using oligo(dT)-coupled magnetic beads according to the manufacturer’s instructions (Ambion). .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Article Title: Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome
    Article Snippet: Total RNA was extracted from PBMCs or cell lines with Trizol reagent (Invitrogen). .. Primary microRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNAs were synthesized with the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and used as the library template.

    Article Title: MicroRNA miR-23a cluster promotes osteocyte differentiation by regulating TGF-β signalling in osteoblasts
    Article Snippet: Total RNA was extracted by the same method used for qRT–PCR. .. Primary miRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented by using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNAs were synthesized with the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and used as the library template.

    Article Title: mTORC1 Signaling is a Critical Regulator of Postnatal Tendon Development
    Article Snippet: RNA extraction was performed with the Fibrous Connective Tissue kit (Qiagen). .. Primary mRNA was isolated using Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNA was synthesized with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) to prepare the library templates.

    Mutagenesis:

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: Total RNA was extracted from two wild-type and two mutant samples (frozen hippocampus) using TRIzol. .. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity.

    Isolation:

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: For isolation of poly(A) RNA, total RNA was subjected to two rounds of purification using oligo(dT)-coupled magnetic beads according to the manufacturer’s instructions (Ambion). .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: Paragraph title: RNA isolation, RT-qPCR analysis and RNA-seq ... 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).

    Article Title: mTORC1 Signaling is a Critical Regulator of Postnatal Tendon Development
    Article Snippet: RNA extraction was performed with the Fibrous Connective Tissue kit (Qiagen). .. Primary mRNA was isolated using Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. Double-stranded cDNA was synthesized with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) to prepare the library templates.

    Multiplex Assay:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: Equal amounts of samples were used to construct the PARE libraries using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Purification:

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: For isolation of poly(A) RNA, total RNA was subjected to two rounds of purification using oligo(dT)-coupled magnetic beads according to the manufacturer’s instructions (Ambion). .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: RNA concentrations were determined throughout the purification procedure using a Qubit 2.0 fluorometer (Life Technologies). .. A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. The resulting product was PCR amplified with barcoded reverse primer for 15 cycles and subjected to polyacrylamide gel extraction to purify the cDNA (50 to 200 nt) devoid of library adapters and primers.

    Article Title: Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection
    Article Snippet: A total of 20 μg total RNA was used for two rounds of mRNA purification using Dynabeads (610.06, Invitrogen, USA). .. About 100 ng mRNA was fragmented using NEB Next Magnesium RNA Fragmentation Module (E6150, NEB), purified with an RNA clean up kit (R6247, Omega, USA), end repaired with T4 Polynucleotide Kinase (T4 PNK) (M0201, NEB) and cleaned up again with a kit (R6247, Omega). .. The end-repaired RNAs were used to prepare the strand specific transcriptome, using the Small RNA Sample Preparation kit (E6160, NEB) according to the manufacturer protocol with some minor modification, including the SR Primer F3 being replaced with barcode primers.

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: After RNA isolation, 10 μg total RNA were treated with DNase I (Thermo Scientific) and purified using the RNeasy MinElute Cleanup Kit (Qiagen). .. 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen). .. SuperScript III reverse transcriptase (Life Technologies, Carlsbad, CA) was used for first strand synthesis.

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: Then total RNA was treated with DNase (Qiagen, 79254) and purified using an RNeasy MinElute Cleanup Kit (Qiagen, 74204). .. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity.

    Article Title: Global repositioning of transcription start sites in a plant-fermenting bacterium
    Article Snippet: RNA was 5′ capped using VCE (NEB M2080) at 3 U μg−1 RNA with 0.1 mM SAM and 0.5 mM 3′ biotin-GTP (NEB N0760) for 30 min at 37 °C and purified by Zymo Concentrator-5 ( > 200 bp capture) with two additional washes into 45 μl water. .. RNA was fragmented for 30 s at 94 °C using NEBNext Magnesium-based RNA fragmentation buffer (NEB E6101) and purified by Zymo Concentrator-5 (total RNA capture) into 100 μl water. .. Streptavidin magnetic beads (NEB S1421S) were pre-washed twice with low-salt buffer (10 mM Tris, 50 mM NaCl, 1 mM EDTA), twice with binding buffer (10 mM Tris, 500 mM NaCl, 1 mM EDTA) and resuspended at 4 mg ml−1 beads in binding buffer.

    Article Title: Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species
    Article Snippet: RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (NEB) and ethanol Na-acetate precipitated with the addition of 2 μl of linear acrylamide (NEB). .. Precipitated RNA was resuspended in 14 μl of nuclease-free H2 O. Sequencing libraries of fragmented RNA were assembled using the NEBNext sRNA library prep kit (NEB) per the manufacturer’s instructions.

    Polymerase Chain Reaction:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added. .. The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added.

    Article Title: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
    Article Snippet: CLIP-seq was performed with modifications according to ( , ). .. Briefly, RNAse I was used for RNA fragmentation, pre-adenylated 3′ linker and truncated RNA ligase 2 (NEB) was used for on-beads 3′ linker ligation and cDNA library was amplified by 25 PCR cycles (Detailed CLIP-seq procedure can be found in ). .. Cells expressing FLAG-tagged FTO were grown to 90% confluence, washed with ice cold PBS and lysed in lysis buffer (LB) containing 150 mM NaCl, 50 mM Tris pH 7.6, 1% Triton X-100, EDTA-free Complete Protease Inhibitor Cocktail (Roche), 1 mM DTT, RNase In (Promega).

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood.

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA).

    Article Title: Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection
    Article Snippet: Paragraph title: DNA and RNA library preparation, emulsion PCR and sequencing ... About 100 ng mRNA was fragmented using NEB Next Magnesium RNA Fragmentation Module (E6150, NEB), purified with an RNA clean up kit (R6247, Omega, USA), end repaired with T4 Polynucleotide Kinase (T4 PNK) (M0201, NEB) and cleaned up again with a kit (R6247, Omega).

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen). .. Samples were purified using Mini Quick Spin Columns (Roche) and second strand synthesis was done with the NEBNext mRNA Second Strand Synthesis Module (New England Biolabs).

    Quantitative RT-PCR:

    Article Title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
    Article Snippet: Paragraph title: RNA isolation, RT-qPCR analysis and RNA-seq ... 5 μg DNase treated RNA were used for rRNA depletion with the RiboMinus Eukaryote System v2 (Life Technologies, Carlsbad, CA). rRNA depleted samples were fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).

    Article Title: MicroRNA miR-23a cluster promotes osteocyte differentiation by regulating TGF-β signalling in osteoblasts
    Article Snippet: Total RNA was extracted by the same method used for qRT–PCR. .. Primary miRNAs and mRNAs were captured by Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented by using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    cDNA Library Assay:

    Article Title: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
    Article Snippet: CLIP-seq was performed with modifications according to ( , ). .. Briefly, RNAse I was used for RNA fragmentation, pre-adenylated 3′ linker and truncated RNA ligase 2 (NEB) was used for on-beads 3′ linker ligation and cDNA library was amplified by 25 PCR cycles (Detailed CLIP-seq procedure can be found in ). .. Cells expressing FLAG-tagged FTO were grown to 90% confluence, washed with ice cold PBS and lysed in lysis buffer (LB) containing 150 mM NaCl, 50 mM Tris pH 7.6, 1% Triton X-100, EDTA-free Complete Protease Inhibitor Cocktail (Roche), 1 mM DTT, RNase In (Promega).

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. The resulting product was PCR amplified with barcoded reverse primer for 15 cycles and subjected to polyacrylamide gel extraction to purify the cDNA (50 to 200 nt) devoid of library adapters and primers.

    Mouse Assay:

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: Transgenic tissue-specific Cre recombinase mice (e.g., Tie2:Cre ( B6.Cg-Tg(Tek-cre)1Ywa/J ): The Jackson Laboratory, stock no. 008863) Transgenic CA > GFPstop > HA-UPRT mice (The Jackson Laboratory, stock no. 021469) !CAUTION All mouse procedures must be authorized by your institutional animal care and use committee in compliance with institutional and national animal care guidelines DMSO (Sigma, cat. no. D1435) Corn oil (Sigma, cat. no. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood.

    Chromatin Immunoprecipitation:

    Article Title: Peregrine
    Article Snippet: In all cases, 200 ng aliquots of RNA (total or rRNA-depleted via Ribo-Zero) were subjected to random fragmentation in 20 μl reactions, through addition of 2 μl of 10X NEBNext RNA fragmentation buffer (New England BioLabs) and incubation at 94°C for 3 min, followed by immediate cooling on ice and addition of 2 μl of NEBNext RNA fragmentation stop solution (New England Biolabs). .. In all cases, 200 ng aliquots of RNA (total or rRNA-depleted via Ribo-Zero) were subjected to random fragmentation in 20 μl reactions, through addition of 2 μl of 10X NEBNext RNA fragmentation buffer (New England BioLabs) and incubation at 94°C for 3 min, followed by immediate cooling on ice and addition of 2 μl of NEBNext RNA fragmentation stop solution (New England Biolabs).

    RNA Extraction:

    Article Title: A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing
    Article Snippet: Paragraph title: RNA extraction and cDNA Synthesis ... The RNA was next fragmented using the NEBNext Magnesium RNA Fragmentation Module [ ] with a 3 minute incubation at 94°C followed by a cleanup step using the RNA Clean & Concentrator-5 (Zymo Research).

    Article Title: mTORC1 Signaling is a Critical Regulator of Postnatal Tendon Development
    Article Snippet: RNA extraction was performed with the Fibrous Connective Tissue kit (Qiagen). .. Primary mRNA was isolated using Dynabeads Oligo (dT)25 magnetic beads (Invitrogen) and fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Selection:

    Article Title: Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    Article Snippet: A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs). .. A “RiboMinus™ spike-in” library (for assessing mRNA coverage and PCR duplication, was generated by mixing RiboMinus™-treated RNA (Life Technologies, generated as per manufacturer’s instructions) with total RNA in a 1:4 ratio and fragmenting for 6 minutes at 94°C.

    Agarose Gel Electrophoresis:

    Article Title: Mapping of internal monophosphate 5′ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
    Article Snippet: The RNA was fragmented using the NEBNext® Magnesium RNA Fragmentation Module at 94°C for 4 min, and 2 μl of stop solution was added. .. After addition of the RT primer, the reaction volume was adjusted to 30 μl and RT/PCR amplification reactions were performed as per the manufacturer's protocol, using barcoded primers.

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: Then, mRNA concentration was measured by Qubit 2.0 (Invitrogen) and the integrity was tested by agarose gel electrophoresis and Agilent 2100 bioanalyzer. .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. After another ethanol precipitation cleanup step, sequencing library preparation was performed using the Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs).

    Transgenic Assay:

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: Transgenic tissue-specific Cre recombinase mice (e.g., Tie2:Cre ( B6.Cg-Tg(Tek-cre)1Ywa/J ): The Jackson Laboratory, stock no. 008863) Transgenic CA > GFPstop > HA-UPRT mice (The Jackson Laboratory, stock no. 021469) !CAUTION All mouse procedures must be authorized by your institutional animal care and use committee in compliance with institutional and national animal care guidelines DMSO (Sigma, cat. no. D1435) Corn oil (Sigma, cat. no. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood.

    Ethanol Precipitation:

    Article Title: The E. coli molecular phenotype under different growth conditions
    Article Snippet: A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). .. A fraction of the RNA was then fragmented to ~250 bp using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs).

    Article Title: The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis
    Article Snippet: Five micrograms of mRNA was used for each m6 A-IP sample. mRNA was fragmented into ∼200-nucleotide molecules with RNA fragmentation reagents (NEB) and incubated with 5 μg m6 A antibody (Synaptic Systems) for 4 h at 4°C. .. The m6 A-containing fragments were immunoprecipitated with preblocked Protein A Dynabeads (Thermo Scientific) and eluted with 7 mM m6 A nucleoside-containing solution.

    Article Title: Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage
    Article Snippet: A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs). .. A “total” RNA library (used for sequencing) was generated by Mg+2 -mediated cleavage of intact RNA for 8 minutes at 94°C using the NEBNext Mg+2 RNA fragmentation module (New England Biolabs).

    Random Hexamer Labeling:

    Article Title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration
    Article Snippet: Then, the RNA was washed and resuspended in 36 µl of RNase-free water. .. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution, and the RNA was fragmented by incubation at 95°C for 3 min. For reverse transcription, cDNA first-strand synthesis was performed with random hexamer primers. cDNA second-strand synthesis was performed with dNTPs to ensure strand specificity. .. The RNA-seq library was synthesized using a KAPA Hyper prep kit (KK8504), and a treatment with USER enzyme (NEB, M5505L) was added to digest the non-specific strand.

    Spectrophotometry:

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: NanoDrop spectrophotometer (Thermo Scientific) was used to measure the concentration of RNA, and the integrity were tested by Agilent 2100 bioanalyzer. .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Concentration Assay:

    Article Title: mRNA N6-methyladenosine methylation of postnatal liver development in pig
    Article Snippet: Then, mRNA concentration was measured by Qubit 2.0 (Invitrogen) and the integrity was tested by agarose gel electrophoresis and Agilent 2100 bioanalyzer. .. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol.

    Article Title: Staphylococcus aureus Shifts toward Commensalism in Response to Corynebacterium Species
    Article Snippet: RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (NEB) and ethanol Na-acetate precipitated with the addition of 2 μl of linear acrylamide (NEB). .. Assembled libraries were run on 6% polyacrylamide TBE gels and bands between 130 and 300 bp were gel purified and extracted as per the NEBNext sRNA library kit instructions.

    Gel Extraction:

    Article Title: Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans
    Article Snippet: To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA). .. To generate RNA optimal for sequencing rRNA-depleted RNA samples were fragmented to ~100 nt using NEBNext Magnesium RNA fragmentation module (Cat. No E6150S, NEB, Ipswich, MA).

    Cross-linking Immunoprecipitation:

    Article Title: N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
    Article Snippet: CLIP-seq was performed with modifications according to ( , ). .. Briefly, RNAse I was used for RNA fragmentation, pre-adenylated 3′ linker and truncated RNA ligase 2 (NEB) was used for on-beads 3′ linker ligation and cDNA library was amplified by 25 PCR cycles (Detailed CLIP-seq procedure can be found in ). .. Cells expressing FLAG-tagged FTO were grown to 90% confluence, washed with ice cold PBS and lysed in lysis buffer (LB) containing 150 mM NaCl, 50 mM Tris pH 7.6, 1% Triton X-100, EDTA-free Complete Protease Inhibitor Cocktail (Roche), 1 mM DTT, RNase In (Promega).

    Hood:

    Article Title: Applying thiouracil (TU)-tagging for mouse transcriptome analysis
    Article Snippet: 4-thiouracil (4TU) (Sigma, cat. no. 440736) TRIzol (Invitrogen, cat. no. 15596-026) Chloroform (Macron Fine Chemicals, cat. no. 444004) !CAUTION TRIzol and chloroform are toxic and should be used in a fume hood while wearing gloves and a lab coat. .. Isopropyl alcohol (Macron Fine Chemicals, cat. no. MK303202) Ethanol (EtOH) (Pharmco Aaper, cat. no. 11100020G) RNase-free water (H2 O) (Ambion cat. no. AM9938) 1M Tris pH 8.0 RNase-free (Ambion cat. no. AM9855G) 0.5M EDTA pH 8.0 RNase-free (Ambion cat. no. AM9260G) TURBO DNase (Invitrogen cat. no. AM2238) RNeasy Mini Kit (Qiagen cat. no. 74101) Qubit RNA BR Assay Kit (Invitrogen, cat. no. ) Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. ) Qubit assay tubes (Invitrogen, cat. no. ) NEBNext magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) Ribo-Zero Magnetic Kit (Epicentre, cat. no. MRZH11124) N,N-Dimethylformamide (Sigma, cat. no. D4551) EZ-Link Biotin-HDPD (Thermo Scientific, cat. no. 21341) μMacs Streptavidin Kit (Miltenyi Biotec, cat. no. 130-074-101) 2-mercaptoethanol (Sigma, cat. no. M3148) !CAUTION 2-mercaptoethanol is toxic and should only be used in a fume hood. .. Glove and lab coat should be worn when handling.

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    New England Biolabs next magnesium rna fragmentation module
    Next Magnesium Rna Fragmentation Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/next magnesium rna fragmentation module/product/New England Biolabs
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