neb e7490 poly  (New England Biolabs)


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  • 99
    Name:
    NEBNext Poly A mRNA Magnetic Isolation Module
    Description:
    NEBNext Poly A mRNA Magnetic Isolation Module 96 rxns
    Catalog Number:
    E7490L
    Price:
    242
    Size:
    96 rxns
    Category:
    mRNA Purification Kits
    Buy from Supplier


    Structured Review

    New England Biolabs neb e7490 poly
    NEBNext Poly A mRNA Magnetic Isolation Module
    NEBNext Poly A mRNA Magnetic Isolation Module 96 rxns
    https://www.bioz.com/result/neb e7490 poly/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    neb e7490 poly - by Bioz Stars, 2019-07
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide. .. 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: Fragment interruption, cDNA synthesis, addition of adapters, PCR amplification and RNA-Seq were performed by Beijing BioMarker Technologies (Beijing, China). .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA).

    Construct:

    Article Title: Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis
    Article Snippet: Paragraph title: Plasmid constructs and in vitro transcription ... The EMCV IRES containing mRNA was uncapped, whereas for all other transcripts Vaccinia Capping System (NEB) was used to obtain 100% capped products.

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S). .. RNA-seq libraries were constructed using NEB kits E7530S (library prep), and E7335S (Oligos).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: The standard Illumina methods and protocols were adopted to prepare and sequence the cDNA libraries. .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA). .. The size of the library insert fragments was determined by 1.8% agarose gel electrophoresis, and the fragments were quantified using a Library Quantification Kit/Illumina GA Universal (Kapa, USA).

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

    Real-time Polymerase Chain Reaction:

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. After indexing via PCR (11 cycles) enrichment, the amplified libraries together with library preparation negative control were cleaned up by AMPure XP beads (Beckman Coulter, Brea, CA) for QC analysis using Bioanalyzer High Sensitivity chip (Agilent).

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA). .. Libraries were gel purified using 2% E-Gel SizeSelect (Thermo Fisher Scientific, Waltham, MA, USA) and quality control was performed using bioanalyser HS kit (Agilent biotechnologies, Palo Alto, CA, USA).

    Microarray:

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: The mixed library was sequenced with PE-150 bp run using 64% of a single Illumina lane on HiSeq 2500 at UT Southwestern Medical Center Genomics and Microarray Core Facility. .. We further isolated mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, MA USA).

    Incubation:

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA). .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    Expressing:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: RNA library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF). .. 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Article Title: miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking
    Article Snippet: Paragraph title: RNA‐seq library preparation, gene expression and alternative splicing analysis ... Poly(A) RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module columns according to the manufacturer's instructions.

    Article Title: Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest
    Article Snippet: The mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and libraries were prepared with NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB). .. RNA-seq data were processed using RSEM (v1.2.0) ( ).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA). .. In order to obtain clean and high-quality reads for sequence assembly, the raw reads were filtered by removing adaptor sequences, low-quality sequences (reads with ambiguous bases ‘N’) and reads with 10% > Q < 20% bases [ , ].

    Derivative Assay:

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: A total of six locally grown winged bean accessions (two derived from Malaysian Agricultural Research and Development Institute (MARDI) and four from local planters) were grown from August to December 2012 at Lady Bird Farm, Broga, Semenyih, Malaysia (Latitude: 2.9394 N; Longitude: 101.8971 E; Altitude: 45m asl). .. A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA).

    Flow Cytometry:

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs). .. One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs).

    Transfection:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: Paragraph title: Cell cultures, transfections and library preparations. ... For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations.

    Ligation:

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA). .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    Biomarker Assay:

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA).

    Infection:

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ].

    Generated:

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

    Article Title: Exosomes play an important role in the process of psoralen reverse multidrug resistance of breast cancer
    Article Snippet: ND-1000 Nanodrop and Agilent 2200 TapeStation were used to explore the sample quality. .. RNA libraries were then generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module from Illumina (San Diego, CA, USA) according to the manufacturer’s instructions. .. The cDNA fragments were sequenced in paired end lane for 101 cycles using the Illumina HiSeq3000.

    Inhibition:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics.

    Negative Control:

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Sequencing:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: Paragraph title: RNA-Seq library preparation and sequencing ... 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Paragraph title: RNA-Seq Library Preparation, Sequencing and Analysis ... Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking
    Article Snippet: Poly(A) RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module columns according to the manufacturer's instructions. .. The poly(A) fraction was size‐fractionated and concentrated using 3.53 AMPure RNAClean XP sample preparation (New England Biolabs) and eluted with water.

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Prior to cDNA library constructions, the RNA quality and concentration were checked with the Agilent Bioanalyzer 2100 using an Agilent RNA 6000 Nano Chip (Agilent Technologies, USA) and 0.5 µg of each cDNA library was used to prepare Illumina cDNA sequencing libraries. .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: We used the information on the deep sequencing experiments performed by Shabman et al. [ ] available in Supplementary Material Table S2 to their article, as well as in NCBI BioProjects under accession numbers PRJNA258131 (for Zaire ebolavirus ) and PRJNA264121 (for Marburg virus ). .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ].

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

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs). .. One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: Paragraph title: Library construction, Illumina sequencing and read assembly ... NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA).

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

    Article Title: Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells
    Article Snippet: The quality of total RNA was evaluated using the Agilent 2100 BioAnalyzer and the Agilent RNA 6000 Nano Kit (#5067-1511) according to the manufacturer’s instructions. .. For all samples, RNA integrity numbers were sufficiently high ( > 9.5) to perform mRNA sequencing. mRNA was purified from 5 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Whitby, Ontario) following manufacturer’s instructions. cDNA libraries were then prepared with 25 ng mRNA of each sample using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420, New England Biolabs) and barcoded by PCR for subsequent multiplexed sequencing. .. The quality and quantity of the librairies were assessed using the Agilent High Sensitivity DNA Kit (#5067-4626) on Agilent 2100 BioAnalyzer.

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: Paragraph title: Transcriptome sequencing and analysis ... Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA).

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: Paragraph title: Library preparation and sequencing ... We further isolated mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, MA USA).

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: Paragraph title: 2.1. Plant Material, RNA Extraction, Complementary DNA (cDNA) Library Construction, and Sequencing ... A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA).

    RNA Sequencing Assay:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: Paragraph title: RNA-Seq library preparation and sequencing ... 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Paragraph title: RNA-Seq Library Preparation, Sequencing and Analysis ... Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking
    Article Snippet: Paragraph title: RNA‐seq library preparation, gene expression and alternative splicing analysis ... Poly(A) RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module columns according to the manufacturer's instructions.

    Article Title: Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest
    Article Snippet: Paragraph title: RNA-Seq ... The mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and libraries were prepared with NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB).

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ]. .. Obtained Illumina HiSeq 100 nt reads were mapped to the reference Zaire ebolavirus and Marburg virus sequences mentioned above by using the TopHat/Cufflinks software suite v2 with the default settings [ ].

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

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: Paragraph title: RNA sequencing ... One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs).

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Paragraph title: Sample preparation for RNA-seq ... Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: Fragment interruption, cDNA synthesis, addition of adapters, PCR amplification and RNA-Seq were performed by Beijing BioMarker Technologies (Beijing, China). .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA).

    Article Title: Exosomes play an important role in the process of psoralen reverse multidrug resistance of breast cancer
    Article Snippet: Paragraph title: Preparation of a cDNA library for RNA-seq ... RNA libraries were then generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module from Illumina (San Diego, CA, USA) according to the manufacturer’s instructions.

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

    Article Title: Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells
    Article Snippet: Paragraph title: RNA-seq sample preparation and analysis ... For all samples, RNA integrity numbers were sufficiently high ( > 9.5) to perform mRNA sequencing. mRNA was purified from 5 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Whitby, Ontario) following manufacturer’s instructions. cDNA libraries were then prepared with 25 ng mRNA of each sample using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420, New England Biolabs) and barcoded by PCR for subsequent multiplexed sequencing.

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

    Magnetic Beads:

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ]. .. Obtained Illumina HiSeq 100 nt reads were mapped to the reference Zaire ebolavirus and Marburg virus sequences mentioned above by using the TopHat/Cufflinks software suite v2 with the default settings [ ].

    Isolation:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: The RINs of all total RNA samples were 9.7–10. .. 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide. .. Specifically, 100 ng of total RNA together with 2 μL of 1:2000 diluted ERCC was added to extracted mRNA with 15 μL of NEBNext Magnetic Oligo d(T)25 and fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for 8 min, followed by first-strand cDNA synthesis using reverse transcriptase and random primers.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: A total of 1 μg RNA for each sample with RNA integrity number (RIN) values > 8 was used for sequencing library construction. .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Using the polyA RNA as input, the library for RNA-seq was prepared by using NEBNext Ultra Directional RNA Library Prep kit.

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: Total RNA was extracted using RNeasy Plus (Qiagen). .. For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics.

    Article Title: miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking
    Article Snippet: Microarray data for all data sets are provided in . .. Poly(A) RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module columns according to the manufacturer's instructions. .. The poly(A) fraction was size‐fractionated and concentrated using 3.53 AMPure RNAClean XP sample preparation (New England Biolabs) and eluted with water.

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Prior to cDNA library constructions, the RNA quality and concentration were checked with the Agilent Bioanalyzer 2100 using an Agilent RNA 6000 Nano Chip (Agilent Technologies, USA) and 0.5 µg of each cDNA library was used to prepare Illumina cDNA sequencing libraries. .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA). .. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) for Illumina and indexed with the NEBNext Mulitplex Oligos for Illumina (NEB).

    Article Title: Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest
    Article Snippet: RNA quality was assessed using a Bioanalyzer (Agilent Technologies) and all RNA integrity number (RIN) values were above 9.4. .. The mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and libraries were prepared with NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB). .. Samples were multiplexed with seven or eight samples per sequencing lane (samples indexed with NEBNext Multiplex Oligos for Illumina).

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ].

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

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: For each genotype, more than 300 day 1 adult worms were collected in Trizol in three independent biological replicates. .. One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs). .. RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Embryos were collected to prepare 3 biological replicates and were immediately transferred to Trizol for RNA extraction. .. Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S). .. RNA-seq libraries were constructed using NEB kits E7530S (library prep), and E7335S (Oligos).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: The standard Illumina methods and protocols were adopted to prepare and sequence the cDNA libraries. .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA). .. The size of the library insert fragments was determined by 1.8% agarose gel electrophoresis, and the fragments were quantified using a Library Quantification Kit/Illumina GA Universal (Kapa, USA).

    Article Title: Exosomes play an important role in the process of psoralen reverse multidrug resistance of breast cancer
    Article Snippet: ND-1000 Nanodrop and Agilent 2200 TapeStation were used to explore the sample quality. .. RNA libraries were then generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module from Illumina (San Diego, CA, USA) according to the manufacturer’s instructions. .. The cDNA fragments were sequenced in paired end lane for 101 cycles using the Illumina HiSeq3000.

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

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    Article Title: Complete genome ofPieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins
    Article Snippet: Part of specimen NVG-3537 was used to extract RNA using QIAGEN RNeasy Mini Kit (QIAGEN Inc., Valencia, CA USA). .. We further isolated mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs Inc., Ipswich, MA USA). .. RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs Inc., Ipswich, MA USA) for Illumina following manufacturer’s protocol.

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: Total RNA was measured using the Qubit RNA BR assay kit (Thermo Fisher Scientific, Waltham, MA, USA). .. A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA). .. RNA fragmentation was done using NEBNext Magnesium RNA Fragmentation Module (New England Biolabs, Beverly, MA, USA).

    Multiplex Assay:

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: The standard Illumina methods and protocols were adopted to prepare and sequence the cDNA libraries. .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA). .. The size of the library insert fragments was determined by 1.8% agarose gel electrophoresis, and the fragments were quantified using a Library Quantification Kit/Illumina GA Universal (Kapa, USA).

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    Purification:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide. .. 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: A total of 1 μg RNA for each sample with RNA integrity number (RIN) values > 8 was used for sequencing library construction. .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Using the polyA RNA as input, the library for RNA-seq was prepared by using NEBNext Ultra Directional RNA Library Prep kit.

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Prior to cDNA library constructions, the RNA quality and concentration were checked with the Agilent Bioanalyzer 2100 using an Agilent RNA 6000 Nano Chip (Agilent Technologies, USA) and 0.5 µg of each cDNA library was used to prepare Illumina cDNA sequencing libraries. .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA). .. Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (NEB) for Illumina and indexed with the NEBNext Mulitplex Oligos for Illumina (NEB).

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ]. .. Obtained Illumina HiSeq 100 nt reads were mapped to the reference Zaire ebolavirus and Marburg virus sequences mentioned above by using the TopHat/Cufflinks software suite v2 with the default settings [ ].

    Article Title: Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells
    Article Snippet: The quality of total RNA was evaluated using the Agilent 2100 BioAnalyzer and the Agilent RNA 6000 Nano Kit (#5067-1511) according to the manufacturer’s instructions. .. For all samples, RNA integrity numbers were sufficiently high ( > 9.5) to perform mRNA sequencing. mRNA was purified from 5 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Whitby, Ontario) following manufacturer’s instructions. cDNA libraries were then prepared with 25 ng mRNA of each sample using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420, New England Biolabs) and barcoded by PCR for subsequent multiplexed sequencing. .. The quality and quantity of the librairies were assessed using the Agilent High Sensitivity DNA Kit (#5067-4626) on Agilent 2100 BioAnalyzer.

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA).

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: Extraction was performed from different tissue groups separately using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA, USA) followed by another round of purification using RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) before library preparation. .. A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA).

    Polymerase Chain Reaction:

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus
    Article Snippet: Total RNA in the abovementioned experiment was isolated by using Trizol (Invitrogen) from Vero cells (African green monkey kidney epithelial cells) or differentiated Thp1 cells (human monocytic leukemia cells) infected with EBOV Mayinga (CDC isolate number 808011) or MARV-Ang (CDC isolate number 200501379) at multiplicity of infection of 3 [ ]. .. RNA molecules containing poly-A tails were purified with Invitrogen Dynal oligo dT magnetic beads and then RNA-Seq libraries have been created using NEB Next mRNA-Seq kit using 18 cycles of PCR [ ]. .. Obtained Illumina HiSeq 100 nt reads were mapped to the reference Zaire ebolavirus and Marburg virus sequences mentioned above by using the TopHat/Cufflinks software suite v2 with the default settings [ ].

    Article Title: Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis
    Article Snippet: PCR templates for synthesis of mRNAs (CA)-Fluc and (CA)uORF-Fluc were obtained using the same strategy directly from the pFluc plasmid with the corresponding T7 promoter-containing forward primers (see Supplementary Figure S2). .. The EMCV IRES containing mRNA was uncapped, whereas for all other transcripts Vaccinia Capping System (NEB) was used to obtain 100% capped products.

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S). .. RNA-seq libraries were constructed using NEB kits E7530S (library prep), and E7335S (Oligos).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: Fragment interruption, cDNA synthesis, addition of adapters, PCR amplification and RNA-Seq were performed by Beijing BioMarker Technologies (Beijing, China). .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA).

    Article Title: Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells
    Article Snippet: The quality of total RNA was evaluated using the Agilent 2100 BioAnalyzer and the Agilent RNA 6000 Nano Kit (#5067-1511) according to the manufacturer’s instructions. .. For all samples, RNA integrity numbers were sufficiently high ( > 9.5) to perform mRNA sequencing. mRNA was purified from 5 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Whitby, Ontario) following manufacturer’s instructions. cDNA libraries were then prepared with 25 ng mRNA of each sample using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420, New England Biolabs) and barcoded by PCR for subsequent multiplexed sequencing. .. The quality and quantity of the librairies were assessed using the Agilent High Sensitivity DNA Kit (#5067-4626) on Agilent 2100 BioAnalyzer.

    Cotransfection:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    cDNA Library Assay:

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Paragraph title: cDNA library constructions and next generation sequencing ... Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    Article Title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains
    Article Snippet: The standard Illumina methods and protocols were adopted to prepare and sequence the cDNA libraries. .. NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, USA) was used to enrich mRNA, and then the cDNA library was constructed using the NEBNext mRNA Library Prep Master Mix Set for Illumina (NEB, USA) and NEBNext Multiplex Oligos for Illumina (NEB, USA). .. The size of the library insert fragments was determined by 1.8% agarose gel electrophoresis, and the fragments were quantified using a Library Quantification Kit/Illumina GA Universal (Kapa, USA).

    Article Title: Exosomes play an important role in the process of psoralen reverse multidrug resistance of breast cancer
    Article Snippet: Paragraph title: Preparation of a cDNA library for RNA-seq ... RNA libraries were then generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module from Illumina (San Diego, CA, USA) according to the manufacturer’s instructions.

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: Paragraph title: 2.1. Plant Material, RNA Extraction, Complementary DNA (cDNA) Library Construction, and Sequencing ... A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA).

    Sample Prep:

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Paragraph title: Sample preparation for RNA-seq ... Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S).

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

    Article Title: Dual leucine zipper kinase regulates expression of axon guidance genes in mouse neuronal cells
    Article Snippet: Paragraph title: RNA-seq sample preparation and analysis ... For all samples, RNA integrity numbers were sufficiently high ( > 9.5) to perform mRNA sequencing. mRNA was purified from 5 μg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Whitby, Ontario) following manufacturer’s instructions. cDNA libraries were then prepared with 25 ng mRNA of each sample using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#E7420, New England Biolabs) and barcoded by PCR for subsequent multiplexed sequencing.

    Chromatin Immunoprecipitation:

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Prior to cDNA library constructions, the RNA quality and concentration were checked with the Agilent Bioanalyzer 2100 using an Agilent RNA 6000 Nano Chip (Agilent Technologies, USA) and 0.5 µg of each cDNA library was used to prepare Illumina cDNA sequencing libraries. .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

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

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

    RNA Extraction:

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Embryos were collected to prepare 3 biological replicates and were immediately transferred to Trizol for RNA extraction. .. Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S).

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

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: For RNA extraction, maxillary and labial palps were pooled from 30 individuals of the naïve 5th instar (3–5 days old, both male and female) were collected and then total RNA was extracted. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA).

    Article Title: Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment
    Article Snippet: Paragraph title: 2.1. Plant Material, RNA Extraction, Complementary DNA (cDNA) Library Construction, and Sequencing ... A total of 5 µg of RNA was used for enrichment of mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Beverly, MA, USA).

    Plasmid Preparation:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Article Title: Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis
    Article Snippet: Paragraph title: Plasmid constructs and in vitro transcription ... The EMCV IRES containing mRNA was uncapped, whereas for all other transcripts Vaccinia Capping System (NEB) was used to obtain 100% capped products.

    Software:

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs). .. One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs).

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    Electrophoresis:

    Article Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
    Article Snippet: One microgram of of RNA was extracted using miRNAeasy Mini Kit (QIAGEN). polyA+ mRNA was isolated from 500 ng total RNA with NEBNext Poly(A) mRNA Magnetics Isolation Module (New England Biolabs). .. RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

    Functional Assay:

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA).

    Agarose Gel Electrophoresis:

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    In Vitro:

    Article Title: Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis
    Article Snippet: Paragraph title: Plasmid constructs and in vitro transcription ... The EMCV IRES containing mRNA was uncapped, whereas for all other transcripts Vaccinia Capping System (NEB) was used to obtain 100% capped products.

    Ethanol Precipitation:

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

    Next-Generation Sequencing:

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Paragraph title: cDNA library constructions and next generation sequencing ... Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    Article Title: A Family of CSαβ Defensins and Defensin-Like Peptides from the Migratory Locust, Locusta migratoria, and Their Expression Dynamics during Mycosis and Nosemosis
    Article Snippet: The RNA sample was purified and tested for purity and integrity on an Agilent 2100 Bioanalyzer based on electropherogram and RNA Integrity Number (RIN) and finally was introduced into an Illumina HiSeqTM 2500 platform by Biomarker sequencing company (Beijing, China) for standard sequencing. .. Briefly, mRNA enriched via the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) were used for library construction (NEBNext® mRNA Library Prep Master Mix Set for Illumina®, E6110 and NEBNext® Multiplex Oligos for Illumina®, NEB #E7500 (Index Primers Set 2)) followed by library quality check on agarose gel and qPCR (Library Quantification Kit for NGS, KK4824, Kapa Biosystems, Inc., MA, USA). .. Raw paired-end sequencing reads were evaluated and trimmed with a customized Perl script (Biomarker, China) to guarantee high reliability of future assembly and annotation.

    Spectrophotometry:

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

    Concentration Assay:

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
    Article Snippet: RNA concentration was determined on Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), RNA quality was assessed using the Agilent 2100 Bioanalyzer. .. 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Article Title: Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome
    Article Snippet: The concentration and integrity of the isolated RNA was quantified using the Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE) and 2100 Bioanalyzer (Agilent, Santa Clara, CA). .. Briefly, polyA RNA was first purified via NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).

    Article Title: An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
    Article Snippet: Prior to cDNA library constructions, the RNA quality and concentration were checked with the Agilent Bioanalyzer 2100 using an Agilent RNA 6000 Nano Chip (Agilent Technologies, USA) and 0.5 µg of each cDNA library was used to prepare Illumina cDNA sequencing libraries. .. Poly-A mRNA was purified using the oligo-dT beads provided in the NEBNExt Poly(A) mRNA Magnetic Isolation Module (New England Biolabs (NEB), USA).

    DNA Purification:

    Article Title: The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster
    Article Snippet: Poly(A)+ RNA was prepared using an NEB mRNA isolation module (E7490S). .. RNA-seq libraries were constructed using NEB kits E7530S (library prep), and E7335S (Oligos).

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  • 99
    New England Biolabs mrna magnetic isolation module
    Cleavage of 3′-UTR regions results in autonomous uncapped <t>RNA</t> fragments. a RNA-seq read coverage ( y -axis) for Ssr1 , Bcl2 , and Rab2a in mouse T cells 12 , B cells 14 , and brain tissue 15 , demonstrating a gap in read coverage (marked by arrows) at 3′-UTRs, as well as uneven levels of RNA upstream and downstream of the gap site. b Three sets of primers were used per gene for qRT-PCR amplification: upstream (blue rectangle), downstream (red), and across the RNA-seq coverage gap (green). Bar plots (bottom) visualize the relative percentage of cytoplasmic (black) and nuclear (gray) expression of each amplicon out of its total (cytoplasm+nuclear) expression. c A model for post-transcriptional processing of <t>mRNA:</t> mRNA is cleaved at an APA site, resulting in a capped “body” and an uncapped 3′-UTR “tail,” sensitive to terminator 5′-phosphate-dependent exonuclease (TEX) treatment. d qRT-PCR analysis shows cytoplasmic degradation of the “tail” unit (in red) compared to the “body” unit (in blue) following TEX treatment. * p
    Mrna Magnetic Isolation Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 211 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mrna magnetic isolation module/product/New England Biolabs
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    mrna magnetic isolation module - by Bioz Stars, 2019-07
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    87
    New England Biolabs ultra directional mrnaseq kit
    Dynamics of H3K4me3 and expression in subsets of genes. ( A ) Genomic regions subject to age-linked CNV detected by comparison between input samples; these were excluded from ChIP analysis. ( B ) Scatter plot of log 2 -transformed <t>mRNAseq</t> read counts from protein coding genes defined in Figure 4A normalised for ORF length comparing log phase cells to 48-hr-aged cells. Data averaged across five replicates per condition. ( C ) Average profile of H3K4me3 ChIP signal for 1 kb either side of the TSS performed as in Figure 4C , for 300 genes least induced with age. ( D ) As ( C ) for 300 most induced genes. ( E ) Hierarchical clustering analysis of log 2 -transformed mRNA levels across age for the 4806 unambiguous genes defined in Figure 4A .
    Ultra Directional Mrnaseq Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ultra directional mrnaseq kit/product/New England Biolabs
    Average 87 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ultra directional mrnaseq kit - by Bioz Stars, 2019-07
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    Cleavage of 3′-UTR regions results in autonomous uncapped RNA fragments. a RNA-seq read coverage ( y -axis) for Ssr1 , Bcl2 , and Rab2a in mouse T cells 12 , B cells 14 , and brain tissue 15 , demonstrating a gap in read coverage (marked by arrows) at 3′-UTRs, as well as uneven levels of RNA upstream and downstream of the gap site. b Three sets of primers were used per gene for qRT-PCR amplification: upstream (blue rectangle), downstream (red), and across the RNA-seq coverage gap (green). Bar plots (bottom) visualize the relative percentage of cytoplasmic (black) and nuclear (gray) expression of each amplicon out of its total (cytoplasm+nuclear) expression. c A model for post-transcriptional processing of mRNA: mRNA is cleaved at an APA site, resulting in a capped “body” and an uncapped 3′-UTR “tail,” sensitive to terminator 5′-phosphate-dependent exonuclease (TEX) treatment. d qRT-PCR analysis shows cytoplasmic degradation of the “tail” unit (in red) compared to the “body” unit (in blue) following TEX treatment. * p

    Journal: Nature Communications

    Article Title: Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

    doi: 10.1038/s41467-017-02099-7

    Figure Lengend Snippet: Cleavage of 3′-UTR regions results in autonomous uncapped RNA fragments. a RNA-seq read coverage ( y -axis) for Ssr1 , Bcl2 , and Rab2a in mouse T cells 12 , B cells 14 , and brain tissue 15 , demonstrating a gap in read coverage (marked by arrows) at 3′-UTRs, as well as uneven levels of RNA upstream and downstream of the gap site. b Three sets of primers were used per gene for qRT-PCR amplification: upstream (blue rectangle), downstream (red), and across the RNA-seq coverage gap (green). Bar plots (bottom) visualize the relative percentage of cytoplasmic (black) and nuclear (gray) expression of each amplicon out of its total (cytoplasm+nuclear) expression. c A model for post-transcriptional processing of mRNA: mRNA is cleaved at an APA site, resulting in a capped “body” and an uncapped 3′-UTR “tail,” sensitive to terminator 5′-phosphate-dependent exonuclease (TEX) treatment. d qRT-PCR analysis shows cytoplasmic degradation of the “tail” unit (in red) compared to the “body” unit (in blue) following TEX treatment. * p

    Article Snippet: Five micrograms of RNA for each sample was processed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

    Techniques: RNA Sequencing Assay, Quantitative RT-PCR, Amplification, Expressing

    Orthogonal validation of RNA-Seq data. a-d Expression of select genes was validated by qPCR; ESR1 ( a ), Connective tissue growth factor ( CTGF, b ), VIM ( c ), and Matrix metalloproteinase 2 ( MMP2 , d ), in an identical and independent experiment. Bars represent expression [Log2(Fold Change)] of each gene in the RNA-Seq analysis, and black dots represent expression [Log2(Fold Change)] in each sample ( n = 6) in the orthogonal experiment as determined by qPCR relative to vehicle control (DMSO). Target gene expression as measured by qPCR was normalized to GAPDH mRNA expression and quantified as fold change to control using the relative ΔΔCq method. Asterisks (*) indicate differential expression compared to controls [Log2(Fold Change) ≥ |0.6| and FDR-corrected p -value

    Journal: Respiratory Research

    Article Title: Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells

    doi: 10.1186/s12931-018-0861-5

    Figure Lengend Snippet: Orthogonal validation of RNA-Seq data. a-d Expression of select genes was validated by qPCR; ESR1 ( a ), Connective tissue growth factor ( CTGF, b ), VIM ( c ), and Matrix metalloproteinase 2 ( MMP2 , d ), in an identical and independent experiment. Bars represent expression [Log2(Fold Change)] of each gene in the RNA-Seq analysis, and black dots represent expression [Log2(Fold Change)] in each sample ( n = 6) in the orthogonal experiment as determined by qPCR relative to vehicle control (DMSO). Target gene expression as measured by qPCR was normalized to GAPDH mRNA expression and quantified as fold change to control using the relative ΔΔCq method. Asterisks (*) indicate differential expression compared to controls [Log2(Fold Change) ≥ |0.6| and FDR-corrected p -value

    Article Snippet: 2 μL of 1:2000 diluted External RNA Controls Consortium (ERCC) Spike-In Mix (Ambion™ 4,456,740, ThermoFisher Scientific Inc.) was added to 100 ng of high-quality total RNA followed by mRNA isolation using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer’s user guide.

    Techniques: RNA Sequencing Assay, Expressing, Real-time Polymerase Chain Reaction

    Expression pattern analysis of 13 TF and 2 zein genes by qRT-PCR and RNA-seq. The y- axis shows the mRNA levels. The scale on the right indicates gene expression level based on RNA-Seq. The scale on the left shows relative gene expression levels based on qRT-PCR. The x -axis indicates the day of endosperm sampling after pollination. The letters correspond to the genes. The blue lines correspond with RNA-seq; and the gold lines correspond with qRT-PCR.

    Journal: PLoS ONE

    Article Title: Transcriptome Dynamics during Maize Endosperm Development

    doi: 10.1371/journal.pone.0163814

    Figure Lengend Snippet: Expression pattern analysis of 13 TF and 2 zein genes by qRT-PCR and RNA-seq. The y- axis shows the mRNA levels. The scale on the right indicates gene expression level based on RNA-Seq. The scale on the left shows relative gene expression levels based on qRT-PCR. The x -axis indicates the day of endosperm sampling after pollination. The letters correspond to the genes. The blue lines correspond with RNA-seq; and the gold lines correspond with qRT-PCR.

    Article Snippet: RNA enrichment was achieved with an NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).

    Techniques: Expressing, Quantitative RT-PCR, RNA Sequencing Assay, Sampling

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

    Journal: eLife

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

    doi: 10.7554/eLife.34081

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

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

    Techniques: Expressing, Chromatin Immunoprecipitation, Transformation Assay