strand specific rna seq library preparation  (New England Biolabs)


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  • 99
    Name:
    NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module
    Description:
    NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module 100 rxns
    Catalog Number:
    e6111l
    Price:
    1180
    Size:
    100 rxns
    Category:
    mRNA Template Preparation for PCR
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    Structured Review

    New England Biolabs strand specific rna seq library preparation
    NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module
    NEBNext Ultra II Non Directional RNA Second Strand Synthesis Module 100 rxns
    https://www.bioz.com/result/strand specific rna seq library preparation/product/New England Biolabs
    Average 99 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    strand specific rna seq library preparation - by Bioz Stars, 2020-08
    99/100 stars

    Images

    1) Product Images from "Cooperative molecular networks drive a mammalian cell state transition"

    Article Title: Cooperative molecular networks drive a mammalian cell state transition

    Journal: bioRxiv

    doi: 10.1101/2020.03.23.000109

    (A) The top 15 candidate genes from the haploid screen ordered by the number of times the hit was found in the 35 screens, including the number of independent integration sites and the calculated FDR. (B) Significantly enriched pathways among screen hits ranked according to fold enrichment; colours represent FDR in screen analysis. Numbers next to bars indicate number of hit-genes within category, (C) Significantly enriched GO terms among screen hits as in (B) (D) Workflow to generate Cas9 knockouts in RC9 ESCs. (E) Idealized strategy illustrating gRNAs and genotyping primers. (F) Western analysis using indicated KOs and indicated antibodies. Tubulin or Gapdh were used as loading controls, as indicated. (G) Anti-flag specific Westerns in indicated KO rescue ESCs upon stable forced expression of 3xflag rescue cDNAs driven from a CAG promoter. (H) Rex1GFP levels measured by FACS showing restoration of differentiation behaviour in the indicated rescue cell lines at N30. (I) t-SNE visualization of RNA-seq profiles in 2i and at N24 before and after batch correction. (J) GO enrichment analysis of the top 10% of genes (by absolute logFC) that were differentially expressed between 2i and N24 in WT ESCs (FDR ≤ 0.05, H0: |FC|
    Figure Legend Snippet: (A) The top 15 candidate genes from the haploid screen ordered by the number of times the hit was found in the 35 screens, including the number of independent integration sites and the calculated FDR. (B) Significantly enriched pathways among screen hits ranked according to fold enrichment; colours represent FDR in screen analysis. Numbers next to bars indicate number of hit-genes within category, (C) Significantly enriched GO terms among screen hits as in (B) (D) Workflow to generate Cas9 knockouts in RC9 ESCs. (E) Idealized strategy illustrating gRNAs and genotyping primers. (F) Western analysis using indicated KOs and indicated antibodies. Tubulin or Gapdh were used as loading controls, as indicated. (G) Anti-flag specific Westerns in indicated KO rescue ESCs upon stable forced expression of 3xflag rescue cDNAs driven from a CAG promoter. (H) Rex1GFP levels measured by FACS showing restoration of differentiation behaviour in the indicated rescue cell lines at N30. (I) t-SNE visualization of RNA-seq profiles in 2i and at N24 before and after batch correction. (J) GO enrichment analysis of the top 10% of genes (by absolute logFC) that were differentially expressed between 2i and N24 in WT ESCs (FDR ≤ 0.05, H0: |FC|

    Techniques Used: Western Blot, Expressing, FACS, RNA Sequencing Assay

    2) Product Images from "Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs"

    Article Title: Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

    Journal: The Plant Cell

    doi: 10.1105/tpc.16.00751

    Transcriptome-Wide Mapping of m 5 C Using bsRNA-Seq in Arabidopsis. (A) Venn diagram showing the number of m 5 /RBS-seq ( n ≤ 0.3 and ≥1% methylation. (B) Gene schematic and genome browser view of a differentially methylated gene, MAG5 , in three different tissue types. In the MAG5 gene schematic, the methylated cytosine C3349 is indicated. Boxes represent exons; lines represent introns. In the genome browser view, black arrows indicate m 5 C position C3349 (chr5: 19, 262, 126). Top: m 5 reads mapped to the MAG5 locus (chr5: 19, 262, 122-19, 262, 130) from the separate tissue data sets: siliques, shoots, and roots. Each row represents one sequence read and each column a nucleotide. Gray boxes represent nucleotides matching with the MAG5 reference sequence, and red boxes indicate mismatching nucleotides and/or nonmethylated, bisulfite converted cytosines. Sequencing gaps are shown in white. (C) Distribution of m 5 C sites within different RNA types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower mRNA abundance in Arabidopsis roots ( r s = −0.32, *P value ≤ 0.0001, Spearman’s correlation). (E) Histogram showing relative enrichment of observed m 5 C sites versus expected number of m 5 across all three tissue types (*P value ≤ 0.0001, binomial test). (F) Metagene profile of m 5 ≤ 0.3 and ≥2% methylation). (G) Methylation of candidate m 5 results. Heat map depicts log arcsine transformed methylation percentages of five m 5 . The numbers in parentheses are genome coordinates, and + or – indicates the strand.
    Figure Legend Snippet: Transcriptome-Wide Mapping of m 5 C Using bsRNA-Seq in Arabidopsis. (A) Venn diagram showing the number of m 5 /RBS-seq ( n ≤ 0.3 and ≥1% methylation. (B) Gene schematic and genome browser view of a differentially methylated gene, MAG5 , in three different tissue types. In the MAG5 gene schematic, the methylated cytosine C3349 is indicated. Boxes represent exons; lines represent introns. In the genome browser view, black arrows indicate m 5 C position C3349 (chr5: 19, 262, 126). Top: m 5 reads mapped to the MAG5 locus (chr5: 19, 262, 122-19, 262, 130) from the separate tissue data sets: siliques, shoots, and roots. Each row represents one sequence read and each column a nucleotide. Gray boxes represent nucleotides matching with the MAG5 reference sequence, and red boxes indicate mismatching nucleotides and/or nonmethylated, bisulfite converted cytosines. Sequencing gaps are shown in white. (C) Distribution of m 5 C sites within different RNA types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower mRNA abundance in Arabidopsis roots ( r s = −0.32, *P value ≤ 0.0001, Spearman’s correlation). (E) Histogram showing relative enrichment of observed m 5 C sites versus expected number of m 5 across all three tissue types (*P value ≤ 0.0001, binomial test). (F) Metagene profile of m 5 ≤ 0.3 and ≥2% methylation). (G) Methylation of candidate m 5 results. Heat map depicts log arcsine transformed methylation percentages of five m 5 . The numbers in parentheses are genome coordinates, and + or – indicates the strand.

    Techniques Used: Methylation, Sequencing, Transformation Assay

    Related Articles

    RNA Sequencing Assay:

    Article Title: The hyper-activation of transcriptional enhancers in breast cancer
    Article Snippet: .. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). .. Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis.

    Synthesized:

    Article Title: Classic oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer
    Article Snippet: .. Poly-adenylated RNA was enriched from 1ug of RNA for each sample with the NEBNext® PolyA mRNA Magnetic Isolation Module (NEB), incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (Thermo Fisher Scientific) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (NEB). .. Up to 10□ng of cDNA was used for the Illumina sequencing library construction using NEBNext® Ultra™ DNA Library Prep Kit (NEB).

    Isolation:

    Article Title: The hyper-activation of transcriptional enhancers in breast cancer
    Article Snippet: .. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). .. Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis.

    Article Title: Classic oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer
    Article Snippet: .. Poly-adenylated RNA was enriched from 1ug of RNA for each sample with the NEBNext® PolyA mRNA Magnetic Isolation Module (NEB), incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (Thermo Fisher Scientific) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (NEB). .. Up to 10□ng of cDNA was used for the Illumina sequencing library construction using NEBNext® Ultra™ DNA Library Prep Kit (NEB).

    Ligation:

    Article Title: Library preparation for highly accurate population sequencing of RNA viruses
    Article Snippet: .. Random hexamers, 50 μM (Invitrogen, cat. no. N8080127) dNTP mix, 10 mM total (Bioline, cat. no. BIO-39053) SuperScript III reverse transcriptase, 200 U/μl (Invitrogen, cat. no. 18080-044) RNase H, 2 U/μl (Invitrogen, cat. no. 18021-071) NEBNext mRNA second strand synthesis module (New England Biolabs, cat. no. E6111S/L) NEBNext end repair module (New England Biolabs, cat. no. E6050S/L) NEBNext dA-tailing module (New England Biolabs, cat. no. E6053S/L) NEBNext quick ligation module (New England Biolabs, cat. no. E6056S/L) Phusion high-fidelity DNA polymerase (New England Biolabs, cat. no. M053S/L) Bromophenol Blue (Sigma-Aldrich, cat. no. B6131) Xylene cyanol (Affymetrix, cat. no. 23513) Perfect RNA Markers, 0.1–1 kb (EMD Millipore, cat. no. 69924) Low-molecular-weight DNA ladder, supplied with 6× gel loading dye (New England Biolabs, cat. no. N3233S/L) TruSeq indexed adapters and PCR primer cocktail (Illumina, cat. no. FC-121-4001) or equivalent oligonucleotides ▴ CRITICAL Indexed adapter oligonucleotides that are ordered separately should be annealed before use. .. Library quantification kit, Illumina/Universal (Kapa Biosystems, cat. no. KK4824) Sequencing kits, MiSeq reagent kit v2 (300 cycles; Illumina, cat. no. MS-102-2002) or 5× TruSeq rapid SBS kit—HS (50 cycle) and TruSeq rapid SR cluster kit—HS (Illumina, cat. nos.

    Generated:

    Article Title: Monitoring Viral Genetic Variation as a Tool To Improve Molecular Diagnostics for Mumps Virus
    Article Snippet: .. Second-strand cDNA was generated using the NEBNext Ultra II nondirectional RNA second-strand synthesis module (NEB, Ipswich, MA, USA). .. The resulting double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA) and converted into Illumina sequencing libraries using the Nextera XT library preparation kit.

    Construct:

    Article Title: The hyper-activation of transcriptional enhancers in breast cancer
    Article Snippet: .. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). .. Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis.

    Incubation:

    Article Title: Classic oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer
    Article Snippet: .. Poly-adenylated RNA was enriched from 1ug of RNA for each sample with the NEBNext® PolyA mRNA Magnetic Isolation Module (NEB), incubated at 94°C for 15 min and double-strand cDNA was synthesized using SuperScript III reverse transcriptase (Thermo Fisher Scientific) and NEBNext® Ultra™ II Directional RNA Second Strand Synthesis Module (NEB). .. Up to 10□ng of cDNA was used for the Illumina sequencing library construction using NEBNext® Ultra™ DNA Library Prep Kit (NEB).

    Polymerase Chain Reaction:

    Article Title: Library preparation for highly accurate population sequencing of RNA viruses
    Article Snippet: .. Random hexamers, 50 μM (Invitrogen, cat. no. N8080127) dNTP mix, 10 mM total (Bioline, cat. no. BIO-39053) SuperScript III reverse transcriptase, 200 U/μl (Invitrogen, cat. no. 18080-044) RNase H, 2 U/μl (Invitrogen, cat. no. 18021-071) NEBNext mRNA second strand synthesis module (New England Biolabs, cat. no. E6111S/L) NEBNext end repair module (New England Biolabs, cat. no. E6050S/L) NEBNext dA-tailing module (New England Biolabs, cat. no. E6053S/L) NEBNext quick ligation module (New England Biolabs, cat. no. E6056S/L) Phusion high-fidelity DNA polymerase (New England Biolabs, cat. no. M053S/L) Bromophenol Blue (Sigma-Aldrich, cat. no. B6131) Xylene cyanol (Affymetrix, cat. no. 23513) Perfect RNA Markers, 0.1–1 kb (EMD Millipore, cat. no. 69924) Low-molecular-weight DNA ladder, supplied with 6× gel loading dye (New England Biolabs, cat. no. N3233S/L) TruSeq indexed adapters and PCR primer cocktail (Illumina, cat. no. FC-121-4001) or equivalent oligonucleotides ▴ CRITICAL Indexed adapter oligonucleotides that are ordered separately should be annealed before use. .. Library quantification kit, Illumina/Universal (Kapa Biosystems, cat. no. KK4824) Sequencing kits, MiSeq reagent kit v2 (300 cycles; Illumina, cat. no. MS-102-2002) or 5× TruSeq rapid SBS kit—HS (50 cycle) and TruSeq rapid SR cluster kit—HS (Illumina, cat. nos.

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  • 88
    New England Biolabs strand specific rna seq library preparation
    (A) The top 15 candidate genes from the haploid screen ordered by the number of times the hit was found in the 35 screens, including the number of independent integration sites and the calculated FDR. (B) Significantly enriched pathways among screen hits ranked according to fold enrichment; colours represent FDR in screen analysis. Numbers next to bars indicate number of hit-genes within category, (C) Significantly enriched GO terms among screen hits as in (B) (D) <t>Workflow</t> to generate Cas9 knockouts in RC9 ESCs. (E) Idealized strategy illustrating gRNAs and genotyping primers. (F) Western analysis using indicated KOs and indicated antibodies. Tubulin or Gapdh were used as loading controls, as indicated. (G) Anti-flag specific Westerns in indicated KO rescue ESCs upon stable forced expression of 3xflag rescue cDNAs driven from a CAG promoter. (H) Rex1GFP levels measured by FACS showing restoration of differentiation behaviour in the indicated rescue cell lines at N30. (I) t-SNE visualization of <t>RNA-seq</t> profiles in 2i and at N24 before and after batch correction. (J) GO enrichment analysis of the top 10% of genes (by absolute logFC) that were differentially expressed between 2i and N24 in WT ESCs (FDR ≤ 0.05, H0: |FC|
    Strand Specific Rna Seq Library Preparation, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/strand specific rna seq library preparation/product/New England Biolabs
    Average 88 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    strand specific rna seq library preparation - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    Image Search Results


    (A) The top 15 candidate genes from the haploid screen ordered by the number of times the hit was found in the 35 screens, including the number of independent integration sites and the calculated FDR. (B) Significantly enriched pathways among screen hits ranked according to fold enrichment; colours represent FDR in screen analysis. Numbers next to bars indicate number of hit-genes within category, (C) Significantly enriched GO terms among screen hits as in (B) (D) Workflow to generate Cas9 knockouts in RC9 ESCs. (E) Idealized strategy illustrating gRNAs and genotyping primers. (F) Western analysis using indicated KOs and indicated antibodies. Tubulin or Gapdh were used as loading controls, as indicated. (G) Anti-flag specific Westerns in indicated KO rescue ESCs upon stable forced expression of 3xflag rescue cDNAs driven from a CAG promoter. (H) Rex1GFP levels measured by FACS showing restoration of differentiation behaviour in the indicated rescue cell lines at N30. (I) t-SNE visualization of RNA-seq profiles in 2i and at N24 before and after batch correction. (J) GO enrichment analysis of the top 10% of genes (by absolute logFC) that were differentially expressed between 2i and N24 in WT ESCs (FDR ≤ 0.05, H0: |FC|

    Journal: bioRxiv

    Article Title: Cooperative molecular networks drive a mammalian cell state transition

    doi: 10.1101/2020.03.23.000109

    Figure Lengend Snippet: (A) The top 15 candidate genes from the haploid screen ordered by the number of times the hit was found in the 35 screens, including the number of independent integration sites and the calculated FDR. (B) Significantly enriched pathways among screen hits ranked according to fold enrichment; colours represent FDR in screen analysis. Numbers next to bars indicate number of hit-genes within category, (C) Significantly enriched GO terms among screen hits as in (B) (D) Workflow to generate Cas9 knockouts in RC9 ESCs. (E) Idealized strategy illustrating gRNAs and genotyping primers. (F) Western analysis using indicated KOs and indicated antibodies. Tubulin or Gapdh were used as loading controls, as indicated. (G) Anti-flag specific Westerns in indicated KO rescue ESCs upon stable forced expression of 3xflag rescue cDNAs driven from a CAG promoter. (H) Rex1GFP levels measured by FACS showing restoration of differentiation behaviour in the indicated rescue cell lines at N30. (I) t-SNE visualization of RNA-seq profiles in 2i and at N24 before and after batch correction. (J) GO enrichment analysis of the top 10% of genes (by absolute logFC) that were differentially expressed between 2i and N24 in WT ESCs (FDR ≤ 0.05, H0: |FC|

    Article Snippet: After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

    Techniques: Western Blot, Expressing, FACS, RNA Sequencing Assay

    Transcriptome-Wide Mapping of m 5 C Using bsRNA-Seq in Arabidopsis. (A) Venn diagram showing the number of m 5 /RBS-seq ( n ≤ 0.3 and ≥1% methylation. (B) Gene schematic and genome browser view of a differentially methylated gene, MAG5 , in three different tissue types. In the MAG5 gene schematic, the methylated cytosine C3349 is indicated. Boxes represent exons; lines represent introns. In the genome browser view, black arrows indicate m 5 C position C3349 (chr5: 19, 262, 126). Top: m 5 reads mapped to the MAG5 locus (chr5: 19, 262, 122-19, 262, 130) from the separate tissue data sets: siliques, shoots, and roots. Each row represents one sequence read and each column a nucleotide. Gray boxes represent nucleotides matching with the MAG5 reference sequence, and red boxes indicate mismatching nucleotides and/or nonmethylated, bisulfite converted cytosines. Sequencing gaps are shown in white. (C) Distribution of m 5 C sites within different RNA types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower mRNA abundance in Arabidopsis roots ( r s = −0.32, *P value ≤ 0.0001, Spearman’s correlation). (E) Histogram showing relative enrichment of observed m 5 C sites versus expected number of m 5 across all three tissue types (*P value ≤ 0.0001, binomial test). (F) Metagene profile of m 5 ≤ 0.3 and ≥2% methylation). (G) Methylation of candidate m 5 results. Heat map depicts log arcsine transformed methylation percentages of five m 5 . The numbers in parentheses are genome coordinates, and + or – indicates the strand.

    Journal: The Plant Cell

    Article Title: Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

    doi: 10.1105/tpc.16.00751

    Figure Lengend Snippet: Transcriptome-Wide Mapping of m 5 C Using bsRNA-Seq in Arabidopsis. (A) Venn diagram showing the number of m 5 /RBS-seq ( n ≤ 0.3 and ≥1% methylation. (B) Gene schematic and genome browser view of a differentially methylated gene, MAG5 , in three different tissue types. In the MAG5 gene schematic, the methylated cytosine C3349 is indicated. Boxes represent exons; lines represent introns. In the genome browser view, black arrows indicate m 5 C position C3349 (chr5: 19, 262, 126). Top: m 5 reads mapped to the MAG5 locus (chr5: 19, 262, 122-19, 262, 130) from the separate tissue data sets: siliques, shoots, and roots. Each row represents one sequence read and each column a nucleotide. Gray boxes represent nucleotides matching with the MAG5 reference sequence, and red boxes indicate mismatching nucleotides and/or nonmethylated, bisulfite converted cytosines. Sequencing gaps are shown in white. (C) Distribution of m 5 C sites within different RNA types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower mRNA abundance in Arabidopsis roots ( r s = −0.32, *P value ≤ 0.0001, Spearman’s correlation). (E) Histogram showing relative enrichment of observed m 5 C sites versus expected number of m 5 across all three tissue types (*P value ≤ 0.0001, binomial test). (F) Metagene profile of m 5 ≤ 0.3 and ≥2% methylation). (G) Methylation of candidate m 5 results. Heat map depicts log arcsine transformed methylation percentages of five m 5 . The numbers in parentheses are genome coordinates, and + or – indicates the strand.

    Article Snippet: The resulting mRNA-enriched RNA was used as a template for strand-specific RNA-seq library preparation using the NEB Ultra directional RNA library kit.

    Techniques: Methylation, Sequencing, Transformation Assay