strand specific rna seq library preparation  (New England Biolabs)


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    New England Biolabs strand specific rna seq library preparation
    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 <t>RNA</t> types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower <t>mRNA</t> 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.
    Strand Specific Rna Seq Library Preparation, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 9 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 91 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    strand specific rna seq library preparation - by Bioz Stars, 2020-01
    91/100 stars

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    1) 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

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    other:

    Article Title:
    Article Snippet: After chemical fragmentation, the samples were directly subjected to strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

    Article Title:
    Article Snippet: Bisulfite-converted RNA was used as a template for strand-specific RNA-seq library preparation using the NEB Ultra directional RNA library kit.

    Article Title:
    Article Snippet: Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB).

    Article Title:
    Article Snippet: After chemical fragmentation, samples were subjected to strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

    Article Title:
    Article Snippet: Samples were then directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

    Article Title:
    Article Snippet: RNA samples were subjected to the standard workflow for strand-specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB) and were sequenced on an Illumina HiSeq 2500.

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

    Article Title:
    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).

    Article Title:
    Article Snippet: After chemical fragmentation 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).

    Article Title:
    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.

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    New England Biolabs strand specific rna seq library preparation
    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 <t>RNA</t> types from siliques, shoots, and roots. The numbers in parentheses are percentage of total. (D) Scatterplot showing that increased methylation correlates with lower <t>mRNA</t> 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.
    Strand Specific Rna Seq Library Preparation, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 9 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 91 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    strand specific rna seq library preparation - by Bioz Stars, 2020-01
    91/100 stars
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    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