universal pcr primers  (New England Biolabs)


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    Name:
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1
    Description:
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 96 rxns
    Catalog Number:
    e7600s
    Price:
    460
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs universal pcr primers
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 96 rxns
    https://www.bioz.com/result/universal pcr primers/product/New England Biolabs
    Average 97 stars, based on 12946 article reviews
    Price from $9.99 to $1999.99
    universal pcr primers - by Bioz Stars, 2020-05
    97/100 stars

    Images

    1) Product Images from "Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response"

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response

    Journal: Oncotarget

    doi: 10.18632/oncotarget.6841

    Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative PCR for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture oligos and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.
    Figure Legend Snippet: Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative PCR for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture oligos and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.

    Techniques Used: Real-time Polymerase Chain Reaction, Sequencing

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    Multiplex Assay:

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    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
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    Selection:

    Article Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
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    Isolation:

    Article Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
    Article Snippet: .. Sequencing libraries were prepared from 500 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog number E7490, protocol revision 5.0), NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (catalog number E7420, protocol revision 6.0), and NEBNext Multiplex Oligos for Illumina (catalog number E7600, protocol revision 2.0) with the following modifications: E7420, Section1.2 (“mRNA Isolation, Fragmentation and Priming Total RNA”) Step 37, we decreased the incubation time from 15 min to 5 min; E7420, Section 1.3 (“First Strand cDNA Synthesis”), Step 2,we increased the incubation time from 15 min to 50 min; for the size selection we used 40 µL AMPure XP beads for the first bead selection and 20 µL AMPure XP beads for the second bead selection (targeting an insert size of 300–450 bp and a final library size of 400–550 bp); and in E7420, Section 1.9A (“PCR library Enrichment”), Step 2 we used 14 cycles for PCR cycling and dual index primers (i507 and i705–i712). .. Sequencing was performed at UC Berkeley's QB3 Vincent J. Coates Genomics Sequencing Laboratory on an Illumina HiSeq4000 instrument, generating 150 bp paired end reads.

    Next-Generation Sequencing:

    Article Title: Newly emerged enterovirus-A71 C4 sublineage may be more virulent than B5 in the 2015–2016 hand-foot-and-mouth disease outbreak in northern Vietnam
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    Construct:

    Article Title: The Effect of In Vitro Cultivation on the Transcriptome of Adult Brugia malayi
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    Sequencing:

    Article Title: Stochastic processes constrain the within and between host evolution of influenza virus
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    Article Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
    Article Snippet: .. Sequencing libraries were prepared from 500 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog number E7490, protocol revision 5.0), NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (catalog number E7420, protocol revision 6.0), and NEBNext Multiplex Oligos for Illumina (catalog number E7600, protocol revision 2.0) with the following modifications: E7420, Section1.2 (“mRNA Isolation, Fragmentation and Priming Total RNA”) Step 37, we decreased the incubation time from 15 min to 5 min; E7420, Section 1.3 (“First Strand cDNA Synthesis”), Step 2,we increased the incubation time from 15 min to 50 min; for the size selection we used 40 µL AMPure XP beads for the first bead selection and 20 µL AMPure XP beads for the second bead selection (targeting an insert size of 300–450 bp and a final library size of 400–550 bp); and in E7420, Section 1.9A (“PCR library Enrichment”), Step 2 we used 14 cycles for PCR cycling and dual index primers (i507 and i705–i712). .. Sequencing was performed at UC Berkeley's QB3 Vincent J. Coates Genomics Sequencing Laboratory on an Illumina HiSeq4000 instrument, generating 150 bp paired end reads.

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter ), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S). .. The final concentration of each barcoded library was determined by Quanti PicoGreen dsDNA quantification (ThermoFisher Scientific), and equal nanomolar concentrations were pooled.

    Article Title: Newly emerged enterovirus-A71 C4 sublineage may be more virulent than B5 in the 2015–2016 hand-foot-and-mouth disease outbreak in northern Vietnam
    Article Snippet: .. Whole-genome sequencing analysis NGS libraries were prepared from viral RNAs using the NEBNext RNA Library Prep Kit for Illumina (NEB) and the NEBNext Multiplex Oligos for Illumina Dual Index Primer Set 1 (NEB) according to the manufacturer’s instructions, with an average fragment length of 300 bp. .. Whole-genome sequencing analysis NGS libraries were prepared from viral RNAs using the NEBNext RNA Library Prep Kit for Illumina (NEB) and the NEBNext Multiplex Oligos for Illumina Dual Index Primer Set 1 (NEB) according to the manufacturer’s instructions, with an average fragment length of 300 bp.

    Incubation:

    Article Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
    Article Snippet: .. Sequencing libraries were prepared from 500 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog number E7490, protocol revision 5.0), NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (catalog number E7420, protocol revision 6.0), and NEBNext Multiplex Oligos for Illumina (catalog number E7600, protocol revision 2.0) with the following modifications: E7420, Section1.2 (“mRNA Isolation, Fragmentation and Priming Total RNA”) Step 37, we decreased the incubation time from 15 min to 5 min; E7420, Section 1.3 (“First Strand cDNA Synthesis”), Step 2,we increased the incubation time from 15 min to 50 min; for the size selection we used 40 µL AMPure XP beads for the first bead selection and 20 µL AMPure XP beads for the second bead selection (targeting an insert size of 300–450 bp and a final library size of 400–550 bp); and in E7420, Section 1.9A (“PCR library Enrichment”), Step 2 we used 14 cycles for PCR cycling and dual index primers (i507 and i705–i712). .. Sequencing was performed at UC Berkeley's QB3 Vincent J. Coates Genomics Sequencing Laboratory on an Illumina HiSeq4000 instrument, generating 150 bp paired end reads.

    Polymerase Chain Reaction:

    Article Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
    Article Snippet: .. Sequencing libraries were prepared from 500 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (catalog number E7490, protocol revision 5.0), NEBNext Ultra Directional RNA Library Preparation Kit for Illumina (catalog number E7420, protocol revision 6.0), and NEBNext Multiplex Oligos for Illumina (catalog number E7600, protocol revision 2.0) with the following modifications: E7420, Section1.2 (“mRNA Isolation, Fragmentation and Priming Total RNA”) Step 37, we decreased the incubation time from 15 min to 5 min; E7420, Section 1.3 (“First Strand cDNA Synthesis”), Step 2,we increased the incubation time from 15 min to 50 min; for the size selection we used 40 µL AMPure XP beads for the first bead selection and 20 µL AMPure XP beads for the second bead selection (targeting an insert size of 300–450 bp and a final library size of 400–550 bp); and in E7420, Section 1.9A (“PCR library Enrichment”), Step 2 we used 14 cycles for PCR cycling and dual index primers (i507 and i705–i712). .. Sequencing was performed at UC Berkeley's QB3 Vincent J. Coates Genomics Sequencing Laboratory on an Illumina HiSeq4000 instrument, generating 150 bp paired end reads.

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
    Article Snippet: .. The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina. ..

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq
    Article Snippet: .. E7600S) NEBNext adapter for Illumina (New England BioLabs), supplied with NEBNext® Multiplex Oligos for Illumina® Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific, cat.no. ) .. Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, cat.no. )

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    New England Biolabs universal pcr primers
    Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative <t>PCR</t> for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture <t>oligos</t> and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.
    Universal Pcr Primers, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/universal pcr primers/product/New England Biolabs
    Average 97 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    universal pcr primers - by Bioz Stars, 2020-05
    97/100 stars
      Buy from Supplier

    99
    New England Biolabs nebnext multiplex oligos for illumina dual index primers set 1
    Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative <t>PCR</t> for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture <t>oligos</t> and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.
    Nebnext Multiplex Oligos For Illumina Dual Index Primers Set 1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext multiplex oligos for illumina dual index primers set 1/product/New England Biolabs
    Average 99 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    nebnext multiplex oligos for illumina dual index primers set 1 - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

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    Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative PCR for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture oligos and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.

    Journal: Oncotarget

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response

    doi: 10.18632/oncotarget.6841

    Figure Lengend Snippet: Mapping nucleosome distributions following KSHV reactivation using mTSS-seq technique and mTSS-seq validation A. Experimental design for mapping nucleosome distributions following KSHV reactivation using our newly developed mTSS-seq technique. B. Validation of mTSS-seq using quantitative PCR for both on-target regions of the genome (within the sequence-capture region, two-kb region centered on a TSS) and off-target regions of the genome (not within the sequence-capture region, outside the two-region centered on a TSS). Quantitative PCR was performed for on- and off-target regions of the genome for both RHOC and ITGA4. The y-axis shows C t values. On average, C t values between the on- and off-targets of the sequence-captured libraries differ by 10.5 cycles. C. The periodic occurrence of AA/TT/AT/TA dinucleotides was calculated for all nucleosomal-sized fragments (147-148 bp) at the 0 hour time point. The x-axis represents the distance from the dyad axis. The y-axis is the frequency of AA/TT/AT/TA dinucleotides. An A/T-containing dinucleotide periodicity is seen every 10 bp at the 0 hour time point. D. Alignment of the midpoint fragments (purple) from mTSS-seq to the human genome shown in the UCSC Genome Browser ( http://genome.ucsc.edu ). Zooming in 5000X on human chromosome 2 to a six-kb window with two-kb of midpoint fragments at 0 hour time point (purple lines), along with the sequence-capture oligos and previously-published human-nucleosome distribution map for cell line GM18508 (red lines, (Gaffney et al., 2012)) at the TSSs of PUS10 and PEX13. The x-axis is genomic location. The y-axis is scaled reads per million.

    Article Snippet: The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina.

    Techniques: Real-time Polymerase Chain Reaction, Sequencing