dual index nebnext multiplex oligos  (New England Biolabs)


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    Name:
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 2
    Description:
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 2 96 rxns
    Catalog Number:
    e7780s
    Price:
    460
    Size:
    96 rxns
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    Probes and Primers
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    Structured Review

    New England Biolabs dual index nebnext multiplex oligos
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 2
    NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 2 96 rxns
    https://www.bioz.com/result/dual index nebnext multiplex oligos/product/New England Biolabs
    Average 96 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    dual index nebnext multiplex oligos - by Bioz Stars, 2020-08
    96/100 stars

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    Related Articles

    Multiplex Assay:

    Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
    Article Snippet: .. Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). .. Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500.

    Article Title: High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety
    Article Snippet: .. For the Illumina HiSeq 2500 run, a library was prepared with a commercial kit NEBNext Multiplex Oligos for Illumina with Index Primers Set 2 (New England Biolabs Inc., Ipswich, MA, USA) following the manufacturer’s protocol (Paired-End Library Construction). .. The raw sequencing files were submitted to the National Center for Biotechnology Information (NCBI) short read archive under accession numbers with the accession number SRX973821.

    Article Title: Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast
    Article Snippet: .. The ends of the fragmented DNA were repaired and sequencing adapters were ligated using the NEBNext Ultra DNA Library Prep kit reagents and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England Biolabs). .. Junction-containing biotinylated DNA fragments were adsorbed to MyOne Streptavidin C1 dynabeads (ThermoFisher) at room temperature for 15 minutes.

    Article Title: Draft Genome Sequence of Thermaerobacter sp. Strain PB12/4term, a Thermophilic Facultative Anaerobic Bacterium from Bottom Sediments of Lake Baikal, Russia
    Article Snippet: .. The DNA library with an average size of insert of about 600 bp was prepared using a NEBNext Ultra II DNA library prep kit for Illumina (NEB) and dual-index NEBNext multiplex oligos (NEB). .. Whole-genome sequencing of the Thermaerobacter sp. PB12/4term library was conducted with reagent kit version 3 (600-cycle) on a MiSeq genome sequencer (Illumina) at the SB RAS Genomics Core Facility (ICBFM SB RAS, Novosibirsk, Russia).

    Article Title: Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development
    Article Snippet: .. The NEBNext Multiplex Oligos for Illumina (Index Primers Set 2, New England BioLabs Inc.) containing adaptors and primers were used to label libraries facilitating pooling. ..

    Article Title: Rev-Erb co-regulates muscle regeneration via tethered interaction with the NF-Y cistrome
    Article Snippet: .. A library was constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina (New England BioLabs). .. After ligation with bar-coded adapters, fragments corresponding to an original 150 bp in size were selected using AMPure XP Beads (Beckman Coulter) and PCR-amplified.

    Article Title: UNC-16 (JIP3) Acts Through Synapse-Assembly Proteins to Inhibit the Active Transport of Cell Soma Organelles to Caenorhabditis elegans Motor Neuron Axons
    Article Snippet: .. To produce libraries for whole-genome sequencing, we quantified the DNA concentrations using the Qubit fluorimeter (Invitrogen) and the Qubit dsDNA BR Assay Kit (Invitrogen), sheared the DNAs to ∼350 bp by transferring 1080 ng of each DNA in 60 μl of water to Covaris Microtubes using two 25-sec cycles in a Covaris S2 at 4°, and then followed the manufacturer’s instructions for the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7370S) and NEBNext Multiplex Oligos for Illumina (Index Primers set 1 and set 2; E7335S and E7500S). ..

    Article Title: Prostaglandin A1 Inhibits the Cognitive Decline of APP/PS1 Transgenic Mice via PPARγ/ABCA1-dependent Cholesterol Efflux Mechanisms
    Article Snippet: .. 400 ng of RNA were utilized for library preparation by the NEBNext® rRNA Depletion Kit, NEBNext® Ultra II Directional RNA Kit and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, Ipswich, MA). .. The quality control of final reads with a size 350 bp was performed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

    Amplification:

    Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
    Article Snippet: .. Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). .. Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500.

    Ligation:

    Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
    Article Snippet: .. Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). .. Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500.

    Transferring:

    Article Title: UNC-16 (JIP3) Acts Through Synapse-Assembly Proteins to Inhibit the Active Transport of Cell Soma Organelles to Caenorhabditis elegans Motor Neuron Axons
    Article Snippet: .. To produce libraries for whole-genome sequencing, we quantified the DNA concentrations using the Qubit fluorimeter (Invitrogen) and the Qubit dsDNA BR Assay Kit (Invitrogen), sheared the DNAs to ∼350 bp by transferring 1080 ng of each DNA in 60 μl of water to Covaris Microtubes using two 25-sec cycles in a Covaris S2 at 4°, and then followed the manufacturer’s instructions for the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7370S) and NEBNext Multiplex Oligos for Illumina (Index Primers set 1 and set 2; E7335S and E7500S). ..

    Construct:

    Article Title: Rev-Erb co-regulates muscle regeneration via tethered interaction with the NF-Y cistrome
    Article Snippet: .. A library was constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina (New England BioLabs). .. After ligation with bar-coded adapters, fragments corresponding to an original 150 bp in size were selected using AMPure XP Beads (Beckman Coulter) and PCR-amplified.

    Polymerase Chain Reaction:

    Article Title: Batf Pioneers the Reorganization of Chromatin in Developing Effector T Cells via Ets1-Dependent Recruitment of Ctcf
    Article Snippet: .. Biotinylated DNA was captured using magnetic streptavidin beads (Invitrogen), used for adaptor ligation reaction, and PCR amplification using NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set, NEB). .. Hi-C libraries were sequenced with paired-end 50 bp using Illumina HiSeq 2500.

    Sequencing:

    Article Title: Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast
    Article Snippet: .. The ends of the fragmented DNA were repaired and sequencing adapters were ligated using the NEBNext Ultra DNA Library Prep kit reagents and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England Biolabs). .. Junction-containing biotinylated DNA fragments were adsorbed to MyOne Streptavidin C1 dynabeads (ThermoFisher) at room temperature for 15 minutes.

    Article Title: UNC-16 (JIP3) Acts Through Synapse-Assembly Proteins to Inhibit the Active Transport of Cell Soma Organelles to Caenorhabditis elegans Motor Neuron Axons
    Article Snippet: .. To produce libraries for whole-genome sequencing, we quantified the DNA concentrations using the Qubit fluorimeter (Invitrogen) and the Qubit dsDNA BR Assay Kit (Invitrogen), sheared the DNAs to ∼350 bp by transferring 1080 ng of each DNA in 60 μl of water to Covaris Microtubes using two 25-sec cycles in a Covaris S2 at 4°, and then followed the manufacturer’s instructions for the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB E7370S) and NEBNext Multiplex Oligos for Illumina (Index Primers set 1 and set 2; E7335S and E7500S). ..

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  • 99
    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: 99/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 54 article reviews
    Price from $9.99 to $1999.99
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    99
    New England Biolabs nebnext index primer for illumina
    Schistosomula excrete/secrete extracellular miRNAs. Supernatant from 72 h in vitro cultured schistosomula was separated into EV-enriched and EV-depleted fractions (n=3) by preparatory ultracentrifugation. Total RNA from each fraction was extracted using the miRNeasy kit (Qiagen) and prepared for RNA-seq using the <t>NEBNext</t> Small RNA (for <t>Illumina</t> HiSeq sequencing) kit. To identify sma-miRNAs in our samples, the miRDeep2 package was utilized (29). Only miRNAs with at least 10 reads in 2 out of the 3 biological replicates (in at least one of the fractions, EV-enriched OR EV-depleted) were considered in the study. A total of 205 putative sma-miRNAs passed this criterion. sma-miRNA read count data were normalized using the DESeq2 package (33) as described in the Materials and methods . (a) Heatmap depiction of sma-miRNA abundance (represented by Z-scores) found within EV-enriched and EV-depleted supernatant fractions after agglomerative hierarchical clustering and standardization. Each row represents a miRNA and its relative Z-score value in EV-enriched and EV-depleted fractions is displayed in the 2 columns. All sma-miRNA specifics (name, sequence, raw/normalized read counts and cluster location) are included in Supplementary file 3 . (b) sma-miRNA localization found throughout the S. mansoni karyotype (v5.2). Vertical grey bars represent the position of known sma-miRNAs available in miRBase (v.21). Vertical black bars represent the localization of all extracellular sma-miRNAs (within EV-depleted and EV-enriched fractions) newly identified in our study. Black stars above the vertical lines represent 13 sma-miRNAs found in our study that are also present in miRBase. Eighteen miRNAs localized on unmapped scaffolds (16 not mapped at all; 1 unplaced on Ch 7, 4 and 3; 5 unplaced on Ch 1) as well as 15 miRNAs not yet mapped to the current S. mansoni genome assembly were not included in this analysis. All available sma-miRNA localization coordinates are available in Supplementary file 3 .
    Nebnext Index Primer For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext index primer for illumina/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
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    99
    New England Biolabs nebnext multiplex oligos for illumina
    Schistosomula excrete/secrete extracellular miRNAs. Supernatant from 72 h in vitro cultured schistosomula was separated into EV-enriched and EV-depleted fractions (n=3) by preparatory ultracentrifugation. Total RNA from each fraction was extracted using the miRNeasy kit (Qiagen) and prepared for RNA-seq using the <t>NEBNext</t> Small RNA (for <t>Illumina</t> HiSeq sequencing) kit. To identify sma-miRNAs in our samples, the miRDeep2 package was utilized (29). Only miRNAs with at least 10 reads in 2 out of the 3 biological replicates (in at least one of the fractions, EV-enriched OR EV-depleted) were considered in the study. A total of 205 putative sma-miRNAs passed this criterion. sma-miRNA read count data were normalized using the DESeq2 package (33) as described in the Materials and methods . (a) Heatmap depiction of sma-miRNA abundance (represented by Z-scores) found within EV-enriched and EV-depleted supernatant fractions after agglomerative hierarchical clustering and standardization. Each row represents a miRNA and its relative Z-score value in EV-enriched and EV-depleted fractions is displayed in the 2 columns. All sma-miRNA specifics (name, sequence, raw/normalized read counts and cluster location) are included in Supplementary file 3 . (b) sma-miRNA localization found throughout the S. mansoni karyotype (v5.2). Vertical grey bars represent the position of known sma-miRNAs available in miRBase (v.21). Vertical black bars represent the localization of all extracellular sma-miRNAs (within EV-depleted and EV-enriched fractions) newly identified in our study. Black stars above the vertical lines represent 13 sma-miRNAs found in our study that are also present in miRBase. Eighteen miRNAs localized on unmapped scaffolds (16 not mapped at all; 1 unplaced on Ch 7, 4 and 3; 5 unplaced on Ch 1) as well as 15 miRNAs not yet mapped to the current S. mansoni genome assembly were not included in this analysis. All available sma-miRNA localization coordinates are available in Supplementary file 3 .
    Nebnext Multiplex Oligos For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 309 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext multiplex oligos for illumina/product/New England Biolabs
    Average 99 stars, based on 309 article reviews
    Price from $9.99 to $1999.99
    nebnext multiplex oligos for illumina - by Bioz Stars, 2020-08
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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

    Schistosomula excrete/secrete extracellular miRNAs. Supernatant from 72 h in vitro cultured schistosomula was separated into EV-enriched and EV-depleted fractions (n=3) by preparatory ultracentrifugation. Total RNA from each fraction was extracted using the miRNeasy kit (Qiagen) and prepared for RNA-seq using the NEBNext Small RNA (for Illumina HiSeq sequencing) kit. To identify sma-miRNAs in our samples, the miRDeep2 package was utilized (29). Only miRNAs with at least 10 reads in 2 out of the 3 biological replicates (in at least one of the fractions, EV-enriched OR EV-depleted) were considered in the study. A total of 205 putative sma-miRNAs passed this criterion. sma-miRNA read count data were normalized using the DESeq2 package (33) as described in the Materials and methods . (a) Heatmap depiction of sma-miRNA abundance (represented by Z-scores) found within EV-enriched and EV-depleted supernatant fractions after agglomerative hierarchical clustering and standardization. Each row represents a miRNA and its relative Z-score value in EV-enriched and EV-depleted fractions is displayed in the 2 columns. All sma-miRNA specifics (name, sequence, raw/normalized read counts and cluster location) are included in Supplementary file 3 . (b) sma-miRNA localization found throughout the S. mansoni karyotype (v5.2). Vertical grey bars represent the position of known sma-miRNAs available in miRBase (v.21). Vertical black bars represent the localization of all extracellular sma-miRNAs (within EV-depleted and EV-enriched fractions) newly identified in our study. Black stars above the vertical lines represent 13 sma-miRNAs found in our study that are also present in miRBase. Eighteen miRNAs localized on unmapped scaffolds (16 not mapped at all; 1 unplaced on Ch 7, 4 and 3; 5 unplaced on Ch 1) as well as 15 miRNAs not yet mapped to the current S. mansoni genome assembly were not included in this analysis. All available sma-miRNA localization coordinates are available in Supplementary file 3 .

    Journal: Journal of Extracellular Vesicles

    Article Title: Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni

    doi: 10.3402/jev.v4.28665

    Figure Lengend Snippet: Schistosomula excrete/secrete extracellular miRNAs. Supernatant from 72 h in vitro cultured schistosomula was separated into EV-enriched and EV-depleted fractions (n=3) by preparatory ultracentrifugation. Total RNA from each fraction was extracted using the miRNeasy kit (Qiagen) and prepared for RNA-seq using the NEBNext Small RNA (for Illumina HiSeq sequencing) kit. To identify sma-miRNAs in our samples, the miRDeep2 package was utilized (29). Only miRNAs with at least 10 reads in 2 out of the 3 biological replicates (in at least one of the fractions, EV-enriched OR EV-depleted) were considered in the study. A total of 205 putative sma-miRNAs passed this criterion. sma-miRNA read count data were normalized using the DESeq2 package (33) as described in the Materials and methods . (a) Heatmap depiction of sma-miRNA abundance (represented by Z-scores) found within EV-enriched and EV-depleted supernatant fractions after agglomerative hierarchical clustering and standardization. Each row represents a miRNA and its relative Z-score value in EV-enriched and EV-depleted fractions is displayed in the 2 columns. All sma-miRNA specifics (name, sequence, raw/normalized read counts and cluster location) are included in Supplementary file 3 . (b) sma-miRNA localization found throughout the S. mansoni karyotype (v5.2). Vertical grey bars represent the position of known sma-miRNAs available in miRBase (v.21). Vertical black bars represent the localization of all extracellular sma-miRNAs (within EV-depleted and EV-enriched fractions) newly identified in our study. Black stars above the vertical lines represent 13 sma-miRNAs found in our study that are also present in miRBase. Eighteen miRNAs localized on unmapped scaffolds (16 not mapped at all; 1 unplaced on Ch 7, 4 and 3; 5 unplaced on Ch 1) as well as 15 miRNAs not yet mapped to the current S. mansoni genome assembly were not included in this analysis. All available sma-miRNA localization coordinates are available in Supplementary file 3 .

    Article Snippet: Small RNA concentrations ranged from 60 pg/ml (EV-enriched fraction) to 750 pg/ml (EV-depleted fraction) as determined by the Bioanalyzer. sncRNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set and NEBNext index primer for Illumina (New England Biolabs, Ipswich, MA, USA), according to the manufacturer's protocol.

    Techniques: In Vitro, Cell Culture, RNA Sequencing Assay, Sequencing